psi-ms Ontology

Table 1. Metadata
format-version	1.2
data-version	4.1.49
date	03:05:2021 11:30
saved-by	Matthew Robey
auto-generated-by	OBO-Edit 2.3.1
import	http://ontologies.berkeleybop.org/pato.obo
import	http://ontologies.berkeleybop.org/uo.obo
default-namespace	MS
namespace-id-rule	* MS:$sequence(7,0,9999999)$
namespace-id-rule	* PEFF:$sequence(7,0,9999999)$
remark	namespace: MS
remark	namespace: PEFF
remark	coverage: Mass spectrometer output files and spectra interpretation
remark	creator: Yasset Perez-Riverol <yperez ←at→ ebi.ac.uk>
remark	creator: Matt Chambers <matt.chambers ←at→ vanderbilt.edu>
remark	creator: Andreas Bertsch <bertsch ←at→ informatik.uni-tuebingen.de>
remark	creator: Marius Kallhardt <Marius.Kallhardt ←at→ bdal.de>
remark	creator: Eric Deutsch <edeutsch ←at→ systemsbiology.org>
remark	creator: Fredrik Levander <fredrik.levander ←at→ immun.lth.se>
remark	creator: Pierre-Alain Binz <pierre-alain.binz ←at→ chuv.ch>
remark	creator: Gerhard Mayer <mayerg97 ←at→ rub.de>
remark	publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group
remark	When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page
remark	For any queries contact psidev-ms-vocab@lists.sourceforge.net
remark	URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
remark	This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
remark	To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
ontology	ms

Table 2. Typedef [has_regexp]
id	has_regexp
name	has regexp

2.1. has_units has_units

Table 3. Typedef [has_units]
id	has_units
name	has_units

2.2. part_of part_of

Table 4. Typedef [part_of]
id	part_of
name	part_of
is_transitive	true

2.3. has_order has_order

Table 5. Typedef [has_order]
id	has_order
name	has_order

2.4. has_domain has_domain

Table 6. Typedef [has_domain]
id	has_domain
name	has_domain

2.5. MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies

Table 7. Term [MS:0000000]
id	MS:0000000
name	Proteomics Standards Initiative Mass Spectrometry Vocabularies
def	"Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS]

2.6. MS:1000001 sample number

Table 8. Term [MS:1000001]
id	MS:1000001
name	sample number
def	"A reference number relevant to the sample under study." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute

2.7. MS:1000002 sample name

Table 9. Term [MS:1000002]
id	MS:1000002
name	sample name
def	"A reference string relevant to the sample under study." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute

2.8. MS:1000003 sample state

Table 10. Term [MS:1000003]
id	MS:1000003
name	sample state
def	"The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS]
is_a	MS:1000548 sample attribute ! sample attribute

2.9. MS:1000004 sample mass

Table 11. Term [MS:1000004]
id	MS:1000004
name	sample mass
def	"Total mass of sample used." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute
relationship	has_units [UO:0000021] ! gram

2.10. MS:1000005 sample volume

Table 12. Term [MS:1000005]
id	MS:1000005
name	sample volume
def	"Total volume of solution used." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute
relationship	has_units [UO:0000098] ! milliliter

2.11. MS:1000006 sample concentration

Table 13. Term [MS:1000006]
id	MS:1000006
name	sample concentration
def	"Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute
relationship	has_units [UO:0000175] ! gram per liter

2.12. MS:1000007 inlet type

Table 14. Term [MS:1000007]
id	MS:1000007
name	inlet type
def	"The nature of the sample inlet." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.13. MS:1000008 ionization type

Table 15. Term [MS:1000008]
id	MS:1000008
name	ionization type
def	"The method by which gas phase ions are generated from the sample." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.14. MS:1000009 ionization mode

Table 16. Term [MS:1000009]
id	MS:1000009
name	ionization mode
def	"OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS]
comment	This term was made obsolete because it was replaced by scan polarity (MS:1000465).
is_obsolete	true

2.15. MS:1000010 analyzer type

Table 17. Term [MS:1000010]
id	MS:1000010
name	analyzer type
def	"OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.16. MS:1000011 mass resolution

Table 18. Term [MS:1000011]
id	MS:1000011
name	mass resolution
def	"Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute

2.17. MS:1000012 resolution measurement method

Table 19. Term [MS:1000012]
id	MS:1000012
name	resolution measurement method
def	"Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS]
is_a	MS:1000596 measurement method ! measurement method

2.18. MS:1000013 resolution type

Table 20. Term [MS:1000013]
id	MS:1000013
name	resolution type
def	"OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.19. MS:1000014 accuracy

Table 21. Term [MS:1000014]
id	MS:1000014
name	accuracy
def	"Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000480 mass analyzer attribute ! mass analyzer attribute
relationship	has_units MS:1000040 m/z ! m/z
relationship	has_units [UO:0000169] ! parts per million

2.20. MS:1000015 scan rate

Table 22. Term [MS:1000015]
id	MS:1000015
name	scan rate
def	"Rate in Th/sec for scanning analyzers." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units MS:1000807 Th/s ! Th/s

2.21. MS:1000016 scan start time

Table 23. Term [MS:1000016]
id	MS:1000016
name	scan start time
def	"The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
is_a	MS:1002345 PSM-level attribute ! PSM-level attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.22. MS:1000017 Scan Function

Table 24. Term [MS:1000017]
id	MS:1000017
name	Scan Function
def	"OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum." [PSI:MS]
comment	OBSOLETE This former purgatory term was made obsolete.
is_obsolete	true

2.23. MS:1000018 scan direction

Table 25. Term [MS:1000018]
id	MS:1000018
name	scan direction
def	"Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS]
relationship	part_of MS:1000441 scan ! scan

2.24. MS:1000019 scan law

Table 26. Term [MS:1000019]
id	MS:1000019
name	scan law
def	"Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used." [PSI:MS]
relationship	part_of MS:1000441 scan ! scan

2.25. MS:1000020 scanning method

Table 27. Term [MS:1000020]
id	MS:1000020
name	scanning method
def	"Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS]
comment	OBSOLETE This former purgatory term was made obsolete.
synonym	"Tandem Scanning Method" RELATED []
is_obsolete	true

2.26. MS:1000021 reflectron state

Table 28. Term [MS:1000021]
id	MS:1000021
name	reflectron state
def	"Status of the reflectron, turned on or off." [PSI:MS]
is_a	MS:1000480 mass analyzer attribute ! mass analyzer attribute

2.27. MS:1000022 TOF Total Path Length

Table 29. Term [MS:1000022]
id	MS:1000022
name	TOF Total Path Length
def	"The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000480 mass analyzer attribute ! mass analyzer attribute
relationship	has_units [UO:0000008] ! meter

2.28. MS:1000023 isolation width

Table 30. Term [MS:1000023]
id	MS:1000023
name	isolation width
def	"OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS]
comment	This former purgatory term was made obsolete.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
relationship	has_units MS:1000040 m/z ! m/z
is_obsolete	true

2.29. MS:1000024 final MS exponent

Table 31. Term [MS:1000024]
id	MS:1000024
name	final MS exponent
def	"Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1000480 mass analyzer attribute ! mass analyzer attribute

2.30. MS:1000025 magnetic field strength

Table 32. Term [MS:1000025]
id	MS:1000025
name	magnetic field strength
def	"A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS]
synonym	"B" EXACT []
synonym	"Magnetic Field" RELATED []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000480 mass analyzer attribute ! mass analyzer attribute
relationship	has_units [UO:0000228] ! tesla

2.31. MS:1000026 detector type

Table 33. Term [MS:1000026]
id	MS:1000026
name	detector type
def	"Type of detector used in the mass spectrometer." [PSI:MS]
relationship	part_of MS:1000453 detector ! detector

2.32. MS:1000027 detector acquisition mode

Table 34. Term [MS:1000027]
id	MS:1000027
name	detector acquisition mode
def	"Method by which detector signal is acquired by the data system." [PSI:MS]
relationship	part_of MS:1000453 detector ! detector

2.33. MS:1000028 detector resolution

Table 35. Term [MS:1000028]
id	MS:1000028
name	detector resolution
def	"The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000481 detector attribute ! detector attribute

2.34. MS:1000029 sampling frequency

Table 36. Term [MS:1000029]
id	MS:1000029
name	sampling frequency
def	"The rate of signal sampling (measurement) with respect to time." [PSI:MS]
synonym	"ADC Sampling Frequency" NARROW []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000481 detector attribute ! detector attribute
relationship	has_units [UO:0000106] ! hertz

2.35. MS:1000030 vendor

Table 37. Term [MS:1000030]
id	MS:1000030
name	vendor
def	"OBSOLETE Name of instrument vendor." [PSI:MS]
comment	This term was made obsolete because it was replaced by instrument model (MS:1000031).
is_obsolete	true

2.36. MS:1000031 instrument model

Table 38. Term [MS:1000031]
id	MS:1000031
name	instrument model
def	"Instrument model name not including the vendor’s name." [PSI:MS]
relationship	part_of MS:1000463 instrument ! instrument

2.37. MS:1000032 customization

Table 39. Term [MS:1000032]
id	MS:1000032
name	customization
def	"Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000496 instrument attribute ! instrument attribute

2.38. MS:1000033 deisotoping

Table 40. Term [MS:1000033]
id	MS:1000033
name	deisotoping
def	"The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.39. MS:1000034 charge deconvolution

Table 41. Term [MS:1000034]
id	MS:1000034
name	charge deconvolution
def	"The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.40. MS:1000035 peak picking

Table 42. Term [MS:1000035]
id	MS:1000035
name	peak picking
def	"Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.41. MS:1000036 scan mode

Table 43. Term [MS:1000036]
id	MS:1000036
name	scan mode
def	"OBSOLETE." [PSI:MS]
comment	This term was made obsolete because .
is_obsolete	true

2.42. MS:1000037 polarity

Table 44. Term [MS:1000037]
id	MS:1000037
name	polarity
def	"OBSOLETE Terms to describe the polarity setting of the instrument." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186).
is_obsolete	true

2.43. MS:1000038 minute

Table 45. Term [MS:1000038]
id	MS:1000038
name	minute
def	"OBSOLETE Acquisition time in minutes." [PSI:MS]
comment	This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031).
is_obsolete	true

2.44. MS:1000039 second

Table 46. Term [MS:1000039]
id	MS:1000039
name	second
def	"OBSOLETE Acquisition time in seconds." [PSI:MS]
comment	This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010).
is_obsolete	true

2.45. MS:1000040 m/z

Table 47. Term [MS:1000040]
id	MS:1000040
name	m/z
def	"Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion’s mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated." [PSI:MS]
synonym	"mass-to-charge ratio" EXACT []
synonym	"Th" EXACT []
synonym	"thomson" EXACT []
is_a	[UO:0000000] ! unit

2.46. MS:1000041 charge state

Table 48. Term [MS:1000041]
id	MS:1000041
name	charge state
def	"Number of net charges, positive or negative, on an ion." [PSI:MS]
synonym	"z" EXACT []
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
is_a	MS:1000507 ion property ! ion property

2.47. MS:1000042 peak intensity

Table 49. Term [MS:1000042]
id	MS:1000042
name	peak intensity
def	"Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit
relationship	part_of MS:1000231 peak ! peak

2.48. MS:1000043 intensity unit

Table 50. Term [MS:1000043]
id	MS:1000043
name	intensity unit
def	"Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors." [PSI:MS]
is_a	[UO:0000000] ! unit

2.49. MS:1000044 dissociation method

Table 51. Term [MS:1000044]
id	MS:1000044
name	dissociation method
def	"Fragmentation method used for dissociation or fragmentation." [PSI:MS]
synonym	"Activation Method" RELATED []
relationship	part_of MS:1000456 precursor activation ! precursor activation

2.50. MS:1000045 collision energy

Table 52. Term [MS:1000045]
id	MS:1000045
name	collision energy
def	"Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000266] ! electronvolt

2.51. MS:1000046 energy unit

Table 53. Term [MS:1000046]
id	MS:1000046
name	energy unit
def	"OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111).
is_a	[UO:0000000] ! unit
is_obsolete	true

2.52. MS:1000047 emulsion

Table 54. Term [MS:1000047]
id	MS:1000047
name	emulsion
def	"State if the sample is in emulsion form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.53. MS:1000048 gaseous sample state

Table 55. Term [MS:1000048]
id	MS:1000048
name	gaseous sample state
def	"State if the sample is in gaseous form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.54. MS:1000049 liquid sample state

Table 56. Term [MS:1000049]
id	MS:1000049
name	liquid sample state
def	"State if the sample is in liquid form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.55. MS:1000050 solid sample state

Table 57. Term [MS:1000050]
id	MS:1000050
name	solid sample state
def	"State if the sample is in solid form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.56. MS:1000051 solution

Table 58. Term [MS:1000051]
id	MS:1000051
name	solution
def	"State if the sample is in solution form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.57. MS:1000052 suspension

Table 59. Term [MS:1000052]
id	MS:1000052
name	suspension
def	"State if the sample is in suspension form." [PSI:MS]
is_a	MS:1000003 sample state ! sample state

2.58. MS:1000053 sample batch

Table 60. Term [MS:1000053]
id	MS:1000053
name	sample batch
def	"Sample batch lot identifier." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000548 sample attribute ! sample attribute

2.59. MS:1000054 chromatography

Table 61. Term [MS:1000054]
id	MS:1000054
name	chromatography
def	"OBSOLETE Chromatographic conditions used to obtain the sample." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.60. MS:1000055 continuous flow fast atom bombardment

Table 62. Term [MS:1000055]
id	MS:1000055
name	continuous flow fast atom bombardment
def	"Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS]
synonym	"CF-FAB" EXACT []
is_a	MS:1000007 inlet type ! inlet type

2.61. MS:1000056 direct inlet

Table 63. Term [MS:1000056]
id	MS:1000056
name	direct inlet
def	"The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.62. MS:1000057 electrospray inlet

Table 64. Term [MS:1000057]
id	MS:1000057
name	electrospray inlet
def	"Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.63. MS:1000058 flow injection analysis

Table 65. Term [MS:1000058]
id	MS:1000058
name	flow injection analysis
def	"Sample is directly injected or infused into the ionization source." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.64. MS:1000059 inductively coupled plasma

Table 66. Term [MS:1000059]
id	MS:1000059
name	inductively coupled plasma
def	"A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.65. MS:1000060 infusion

Table 67. Term [MS:1000060]
id	MS:1000060
name	infusion
def	"The continuous flow of solution of a sample into the ionization source." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.66. MS:1000061 jet separator

Table 68. Term [MS:1000061]
id	MS:1000061
name	jet separator
def	"A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.67. MS:1000062 membrane separator

Table 69. Term [MS:1000062]
id	MS:1000062
name	membrane separator
def	"A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.68. MS:1000063 moving belt

Table 70. Term [MS:1000063]
id	MS:1000063
name	moving belt
def	"Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.69. MS:1000064 moving wire

Table 71. Term [MS:1000064]
id	MS:1000064
name	moving wire
def	"Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.70. MS:1000065 open split

Table 72. Term [MS:1000065]
id	MS:1000065
name	open split
def	"A division of flowing stream of liquid into two streams." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.71. MS:1000066 particle beam

Table 73. Term [MS:1000066]
id	MS:1000066
name	particle beam
def	"Method for generating ions from a solution of an analyte." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.72. MS:1000067 reservoir

Table 74. Term [MS:1000067]
id	MS:1000067
name	reservoir
def	"A sample inlet method involving a reservoir." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.73. MS:1000068 septum

Table 75. Term [MS:1000068]
id	MS:1000068
name	septum
def	"A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.74. MS:1000069 thermospray inlet

Table 76. Term [MS:1000069]
id	MS:1000069
name	thermospray inlet
def	"A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.75. MS:1000070 atmospheric pressure chemical ionization

Table 77. Term [MS:1000070]
id	MS:1000070
name	atmospheric pressure chemical ionization
def	"Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS]
synonym	"APCI" EXACT []
is_a	MS:1000240 atmospheric pressure ionization ! atmospheric pressure ionization

2.76. MS:1000071 chemical ionization

Table 78. Term [MS:1000071]
id	MS:1000071
name	chemical ionization
def	"The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization." [PSI:MS]
synonym	"CI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.77. MS:1000072 Electronic Ionization

Table 79. Term [MS:1000072]
id	MS:1000072
name	Electronic Ionization
def	"OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS]
comment	This term was made obsolete because it was replaced by electron ionization (MS:1000389).
synonym	"EI" EXACT []
is_obsolete	true

2.78. MS:1000073 electrospray ionization

Table 80. Term [MS:1000073]
id	MS:1000073
name	electrospray ionization
def	"A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended." [PSI:MS]
synonym	"ESI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.79. MS:1000074 fast atom bombardment ionization

Table 81. Term [MS:1000074]
id	MS:1000074
name	fast atom bombardment ionization
def	"The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization." [PSI:MS]
synonym	"FAB" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.80. MS:1000075 matrix-assisted laser desorption ionization

Table 82. Term [MS:1000075]
id	MS:1000075
name	matrix-assisted laser desorption ionization
def	"The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization." [PSI:MS]
synonym	"MALDI" EXACT []
is_a	MS:1000247 desorption ionization ! desorption ionization

2.81. MS:1000076 negative ion mode

Table 83. Term [MS:1000076]
id	MS:1000076
name	negative ion mode
def	"OBSOLETE." [PSI:MS]
comment	This term was made obsolete because it was replaced by negative scan (MS:1000129).
is_obsolete	true

2.82. MS:1000077 positive ion mode

Table 84. Term [MS:1000077]
id	MS:1000077
name	positive ion mode
def	"OBSOLETE." [PSI:MS]
comment	This term was made obsolete because it was replaced by positive scan (MS:1000130).
is_obsolete	true

2.83. MS:1000078 axial ejection linear ion trap

Table 85. Term [MS:1000078]
id	MS:1000078
name	axial ejection linear ion trap
def	"A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS]
is_a	MS:1000291 linear ion trap ! linear ion trap

2.84. MS:1000079 fourier transform ion cyclotron resonance mass spectrometer

Table 86. Term [MS:1000079]
id	MS:1000079
name	fourier transform ion cyclotron resonance mass spectrometer
def	"A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS]
synonym	"FT_ICR" EXACT []
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.85. MS:1000080 magnetic sector

Table 87. Term [MS:1000080]
id	MS:1000080
name	magnetic sector
def	"A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z." [PSI:MS]
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.86. MS:1000081 quadrupole

Table 88. Term [MS:1000081]
id	MS:1000081
name	quadrupole
def	"A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS]
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.87. MS:1000082 quadrupole ion trap

Table 89. Term [MS:1000082]
id	MS:1000082
name	quadrupole ion trap
def	"Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials." [PSI:MS]
synonym	"Paul Ion trap" EXACT []
synonym	"QIT" EXACT []
synonym	"Quistor" EXACT []
is_a	MS:1000264 ion trap ! ion trap

2.88. MS:1000083 radial ejection linear ion trap

Table 90. Term [MS:1000083]
id	MS:1000083
name	radial ejection linear ion trap
def	"A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS]
is_a	MS:1000291 linear ion trap ! linear ion trap

2.89. MS:1000084 time-of-flight

Table 91. Term [MS:1000084]
id	MS:1000084
name	time-of-flight
def	"Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS]
synonym	"TOF" EXACT []
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.90. MS:1000085 baseline

Table 92. Term [MS:1000085]
id	MS:1000085
name	baseline
def	"An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS]
is_a	MS:1000012 resolution measurement method ! resolution measurement method

2.91. MS:1000086 full width at half-maximum

Table 93. Term [MS:1000086]
id	MS:1000086
name	full width at half-maximum
def	"A measure of resolution represented as width of the peak at half peak height." [PSI:MS]
synonym	"FWHM" EXACT []
is_a	MS:1000012 resolution measurement method ! resolution measurement method

2.92. MS:1000087 ten percent valley

Table 94. Term [MS:1000087]
id	MS:1000087
name	ten percent valley
def	"An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS]
is_a	MS:1000012 resolution measurement method ! resolution measurement method

2.93. MS:1000088 constant

Table 95. Term [MS:1000088]
id	MS:1000088
name	constant
def	"OBSOLETE When resolution is constant with respect to m/z." [PSI:MS]
comment	This child of the former purgatory term resolution type was made obsolete.
is_obsolete	true

2.94. MS:1000089 proportional

Table 96. Term [MS:1000089]
id	MS:1000089
name	proportional
def	"OBSOLETE When resolution is proportional with respect to m/z." [PSI:MS]
comment	This child of the former purgatory term resolution type was made obsolete.
is_obsolete	true

2.95. MS:1000090 mass scan

Table 97. Term [MS:1000090]
id	MS:1000090
name	mass scan
def	"OBSOLETE A variation of instrument where a selected mass is scanned." [PSI:MS]
comment	This child of the former purgatory term Scan Function was made obsolete.
is_obsolete	true

2.96. MS:1000091 selected ion detection

Table 98. Term [MS:1000091]
id	MS:1000091
name	selected ion detection
def	"OBSOLETE Please see Single Ion Monitoring." [PSI:MS]
comment	This child of the former purgatory term Scan Function was made obsolete.
is_obsolete	true

2.97. MS:1000092 decreasing m/z scan

Table 99. Term [MS:1000092]
id	MS:1000092
name	decreasing m/z scan
def	"High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS]
is_a	MS:1000018 scan direction ! scan direction

2.98. MS:1000093 increasing m/z scan

Table 100. Term [MS:1000093]
id	MS:1000093
name	increasing m/z scan
def	"Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS]
is_a	MS:1000018 scan direction ! scan direction

2.99. MS:1000094 exponential

Table 101. Term [MS:1000094]
id	MS:1000094
name	exponential
def	"The mass scan is done in exponential mode." [PSI:MS]
is_a	MS:1000019 scan law ! scan law

2.100. MS:1000095 linear

Table 102. Term [MS:1000095]
id	MS:1000095
name	linear
def	"OBSOLETE The mass scan is done in linear mode." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199).
is_a	MS:1000019 scan law ! scan law
is_obsolete	true

2.101. MS:1000096 quadratic

Table 103. Term [MS:1000096]
id	MS:1000096
name	quadratic
def	"The mass scan is done in quadratic mode." [PSI:MS]
is_a	MS:1000019 scan law ! scan law

2.102. MS:1000097 constant neutral mass loss

Table 104. Term [MS:1000097]
id	MS:1000097
name	constant neutral mass loss
def	"OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.103. MS:1000098 multiple ion monitoring

Table 105. Term [MS:1000098]
id	MS:1000098
name	multiple ion monitoring
def	"OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.104. MS:1000099 multiple reaction monitoring

Table 106. Term [MS:1000099]
id	MS:1000099
name	multiple reaction monitoring
def	"OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]
comment	This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206).
synonym	"MRM" EXACT []
is_obsolete	true

2.105. MS:1000100 precursor ion scan

Table 107. Term [MS:1000100]
id	MS:1000100
name	precursor ion scan
def	"OBSOLETE The specific scan function or process that will record a precursor ion spectrum." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.106. MS:1000101 product ion scan

Table 108. Term [MS:1000101]
id	MS:1000101
name	product ion scan
def	"OBSOLETE The specific scan function or process that records product ion spectrum." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.107. MS:1000102 single ion monitoring

Table 109. Term [MS:1000102]
id	MS:1000102
name	single ion monitoring
def	"OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS]
comment	This term was made obsolete because it was replaced by single ion monitoring (MS:100205).
is_obsolete	true

2.108. MS:1000103 single reaction monitoring

Table 110. Term [MS:1000103]
id	MS:1000103
name	single reaction monitoring
def	"OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]
comment	This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206).
is_obsolete	true

2.109. MS:1000104 None ??

Table 111. Term [MS:1000104]
id	MS:1000104
name	None ??
def	"OBSOLETE None." [PSI:MS]
comment	This term was made obsolete because .
is_obsolete	true

2.110. MS:1000105 reflectron off

Table 112. Term [MS:1000105]
id	MS:1000105
name	reflectron off
def	"Reflectron is off." [PSI:MS]
is_a	MS:1000021 reflectron state ! reflectron state

2.111. MS:1000106 reflectron on

Table 113. Term [MS:1000106]
id	MS:1000106
name	reflectron on
def	"Reflectron is on." [PSI:MS]
is_a	MS:1000021 reflectron state ! reflectron state

2.112. MS:1000107 channeltron

Table 114. Term [MS:1000107]
id	MS:1000107
name	channeltron
def	"A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse." [PSI:MS]
synonym	"Channeltron Detector" EXACT []
is_a	MS:1000026 detector type ! detector type

2.113. MS:1000108 conversion dynode electron multiplier

Table 115. Term [MS:1000108]
id	MS:1000108
name	conversion dynode electron multiplier
def	"A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS]
is_a	MS:1000346 conversion dynode ! conversion dynode

2.114. MS:1000109 conversion dynode photomultiplier

Table 116. Term [MS:1000109]
id	MS:1000109
name	conversion dynode photomultiplier
def	"A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier." [PSI:MS]
synonym	"ion-to-photon detector" RELATED []
is_a	MS:1000346 conversion dynode ! conversion dynode

2.115. MS:1000110 daly detector

Table 117. Term [MS:1000110]
id	MS:1000110
name	daly detector
def	"Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector." [PSI:MS]
synonym	"Daly" EXACT []
is_a	MS:1000026 detector type ! detector type

2.116. MS:1000111 electron multiplier tube

Table 118. Term [MS:1000111]
id	MS:1000111
name	electron multiplier tube
def	"A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons." [PSI:MS]
synonym	"EMT" EXACT []
is_a	MS:1000253 electron multiplier ! electron multiplier

2.117. MS:1000112 faraday cup

Table 119. Term [MS:1000112]
id	MS:1000112
name	faraday cup
def	"A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.118. MS:1000113 focal plane array

Table 120. Term [MS:1000113]
id	MS:1000113
name	focal plane array
def	"An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS]
is_a	MS:1000348 focal plane collector ! focal plane collector

2.119. MS:1000114 microchannel plate detector

Table 121. Term [MS:1000114]
id	MS:1000114
name	microchannel plate detector
def	"A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate." [PSI:MS]
synonym	"multichannel plate" EXACT []
is_a	MS:1000345 array detector ! array detector

2.120. MS:1000115 multi-collector

Table 122. Term [MS:1000115]
id	MS:1000115
name	multi-collector
def	"A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.121. MS:1000116 photomultiplier

Table 123. Term [MS:1000116]
id	MS:1000116
name	photomultiplier
def	"A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS]
synonym	"PMT" EXACT []
is_a	MS:1000026 detector type ! detector type

2.122. MS:1000117 analog-digital converter

Table 124. Term [MS:1000117]
id	MS:1000117
name	analog-digital converter
def	"Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers." [PSI:MS]
synonym	"ADC" EXACT []
is_a	MS:1000027 detector acquisition mode ! detector acquisition mode

2.123. MS:1000118 pulse counting

Table 125. Term [MS:1000118]
id	MS:1000118
name	pulse counting
def	"Definition to do." [PSI:MS]
is_a	MS:1000027 detector acquisition mode ! detector acquisition mode

2.124. MS:1000119 time-digital converter

Table 126. Term [MS:1000119]
id	MS:1000119
name	time-digital converter
def	"A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS]
synonym	"TDC" EXACT []
is_a	MS:1000027 detector acquisition mode ! detector acquisition mode

2.125. MS:1000120 transient recorder

Table 127. Term [MS:1000120]
id	MS:1000120
name	transient recorder
def	"A detector acquisition mode used for detecting transient signals." [PSI:MS]
is_a	MS:1000027 detector acquisition mode ! detector acquisition mode

2.126. MS:1000121 SCIEX instrument model

Table 128. Term [MS:1000121]
id	MS:1000121
name	SCIEX instrument model
def	"The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems\|MDS SCIEX\"." [PSI:MS]
synonym	"Applied Biosystems\|MDS SCIEX" RELATED []
is_a	MS:1000031 instrument model ! instrument model

2.127. MS:1000122 Bruker Daltonics instrument model

Table 129. Term [MS:1000122]
id	MS:1000122
name	Bruker Daltonics instrument model
def	"Bruker Daltonics' instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.128. MS:1000123 IonSpec instrument model

Table 130. Term [MS:1000123]
id	MS:1000123
name	IonSpec instrument model
def	"IonSpec corporation instrument model." [PSI:MS]
is_a	MS:1000489 Varian instrument model ! Varian instrument model

2.129. MS:1000124 Shimadzu instrument model

Table 131. Term [MS:1000124]
id	MS:1000124
name	Shimadzu instrument model
def	"Shimadzu corporation instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.130. MS:1000125 Thermo Finnigan instrument model

Table 132. Term [MS:1000125]
id	MS:1000125
name	Thermo Finnigan instrument model
def	"ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS]
is_a	MS:1000483 Thermo Fisher Scientific instrument model ! Thermo Fisher Scientific instrument model

2.131. MS:1000126 Waters instrument model

Table 133. Term [MS:1000126]
id	MS:1000126
name	Waters instrument model
def	"Waters Corporation instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.132. MS:1000127 centroid spectrum

Table 134. Term [MS:1000127]
id	MS:1000127
name	centroid spectrum
def	"Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS]
synonym	"Discrete Mass Spectrum" EXACT []
is_a	MS:1000525 spectrum representation ! spectrum representation

2.133. MS:1000128 profile spectrum

Table 135. Term [MS:1000128]
id	MS:1000128
name	profile spectrum
def	"A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis." [PSI:MS]
synonym	"continuous mass spectrum" EXACT []
synonym	"Continuum Mass Spectrum" EXACT []
is_a	MS:1000525 spectrum representation ! spectrum representation

2.134. MS:1000129 negative scan

Table 136. Term [MS:1000129]
id	MS:1000129
name	negative scan
def	"Polarity of the scan is negative." [PSI:MS]
is_a	MS:1000465 scan polarity ! scan polarity
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute

2.135. MS:1000130 positive scan

Table 137. Term [MS:1000130]
id	MS:1000130
name	positive scan
def	"Polarity of the scan is positive." [PSI:MS]
is_a	MS:1000465 scan polarity ! scan polarity
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute

2.136. MS:1000131 number of detector counts

Table 138. Term [MS:1000131]
id	MS:1000131
name	number of detector counts
def	"The number of counted events observed in one or a group of elements of a detector." [PSI:MS]
is_a	MS:1000043 intensity unit ! intensity unit

2.137. MS:1000132 percent of base peak

Table 139. Term [MS:1000132]
id	MS:1000132
name	percent of base peak
def	"The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000043 intensity unit ! intensity unit

2.138. MS:1000133 collision-induced dissociation

Table 140. Term [MS:1000133]
id	MS:1000133
name	collision-induced dissociation
def	"The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS]
synonym	"CID" EXACT []
synonym	"CAD" EXACT []
synonym	"collisionally activated dissociation" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.139. MS:1000134 plasma desorption

Table 141. Term [MS:1000134]
id	MS:1000134
name	plasma desorption
def	"The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS]
synonym	"PD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.140. MS:1000135 post-source decay

Table 142. Term [MS:1000135]
id	MS:1000135
name	post-source decay
def	"A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra." [PSI:MS]
synonym	"PSD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.141. MS:1000136 surface-induced dissociation

Table 143. Term [MS:1000136]
id	MS:1000136
name	surface-induced dissociation
def	"Fragmentation that results from the collision of an ion with a surface." [PSI:MS]
synonym	"SID" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.142. MS:1000137 electron volt

Table 144. Term [MS:1000137]
id	MS:1000137
name	electron volt
def	"OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).
is_obsolete	true

2.143. MS:1000138 normalized collision energy

Table 145. Term [MS:1000138]
id	MS:1000138
name	normalized collision energy
def	"Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000187] ! percent

2.144. MS:1000139 4000 QTRAP

Table 146. Term [MS:1000139]
id	MS:1000139
name	4000 QTRAP
def	"Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.145. MS:1000140 4700 Proteomics Analyzer

Table 147. Term [MS:1000140]
id	MS:1000140
name	4700 Proteomics Analyzer
def	"Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS]
is_a	MS:1000495 Applied Biosystems instrument model ! Applied Biosystems instrument model

2.146. MS:1000141 apex IV

Table 148. Term [MS:1000141]
id	MS:1000141
name	apex IV
def	"Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
is_a	MS:1001556 Bruker Daltonics apex series ! Bruker Daltonics apex series

2.147. MS:1000142 apex Q

Table 149. Term [MS:1000142]
id	MS:1000142
name	apex Q
def	"Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
is_a	MS:1001556 Bruker Daltonics apex series ! Bruker Daltonics apex series

2.148. MS:1000143 API 150EX

Table 150. Term [MS:1000143]
id	MS:1000143
name	API 150EX
def	"Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.149. MS:1000144 API 150EX Prep

Table 151. Term [MS:1000144]
id	MS:1000144
name	API 150EX Prep
def	"Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.150. MS:1000145 API 2000

Table 152. Term [MS:1000145]
id	MS:1000145
name	API 2000
def	"Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.151. MS:1000146 API 3000

Table 153. Term [MS:1000146]
id	MS:1000146
name	API 3000
def	"Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.152. MS:1000147 API 4000

Table 154. Term [MS:1000147]
id	MS:1000147
name	API 4000
def	"Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.153. MS:1000148 autoflex II

Table 155. Term [MS:1000148]
id	MS:1000148
name	autoflex II
def	"Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.154. MS:1000149 autoflex TOF/TOF

Table 156. Term [MS:1000149]
id	MS:1000149
name	autoflex TOF/TOF
def	"Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.155. MS:1000150 Auto Spec Ultima NT

Table 157. Term [MS:1000150]
id	MS:1000150
name	Auto Spec Ultima NT
def	"Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.156. MS:1000151 BioTOF II

Table 158. Term [MS:1000151]
id	MS:1000151
name	BioTOF II
def	"Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS]
is_a	MS:1001535 Bruker Daltonics BioTOF series ! Bruker Daltonics BioTOF series

2.157. MS:1000152 BioTOF-Q

Table 159. Term [MS:1000152]
id	MS:1000152
name	BioTOF-Q
def	"Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS]
is_a	MS:1001535 Bruker Daltonics BioTOF series ! Bruker Daltonics BioTOF series

2.158. MS:1000153 DELTA plusAdvantage

Table 160. Term [MS:1000153]
id	MS:1000153
name	DELTA plusAdvantage
def	"ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.159. MS:1000154 DELTAplusXP

Table 161. Term [MS:1000154]
id	MS:1000154
name	DELTAplusXP
def	"ThermoFinnigan DELTAplusXP MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.160. MS:1000155 ELEMENT2

Table 162. Term [MS:1000155]
id	MS:1000155
name	ELEMENT2
def	"OBSOLETE ThermoFinnigan ELEMENT2 MS." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.161. MS:1000156 esquire 4000

Table 163. Term [MS:1000156]
id	MS:1000156
name	esquire 4000
def	"Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001533 Bruker Daltonics esquire series ! Bruker Daltonics esquire series

2.162. MS:1000157 esquire 6000

Table 164. Term [MS:1000157]
id	MS:1000157
name	esquire 6000
def	"Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001533 Bruker Daltonics esquire series ! Bruker Daltonics esquire series

2.163. MS:1000158 explorer

Table 165. Term [MS:1000158]
id	MS:1000158
name	explorer
def	"IonSpec Explorer MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.164. MS:1000159 GCT

Table 166. Term [MS:1000159]
id	MS:1000159
name	GCT
def	"Waters oa-ToF based GCT." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.165. MS:1000160 HCT

Table 167. Term [MS:1000160]
id	MS:1000160
name	HCT
def	"Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1000697 Bruker Daltonics HCT Series ! Bruker Daltonics HCT Series

2.166. MS:1000161 HCTplus

Table 168. Term [MS:1000161]
id	MS:1000161
name	HCTplus
def	"Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1000697 Bruker Daltonics HCT Series ! Bruker Daltonics HCT Series

2.167. MS:1000162 HiRes ESI

Table 169. Term [MS:1000162]
id	MS:1000162
name	HiRes ESI
def	"IonSpec HiResESI MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.168. MS:1000163 HiRes MALDI

Table 170. Term [MS:1000163]
id	MS:1000163
name	HiRes MALDI
def	"IonSpec HiResMALDI MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.169. MS:1000164 IsoPrime

Table 171. Term [MS:1000164]
id	MS:1000164
name	IsoPrime
def	"Waters IsoPrime MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.170. MS:1000165 IsoProbe

Table 172. Term [MS:1000165]
id	MS:1000165
name	IsoProbe
def	"Waters IsoProbe MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.171. MS:1000166 IsoProbe T

Table 173. Term [MS:1000166]
id	MS:1000166
name	IsoProbe T
def	"Waters IsoProbe T MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.172. MS:1000167 LCQ Advantage

Table 174. Term [MS:1000167]
id	MS:1000167
name	LCQ Advantage
def	"ThermoFinnigan LCQ Advantage MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.173. MS:1000168 LCQ Classic

Table 175. Term [MS:1000168]
id	MS:1000168
name	LCQ Classic
def	"ThermoFinnigan LCQ Classic MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.174. MS:1000169 LCQ Deca XP Plus

Table 176. Term [MS:1000169]
id	MS:1000169
name	LCQ Deca XP Plus
def	"ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.175. MS:1000170 M@LDI L

Table 177. Term [MS:1000170]
id	MS:1000170
name	M@LDI L
def	"Waters oa-ToF based MALDI L." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.176. MS:1000171 M@LDI LR

Table 178. Term [MS:1000171]
id	MS:1000171
name	M@LDI LR
def	"Waters oa-ToF based MALDI LR." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.177. MS:1000172 MAT253

Table 179. Term [MS:1000172]
id	MS:1000172
name	MAT253
def	"ThermoFinnigan MAT253 MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.178. MS:1000173 MAT900XP

Table 180. Term [MS:1000173]
id	MS:1000173
name	MAT900XP
def	"ThermoFinnigan MAT900XP MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.179. MS:1000174 MAT900XP Trap

Table 181. Term [MS:1000174]
id	MS:1000174
name	MAT900XP Trap
def	"ThermoFinnigan MAT900XP Trap MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.180. MS:1000175 MAT95XP

Table 182. Term [MS:1000175]
id	MS:1000175
name	MAT95XP
def	"ThermoFinnigan MAT95XP MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.181. MS:1000176 MAT95XP Trap

Table 183. Term [MS:1000176]
id	MS:1000176
name	MAT95XP Trap
def	"ThermoFinnigan MAT95XP Trap MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.182. MS:1000177 microflex

Table 184. Term [MS:1000177]
id	MS:1000177
name	microflex
def	"Bruker Daltonics' microflex: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.183. MS:1000178 microTOF LC

Table 185. Term [MS:1000178]
id	MS:1000178
name	microTOF LC
def	"Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.184. MS:1000179 neptune

Table 186. Term [MS:1000179]
id	MS:1000179
name	neptune
def	"ThermoFinnigan NEPTUNE MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.185. MS:1000180 NG-5400

Table 187. Term [MS:1000180]
id	MS:1000180
name	NG-5400
def	"Waters NG-5400 MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.186. MS:1000181 OMEGA

Table 188. Term [MS:1000181]
id	MS:1000181
name	OMEGA
def	"IonSpec OMEGA MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.187. MS:1000182 OMEGA-2001

Table 189. Term [MS:1000182]
id	MS:1000182
name	OMEGA-2001
def	"IonSpec OMEGA-2001 MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.188. MS:1000183 OmniFlex

Table 190. Term [MS:1000183]
id	MS:1000183
name	OmniFlex
def	"Bruker Daltonics' OmniFlex: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.189. MS:1000184 Platform ICP

Table 191. Term [MS:1000184]
id	MS:1000184
name	Platform ICP
def	"Waters Platform ICP MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.190. MS:1000185 PolarisQ

Table 192. Term [MS:1000185]
id	MS:1000185
name	PolarisQ
def	"ThermoFinnigan PolarisQ MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.191. MS:1000186 proteomics solution 1

Table 193. Term [MS:1000186]
id	MS:1000186
name	proteomics solution 1
def	"Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.192. MS:1000187 Q TRAP

Table 194. Term [MS:1000187]
id	MS:1000187
name	Q TRAP
def	"Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.193. MS:1000188 Q-Tof micro

Table 195. Term [MS:1000188]
id	MS:1000188
name	Q-Tof micro
def	"Waters oa-ToF based Q-Tof micro." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.194. MS:1000189 Q-Tof Ultima

Table 196. Term [MS:1000189]
id	MS:1000189
name	Q-Tof Ultima
def	"Waters oa-ToF based Q-Tof Ultima." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.195. MS:1000190 QSTAR

Table 197. Term [MS:1000190]
id	MS:1000190
name	QSTAR
def	"Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.196. MS:1000191 quattro micro

Table 198. Term [MS:1000191]
id	MS:1000191
name	quattro micro
def	"Waters (triple) quadrupole based micro." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.197. MS:1000192 Quattro Ultima

Table 199. Term [MS:1000192]
id	MS:1000192
name	Quattro Ultima
def	"Waters (triple) quadrupole based Ultima." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.198. MS:1000193 Surveyor MSQ

Table 200. Term [MS:1000193]
id	MS:1000193
name	Surveyor MSQ
def	"ThermoFinnigan Surveyor MSQ MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.199. MS:1000194 SymBiot I

Table 201. Term [MS:1000194]
id	MS:1000194
name	SymBiot I
def	"Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.200. MS:1000195 SymBiot XVI

Table 202. Term [MS:1000195]
id	MS:1000195
name	SymBiot XVI
def	"Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.201. MS:1000196 TEMPUS TOF

Table 203. Term [MS:1000196]
id	MS:1000196
name	TEMPUS TOF
def	"ThermoFinnigan TEMPUS TOF MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.202. MS:1000197 TRACE DSQ

Table 204. Term [MS:1000197]
id	MS:1000197
name	TRACE DSQ
def	"ThermoFinnigan TRACE DSQ MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.203. MS:1000198 TRITON

Table 205. Term [MS:1000198]
id	MS:1000198
name	TRITON
def	"ThermoFinnigan TRITON MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.204. MS:1000199 TSQ Quantum

Table 206. Term [MS:1000199]
id	MS:1000199
name	TSQ Quantum
def	"ThermoFinnigan TSQ Quantum MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.205. MS:1000200 ultima

Table 207. Term [MS:1000200]
id	MS:1000200
name	ultima
def	"IonSpec Ultima MS." [PSI:MS]
is_a	MS:1000123 IonSpec instrument model ! IonSpec instrument model

2.206. MS:1000201 ultraflex

Table 208. Term [MS:1000201]
id	MS:1000201
name	ultraflex
def	"Bruker Daltonics' ultraflex: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.207. MS:1000202 ultraflex TOF/TOF

Table 209. Term [MS:1000202]
id	MS:1000202
name	ultraflex TOF/TOF
def	"Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.208. MS:1000203 Voyager-DE PRO

Table 210. Term [MS:1000203]
id	MS:1000203
name	Voyager-DE PRO
def	"Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS]
is_a	MS:1000495 Applied Biosystems instrument model ! Applied Biosystems instrument model

2.209. MS:1000204 Voyager-DE STR

Table 211. Term [MS:1000204]
id	MS:1000204
name	Voyager-DE STR
def	"Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS]
is_a	MS:1000495 Applied Biosystems instrument model ! Applied Biosystems instrument model

2.210. MS:1000205 selected ion monitoring

Table 212. Term [MS:1000205]
id	MS:1000205
name	selected ion monitoring
def	"The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum." [PSI:MS]
synonym	"MIM" RELATED []
synonym	"Multiple Ion Monitoring" EXACT []
synonym	"SIM" EXACT []
is_a	MS:1000596 measurement method ! measurement method

2.211. MS:1000206 selected reaction monitoring

Table 213. Term [MS:1000206]
id	MS:1000206
name	selected reaction monitoring
def	"Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space." [PSI:MS]
synonym	"MRM" RELATED []
synonym	"Multiple Reaction Monitoring" RELATED []
synonym	"SRM" EXACT []
is_a	MS:1000596 measurement method ! measurement method

2.212. MS:1000207 accurate mass

Table 214. Term [MS:1000207]
id	MS:1000207
name	accurate mass
def	"OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.213. MS:1000208 average mass

Table 215. Term [MS:1000208]
id	MS:1000208
name	average mass
def	"OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.214. MS:1000209 appearance energy

Table 216. Term [MS:1000209]
id	MS:1000209
name	appearance energy
def	"OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS]
synonym	"AE" EXACT []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000266] ! electronvolt
is_obsolete	true

2.215. MS:1000210 base peak

Table 217. Term [MS:1000210]
id	MS:1000210
name	base peak
def	"The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures." [PSI:MS]
synonym	"BP" EXACT []
is_a	MS:1000231 peak ! peak

2.216. MS:1000211 OBSOLETE charge number

Table 218. Term [MS:1000211]
id	MS:1000211
name	OBSOLETE charge number
def	"OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_obsolete	true

2.217. MS:1000212 dalton

Table 219. Term [MS:1000212]
id	MS:1000212
name	dalton
def	"OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).
is_obsolete	true

2.218. MS:1000213 electron affinity

Table 220. Term [MS:1000213]
id	MS:1000213
name	electron affinity
def	"OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS]
comment	This child of the former purgatory term ion attribute was made obsolete.
synonym	"EA" EXACT []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete	true

2.219. MS:1000214 electron energy obsolete

Table 221. Term [MS:1000214]
id	MS:1000214
name	electron energy obsolete
def	"OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.220. MS:1000215 exact mass

Table 222. Term [MS:1000215]
id	MS:1000215
name	exact mass
def	"OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.221. MS:1000216 field-free region

Table 223. Term [MS:1000216]
id	MS:1000216
name	field-free region
def	"A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS]
synonym	"FFR" EXACT []
is_a	MS:1000487 ion optics attribute ! ion optics attribute

2.222. MS:1000217 ionization cross section

Table 224. Term [MS:1000217]
id	MS:1000217
name	ionization cross section
def	"OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.223. MS:1000218 ionization efficiency

Table 225. Term [MS:1000218]
id	MS:1000218
name	ionization efficiency
def	"OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
comment	This term was made obsolete because it was replaced by ionization efficiency (MS:1000392).
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete	true

2.224. MS:1000219 ionization energy

Table 226. Term [MS:1000219]
id	MS:1000219
name	ionization energy
def	"OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS]
synonym	"IE" EXACT []
comment	This child of the former purgatory term ion attribute was made obsolete.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
relationship	has_units [UO:0000266] ! electronvolt
is_obsolete	true

2.225. MS:1000220 isotope dilution mass spectrometry

Table 227. Term [MS:1000220]
id	MS:1000220
name	isotope dilution mass spectrometry
def	"OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS]
comment	This child of the former purgatory term mass spectrometry was made obsolete.
synonym	"IDMS" EXACT []
is_obsolete	true

2.226. MS:1000221 magnetic deflection

Table 228. Term [MS:1000221]
id	MS:1000221
name	magnetic deflection
def	"The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.227. MS:1000222 mass defect

Table 229. Term [MS:1000222]
id	MS:1000222
name	mass defect
def	"OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.228. MS:1000223 mass number

Table 230. Term [MS:1000223]
id	MS:1000223
name	mass number
def	"OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
is_obsolete	true

2.229. MS:1000224 molecular mass

Table 231. Term [MS:1000224]
id	MS:1000224
name	molecular mass
def	"Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000861 molecular entity property ! molecular entity property
relationship	has_units [UO:0000002] ! mass unit

2.230. MS:1000225 monoisotopic mass

Table 232. Term [MS:1000225]
id	MS:1000225
name	monoisotopic mass
def	"OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.231. MS:1000226 molecular beam mass spectrometry

Table 233. Term [MS:1000226]
id	MS:1000226
name	molecular beam mass spectrometry
def	"OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"MBMS" EXACT []
is_obsolete	true

2.232. MS:1000227 multiphoton ionization

Table 234. Term [MS:1000227]
id	MS:1000227
name	multiphoton ionization
def	"Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS]
synonym	"MPI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.233. MS:1000228 nitrogen rule

Table 235. Term [MS:1000228]
id	MS:1000228
name	nitrogen rule
def	"OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.234. MS:1000229 nominal mass

Table 236. Term [MS:1000229]
id	MS:1000229
name	nominal mass
def	"OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
comment	This child of the former purgatory term ion attribute was made obsolete.
relationship	has_units [UO:0000002] ! mass unit
is_obsolete	true

2.235. MS:1000230 odd-electron rule

Table 237. Term [MS:1000230]
id	MS:1000230
name	odd-electron rule
def	"OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.236. MS:1000231 peak

Table 238. Term [MS:1000231]
id	MS:1000231
name	peak
def	"A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum

2.237. MS:1000232 peak intensity

Table 239. Term [MS:1000232]
id	MS:1000232
name	peak intensity
def	"OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS]
comment	This term was made obsolete because it was replaced by base peak intensity (MS:1000505).
is_obsolete	true

2.238. MS:1000233 proton affinity

Table 240. Term [MS:1000233]
id	MS:1000233
name	proton affinity
def	"OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ →[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS]
synonym	"PA" EXACT [PSI:MS]
comment	This child of the former purgatory term ion attribute was made obsolete.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete	true

2.239. MS:1000234 mass resolving power

Table 241. Term [MS:1000234]
id	MS:1000234
name	mass resolving power
def	"OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
comment	This term was made obsolete because it was replaced by mass resolving power (MS:1000800).
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete	true

2.240. MS:1000235 total ion current chromatogram

Table 242. Term [MS:1000235]
id	MS:1000235
name	total ion current chromatogram
def	"Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS]
synonym	"TIC chromatogram" EXACT []
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram

2.241. MS:1000236 transmission

Table 243. Term [MS:1000236]
id	MS:1000236
name	transmission
def	"The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000496 instrument attribute ! instrument attribute

2.242. MS:1000237 unified atomic mass unit

Table 244. Term [MS:1000237]
id	MS:1000237
name	unified atomic mass unit
def	"OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS]
comment	This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221).
synonym	"u" EXACT []
is_obsolete	true

2.243. MS:1000238 accelerator mass spectrometry

Table 245. Term [MS:1000238]
id	MS:1000238
name	accelerator mass spectrometry
def	"OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"AMS" EXACT []
is_obsolete	true

2.244. MS:1000239 atmospheric pressure matrix-assisted laser desorption ionization

Table 246. Term [MS:1000239]
id	MS:1000239
name	atmospheric pressure matrix-assisted laser desorption ionization
def	"Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer." [PSI:MS]
synonym	"AP MALDI" EXACT []
is_a	MS:1000240 atmospheric pressure ionization ! atmospheric pressure ionization

2.245. MS:1000240 atmospheric pressure ionization

Table 247. Term [MS:1000240]
id	MS:1000240
name	atmospheric pressure ionization
def	"Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS]
synonym	"API" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.246. MS:1000241 Atmostpheric Pressure Photoionization

Table 248. Term [MS:1000241]
id	MS:1000241
name	Atmostpheric Pressure Photoionization
def	"OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS]
comment	This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382).
synonym	"APPI" EXACT []
is_obsolete	true

2.247. MS:1000242 blackbody infrared radiative dissociation

Table 249. Term [MS:1000242]
id	MS:1000242
name	blackbody infrared radiative dissociation
def	"A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation." [PSI:MS]
synonym	"BIRD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.248. MS:1000243 charge-remote fragmentation

Table 250. Term [MS:1000243]
id	MS:1000243
name	charge-remote fragmentation
def	"OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
synonym	"CRF" EXACT []
is_obsolete	true

2.249. MS:1000244 consecutive reaction monitoring

Table 251. Term [MS:1000244]
id	MS:1000244
name	consecutive reaction monitoring
def	"OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]
comment	This former purgatory term was made obsolete.
synonym	"CRM" EXACT []
is_obsolete	true

2.250. MS:1000245 charge stripping

Table 252. Term [MS:1000245]
id	MS:1000245
name	charge stripping
def	"The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion." [PSI:MS]
synonym	"CS" EXACT []
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute

2.251. MS:1000246 delayed extraction

Table 253. Term [MS:1000246]
id	MS:1000246
name	delayed extraction
def	"The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer." [PSI:MS]
synonym	"DE" EXACT []
is_a	MS:1000597 ion optics type ! ion optics type

2.252. MS:1000247 desorption ionization

Table 254. Term [MS:1000247]
id	MS:1000247
name	desorption ionization
def	"The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS]
synonym	"DI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.253. MS:1000248 direct insertion probe

Table 255. Term [MS:1000248]
id	MS:1000248
name	direct insertion probe
def	"A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS]
synonym	"DIP" EXACT []
is_a	MS:1000007 inlet type ! inlet type

2.254. MS:1000249 direct liquid introduction

Table 256. Term [MS:1000249]
id	MS:1000249
name	direct liquid introduction
def	"The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS]
synonym	"DLI" EXACT []
is_a	MS:1000007 inlet type ! inlet type

2.255. MS:1000250 electron capture dissociation

Table 257. Term [MS:1000250]
id	MS:1000250
name	electron capture dissociation
def	"A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments." [PSI:MS]
synonym	"ECD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.256. MS:1000251 even-electron ion

Table 258. Term [MS:1000251]
id	MS:1000251
name	even-electron ion
def	"OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
synonym	"EE" EXACT []
is_obsolete	true

2.257. MS:1000252 electron-induced excitation in organics

Table 259. Term [MS:1000252]
id	MS:1000252
name	electron-induced excitation in organics
def	"OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
synonym	"EIEIO" EXACT []
is_obsolete	true

2.258. MS:1000253 electron multiplier

Table 260. Term [MS:1000253]
id	MS:1000253
name	electron multiplier
def	"A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons." [PSI:MS]
synonym	"EM" EXACT []
is_a	MS:1000026 detector type ! detector type

2.259. MS:1000254 electrostatic energy analyzer

Table 261. Term [MS:1000254]
id	MS:1000254
name	electrostatic energy analyzer
def	"A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time." [PSI:MS]
synonym	"ESA" EXACT []
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.260. MS:1000255 flowing afterglow

Table 262. Term [MS:1000255]
id	MS:1000255
name	flowing afterglow
def	"An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa." [PSI:MS]
synonym	"FA" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.261. MS:1000256 high-field asymmetric waveform ion mobility spectrometry

Table 263. Term [MS:1000256]
id	MS:1000256
name	high-field asymmetric waveform ion mobility spectrometry
def	"OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"FAIMS" EXACT []
is_obsolete	true

2.262. MS:1000257 field desorption

Table 264. Term [MS:1000257]
id	MS:1000257
name	field desorption
def	"The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization." [PSI:MS]
synonym	"FD" EXACT []
is_a	MS:1000247 desorption ionization ! desorption ionization

2.263. MS:1000258 field ionization

Table 265. Term [MS:1000258]
id	MS:1000258
name	field ionization
def	"The removal of electrons from any species by interaction with a high electric field." [PSI:MS]
synonym	"FI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.264. MS:1000259 glow discharge ionization

Table 266. Term [MS:1000259]
id	MS:1000259
name	glow discharge ionization
def	"The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas." [PSI:MS]
synonym	"GD-MS" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.265. MS:1000260 ion kinetic energy spectrometry

Table 267. Term [MS:1000260]
id	MS:1000260
name	ion kinetic energy spectrometry
def	"OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"IKES" EXACT []
is_obsolete	true

2.266. MS:1000261 ion mobility spectrometry

Table 268. Term [MS:1000261]
id	MS:1000261
name	ion mobility spectrometry
def	"OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"IMS" EXACT []
is_obsolete	true

2.267. MS:1000262 infrared multiphoton dissociation

Table 269. Term [MS:1000262]
id	MS:1000262
name	infrared multiphoton dissociation
def	"Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS]
synonym	"IRMPD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.268. MS:1000263 isotope ratio mass spectrometry

Table 270. Term [MS:1000263]
id	MS:1000263
name	isotope ratio mass spectrometry
def	"OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS]
comment	This child of the former purgatory term mass spectrometry was made obsolete.
synonym	"IRMS" EXACT []
is_obsolete	true

2.269. MS:1000264 ion trap

Table 271. Term [MS:1000264]
id	MS:1000264
name	ion trap
def	"A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS]
synonym	"IT" EXACT []
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.270. MS:1000265 kinetic energy release distribution

Table 272. Term [MS:1000265]
id	MS:1000265
name	kinetic energy release distribution
def	"OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
synonym	"KERD" EXACT []
is_obsolete	true

2.271. MS:1000266 Laser Desorption

Table 273. Term [MS:1000266]
id	MS:1000266
name	Laser Desorption
alt_id	MS:1000393
def	"OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS]
comment	This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393).
synonym	"Laser Ionization MERGE" EXACT []
synonym	"LD" EXACT []
is_obsolete	true

2.272. MS:1000267 mass analyzed ion kinetic energy spectrometry

Table 274. Term [MS:1000267]
id	MS:1000267
name	mass analyzed ion kinetic energy spectrometry
def	"OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"MIKES" EXACT []
is_obsolete	true

2.273. MS:1000268 mass spectrometry

Table 275. Term [MS:1000268]
id	MS:1000268
name	mass spectrometry
def	"OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS]
comment	This former purgatory term was made obsolete.
synonym	"MS" EXACT []
is_obsolete	true

2.274. MS:1000269 mass spectrometry/mass spectrometry

Table 276. Term [MS:1000269]
id	MS:1000269
name	mass spectrometry/mass spectrometry
def	"OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"MS/MS" EXACT []
is_obsolete	true

2.275. MS:1000270 multiple stage mass spectrometry

Table 277. Term [MS:1000270]
id	MS:1000270
name	multiple stage mass spectrometry
def	"OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
synonym	"MSn" EXACT []
is_obsolete	true

2.276. MS:1000271 Negative Ion chemical ionization

Table 278. Term [MS:1000271]
id	MS:1000271
name	Negative Ion chemical ionization
def	"Chemical ionization that results in the formation of negative ions." [PSI:MS]
synonym	"NICI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.277. MS:1000272 neutralization reionization mass spectrometry

Table 279. Term [MS:1000272]
id	MS:1000272
name	neutralization reionization mass spectrometry
def	"With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species." [PSI:MS]
synonym	"NRMS" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.278. MS:1000273 photoionization

Table 280. Term [MS:1000273]
id	MS:1000273
name	photoionization
def	"The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS]
synonym	"PI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.279. MS:1000274 pyrolysis mass spectrometry

Table 281. Term [MS:1000274]
id	MS:1000274
name	pyrolysis mass spectrometry
def	"A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source." [PSI:MS]
synonym	"PyMS" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.280. MS:1000275 collision quadrupole

Table 282. Term [MS:1000275]
id	MS:1000275
name	collision quadrupole
def	"A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation." [PSI:MS]
synonym	"q" EXACT []
is_a	MS:1000597 ion optics type ! ion optics type

2.281. MS:1000276 resonance enhanced multiphoton ionization

Table 283. Term [MS:1000276]
id	MS:1000276
name	resonance enhanced multiphoton ionization
def	"Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species." [PSI:MS]
synonym	"REMPI" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.282. MS:1000277 residual gas analyzer

Table 284. Term [MS:1000277]
id	MS:1000277
name	residual gas analyzer
def	"OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"RGA" EXACT []
is_obsolete	true

2.283. MS:1000278 surface enhanced laser desorption ionization

Table 285. Term [MS:1000278]
id	MS:1000278
name	surface enhanced laser desorption ionization
def	"The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization." [PSI:MS]
synonym	"SELDI" EXACT []
is_a	MS:1000406 surface ionization ! surface ionization

2.284. MS:1000279 surface enhanced neat desorption

Table 286. Term [MS:1000279]
id	MS:1000279
name	surface enhanced neat desorption
def	"Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS]
synonym	"SEND" EXACT []
is_a	MS:1000406 surface ionization ! surface ionization

2.285. MS:1000280 suface ionization

Table 287. Term [MS:1000280]
id	MS:1000280
name	suface ionization
def	"OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS]
comment	This term was made obsolete because it was replaced by surface ionization (MS:1000406).
synonym	"SI" EXACT []
is_obsolete	true

2.286. MS:1000281 selected ion flow tube

Table 288. Term [MS:1000281]
id	MS:1000281
name	selected ion flow tube
def	"A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS]
synonym	"SIFT" EXACT []
is_a	MS:1000597 ion optics type ! ion optics type

2.287. MS:1000282 sustained off-resonance irradiation

Table 289. Term [MS:1000282]
id	MS:1000282
name	sustained off-resonance irradiation
def	"A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion’s orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time." [PSI:MS]
synonym	"SORI" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.288. MS:1000283 Spark Source Mass Spectrometry

Table 290. Term [MS:1000283]
id	MS:1000283
name	Spark Source Mass Spectrometry
def	"OBSOLETE Mass spectrometry using spark ionization." [PSI:MS]
comment	This term was made obsolete because it was replaced by spark ionization (MS:1000404).
synonym	"SSMS" EXACT []
is_obsolete	true

2.289. MS:1000284 stored waveform inverse fourier transform

Table 291. Term [MS:1000284]
id	MS:1000284
name	stored waveform inverse fourier transform
def	"A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments." [PSI:MS]
synonym	"SWIFT" EXACT []
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.290. MS:1000285 total ion current

Table 292. Term [MS:1000285]
id	MS:1000285
name	total ion current
def	"The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS]
synonym	"TIC" EXACT []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003058 spectrum property ! spectrum property

2.291. MS:1000286 time lag focusing

Table 293. Term [MS:1000286]
id	MS:1000286
name	time lag focusing
def	"Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse." [PSI:MS]
synonym	"TLF" EXACT []
is_a	MS:1000597 ion optics type ! ion optics type

2.292. MS:1000287 time-of-flight mass spectrometer

Table 294. Term [MS:1000287]
id	MS:1000287
name	time-of-flight mass spectrometer
def	"OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
synonym	"TOF-MS" EXACT []
is_obsolete	true

2.293. MS:1000288 cyclotron

Table 295. Term [MS:1000288]
id	MS:1000288
name	cyclotron
def	"A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS]
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.294. MS:1000289 double-focusing mass spectrometer

Table 296. Term [MS:1000289]
id	MS:1000289
name	double-focusing mass spectrometer
def	"OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.295. MS:1000290 hybrid mass spectrometer

Table 297. Term [MS:1000290]
id	MS:1000290
name	hybrid mass spectrometer
def	"OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.296. MS:1000291 linear ion trap

Table 298. Term [MS:1000291]
id	MS:1000291
name	linear ion trap
def	"A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap." [PSI:MS]
is_a	MS:1000264 ion trap ! ion trap

2.297. MS:1000292 mass spectrograph obsolete

Table 299. Term [MS:1000292]
id	MS:1000292
name	mass spectrograph obsolete
def	"OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.298. MS:1000293 mass spectrometer

Table 300. Term [MS:1000293]
id	MS:1000293
name	mass spectrometer
def	"OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.299. MS:1000294 mass spectrum

Table 301. Term [MS:1000294]
id	MS:1000294
name	mass spectrum
def	"A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z)." [PSI:MS]
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000559 spectrum type ! spectrum type

2.300. MS:1000295 mattauch-herzog geometry

Table 302. Term [MS:1000295]
id	MS:1000295
name	mattauch-herzog geometry
def	"OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.301. MS:1000296 nier-johnson geometry

Table 303. Term [MS:1000296]
id	MS:1000296
name	nier-johnson geometry
def	"OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.302. MS:1000297 paul ion trap

Table 304. Term [MS:1000297]
id	MS:1000297
name	paul ion trap
def	"OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS]
comment	This term was made obsolete because it is redundant to quadrupole ion trap.
synonym	"quadrupole ion trap" RELATED []
is_obsolete	true

2.303. MS:1000298 prolate traochoidal mass spectrometer

Table 305. Term [MS:1000298]
id	MS:1000298
name	prolate traochoidal mass spectrometer
def	"OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.304. MS:1000299 quistor

Table 306. Term [MS:1000299]
id	MS:1000299
name	quistor
def	"OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.305. MS:1000300 reflectron

Table 307. Term [MS:1000300]
id	MS:1000300
name	reflectron
def	"A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.306. MS:1000301 sector mass spectrometer

Table 308. Term [MS:1000301]
id	MS:1000301
name	sector mass spectrometer
def	"OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.307. MS:1000302 tandem mass spectrometer

Table 309. Term [MS:1000302]
id	MS:1000302
name	tandem mass spectrometer
def	"OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.308. MS:1000303 transmission quadrupole mass spectrometer

Table 310. Term [MS:1000303]
id	MS:1000303
name	transmission quadrupole mass spectrometer
def	"OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.309. MS:1000304 accelerating voltage

Table 311. Term [MS:1000304]
id	MS:1000304
name	accelerating voltage
def	"The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000487 ion optics attribute ! ion optics attribute
relationship	has_units [UO:0000218] ! volt

2.310. MS:1000305 cyclotron motion

Table 312. Term [MS:1000305]
id	MS:1000305
name	cyclotron motion
def	"OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.311. MS:1000306 dynamic mass spectrometry

Table 313. Term [MS:1000306]
id	MS:1000306
name	dynamic mass spectrometry
def	"OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS]
comment	This child of the former purgatory term mass spectrometer was made obsolete.
is_obsolete	true

2.312. MS:1000307 einzel lens

Table 314. Term [MS:1000307]
id	MS:1000307
name	einzel lens
def	"Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.313. MS:1000308 electric field strength

Table 315. Term [MS:1000308]
id	MS:1000308
name	electric field strength
def	"The magnitude of the force per unit charge at a given point in space." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000487 ion optics attribute ! ion optics attribute
relationship	has_units [UO:0000268] ! volt per meter

2.314. MS:1000309 first stability region

Table 316. Term [MS:1000309]
id	MS:1000309
name	first stability region
def	"The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.315. MS:1000310 fringing field

Table 317. Term [MS:1000310]
id	MS:1000310
name	fringing field
def	"The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.316. MS:1000311 kinetic energy analyzer

Table 318. Term [MS:1000311]
id	MS:1000311
name	kinetic energy analyzer
def	"A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.317. MS:1000312 mass limit

Table 319. Term [MS:1000312]
id	MS:1000312
name	mass limit
def	"OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.318. MS:1000313 scan m/z range?

Table 320. Term [MS:1000313]
id	MS:1000313
name	scan m/z range?
def	"OBSOLETE The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.319. MS:1000314 mass selective axial ejection

Table 321. Term [MS:1000314]
id	MS:1000314
name	mass selective axial ejection
def	"OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.320. MS:1000315 mass selective instability

Table 322. Term [MS:1000315]
id	MS:1000315
name	mass selective instability
def	"OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.321. MS:1000316 mathieu stability diagram

Table 323. Term [MS:1000316]
id	MS:1000316
name	mathieu stability diagram
def	"OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.322. MS:1000317 orthogonal extraction

Table 324. Term [MS:1000317]
id	MS:1000317
name	orthogonal extraction
def	"OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.323. MS:1000318 resonance ion ejection

Table 325. Term [MS:1000318]
id	MS:1000318
name	resonance ion ejection
def	"OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.324. MS:1000319 space charge effect

Table 326. Term [MS:1000319]
id	MS:1000319
name	space charge effect
def	"The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time." [PSI:MS]
is_a	MS:1000487 ion optics attribute ! ion optics attribute

2.325. MS:1000320 static field

Table 327. Term [MS:1000320]
id	MS:1000320
name	static field
def	"An electric or magnetic field that does not change in time." [PSI:MS]
is_a	MS:1000597 ion optics type ! ion optics type

2.326. MS:1000321 2E Mass Spectrum

Table 328. Term [MS:1000321]
id	MS:1000321
name	2E Mass Spectrum
def	"OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.327. MS:1000322 charge inversion mass spectrum

Table 329. Term [MS:1000322]
id	MS:1000322
name	charge inversion mass spectrum
def	"The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS]
is_a	MS:1000294 mass spectrum ! mass spectrum

2.328. MS:1000323 constant neutral loss scan

Table 330. Term [MS:1000323]
id	MS:1000323
name	constant neutral loss scan
def	"OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS]
comment	This former purgatory term was made obsolete.
synonym	"constant neutral mass loss scan" RELATED []
synonym	"fixed neutral fragment scan" RELATED []
is_obsolete	true

2.329. MS:1000324 constant neutral gain scan

Table 331. Term [MS:1000324]
id	MS:1000324
name	constant neutral gain scan
def	"OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS]
comment	This former purgatory term was made obsolete.
synonym	"Constant Neutral Mass Gain Scan" EXACT []
is_obsolete	true

2.330. MS:1000325 constant neutral gain spectrum

Table 332. Term [MS:1000325]
id	MS:1000325
name	constant neutral gain spectrum
def	"A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS]
synonym	"constant neutral mass gain spectrum" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.331. MS:1000326 constant neutral loss spectrum

Table 333. Term [MS:1000326]
id	MS:1000326
name	constant neutral loss spectrum
def	"A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS]
synonym	"constant neutral mass loss spectrum" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.332. MS:1000327 consecutive reaction monitoring

Table 334. Term [MS:1000327]
id	MS:1000327
name	consecutive reaction monitoring
def	"OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]
comment	This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244).
is_obsolete	true

2.333. MS:1000328 e/2 mass spectrum

Table 335. Term [MS:1000328]
id	MS:1000328
name	e/2 mass spectrum
def	"A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions." [PSI:MS]
is_a	MS:1000294 mass spectrum ! mass spectrum

2.334. MS:1000329 linked scan

Table 336. Term [MS:1000329]
id	MS:1000329
name	linked scan
def	"OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.335. MS:1000330 linked scan at constant b/e

Table 337. Term [MS:1000330]
id	MS:1000330
name	linked scan at constant b/e
def	"OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors." [PSI:MS]
comment	This child of the former purgatory term linked scan was made obsolete.
is_obsolete	true

2.336. MS:1000331 Linked Scan at Constant E2/V

Table 338. Term [MS:1000331]
id	MS:1000331
name	Linked Scan at Constant E2/V
def	"OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS]
comment	This child of the former purgatory term linked scan was made obsolete.
is_obsolete	true

2.337. MS:1000332 Linked Scan at Constant B2/E

Table 339. Term [MS:1000332]
id	MS:1000332
name	Linked Scan at Constant B2/E
def	"OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended." [PSI:MS]
comment	This child of the former purgatory term linked scan was made obsolete.
is_obsolete	true

2.338. MS:1000333 Linked Scan at Constant B[1-(E/E0)]^1/2 / E

Table 340. Term [MS:1000333]
id	MS:1000333
name	Linked Scan at Constant B[1-(E/E0)]^1/2 / E
def	"OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan." [PSI:MS]
comment	This child of the former purgatory term linked scan was made obsolete.
is_obsolete	true

2.339. MS:1000334 MS/MS in Time

Table 341. Term [MS:1000334]
id	MS:1000334
name	MS/MS in Time
def	"OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.340. MS:1000335 MS/MS in Space

Table 342. Term [MS:1000335]
id	MS:1000335
name	MS/MS in Space
def	"OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition." [PSI:MS]
comment	This child of the former purgatory term m/z Separation Method was made obsolete.
is_obsolete	true

2.341. MS:1000336 neutral loss

Table 343. Term [MS:1000336]
id	MS:1000336
name	neutral loss
def	"The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001055 modification parameters ! modification parameters

2.342. MS:1000337 nth generation product ion

Table 344. Term [MS:1000337]
id	MS:1000337
name	nth generation product ion
def	"OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated." [PSI:MS]
comment	This child of the former purgatory term product ion was made obsolete.
synonym	"granddaughter ion" RELATED []
is_obsolete	true

2.343. MS:1000338 nth generation product ion scan

Table 345. Term [MS:1000338]
id	MS:1000338
name	nth generation product ion scan
def	"OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.344. MS:1000339 nth generation product ion spectrum

Table 346. Term [MS:1000339]
id	MS:1000339
name	nth generation product ion spectrum
def	"OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS]
comment	This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
is_obsolete	true

2.345. MS:1000340 precursor ion

Table 347. Term [MS:1000340]
id	MS:1000340
name	precursor ion
def	"OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated." [PSI:MS]
comment	This child of the former purgatory term ion role was made obsolete.
synonym	"parent ion" RELATED []
is_obsolete	true

2.346. MS:1000341 precursor ion spectrum

Table 348. Term [MS:1000341]
id	MS:1000341
name	precursor ion spectrum
def	"Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS]
is_a	MS:1000294 mass spectrum ! mass spectrum

2.347. MS:1000342 product ion

Table 349. Term [MS:1000342]
id	MS:1000342
name	product ion
def	"OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated." [PSI:MS]
comment	This child of the former purgatory term ion role was made obsolete.
synonym	"daughter ion" RELATED []
is_obsolete	true

2.348. MS:1000343 product ion spectrum

Table 350. Term [MS:1000343]
id	MS:1000343
name	product ion spectrum
def	"OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS]
comment	This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
is_a	MS:1000294 mass spectrum ! mass spectrum
is_obsolete	true

2.349. MS:1000344 progeny ion

Table 351. Term [MS:1000344]
id	MS:1000344
name	progeny ion
def	"OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ → M2+ → M3+ → M4+ → M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
synonym	"Progeny Fragment Ion" EXACT []
is_obsolete	true

2.350. MS:1000345 array detector

Table 352. Term [MS:1000345]
id	MS:1000345
name	array detector
def	"Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.351. MS:1000346 conversion dynode

Table 353. Term [MS:1000346]
id	MS:1000346
name	conversion dynode
def	"A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.352. MS:1000347 dynode

Table 354. Term [MS:1000347]
id	MS:1000347
name	dynode
def	"One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.353. MS:1000348 focal plane collector

Table 355. Term [MS:1000348]
id	MS:1000348
name	focal plane collector
def	"A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.354. MS:1000349 ion-to-photon detector

Table 356. Term [MS:1000349]
id	MS:1000349
name	ion-to-photon detector
def	"A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.355. MS:1000350 point collector

Table 357. Term [MS:1000350]
id	MS:1000350
name	point collector
def	"A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.356. MS:1000351 postacceleration detector

Table 358. Term [MS:1000351]
id	MS:1000351
name	postacceleration detector
def	"A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.357. MS:1000352 secondary electron

Table 359. Term [MS:1000352]
id	MS:1000352
name	secondary electron
def	"OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.358. MS:1000353 adduct ion

Table 360. Term [MS:1000353]
id	MS:1000353
name	adduct ion
def	"Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS]
is_a	MS:1003055 adduct ! adduct

2.359. MS:1000354 aromatic ion

Table 361. Term [MS:1000354]
id	MS:1000354
name	aromatic ion
def	"OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.360. MS:1000355 analog ion

Table 362. Term [MS:1000355]
id	MS:1000355
name	analog ion
def	"OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.361. MS:1000356 anti-aromatic ion

Table 363. Term [MS:1000356]
id	MS:1000356
name	anti-aromatic ion
def	"OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.362. MS:1000357 cationized molecule

Table 364. Term [MS:1000357]
id	MS:1000357
name	cationized molecule
def	"OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.363. MS:1000358 cluster ion

Table 365. Term [MS:1000358]
id	MS:1000358
name	cluster ion
def	"OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as , [(NaCl)nNa] and [(H3PO3)nHPO3]-." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.364. MS:1000359 Conventional ion

Table 366. Term [MS:1000359]
id	MS:1000359
name	Conventional ion
def	"OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.365. MS:1000360 diagnostic ion

Table 367. Term [MS:1000360]
id	MS:1000360
name	diagnostic ion
def	"OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.366. MS:1000361 dimeric ion

Table 368. Term [MS:1000361]
id	MS:1000361
name	dimeric ion
def	"OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.367. MS:1000362 distonic ion

Table 369. Term [MS:1000362]
id	MS:1000362
name	distonic ion
def	"OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.368. MS:1000363 enium ion

Table 370. Term [MS:1000363]
id	MS:1000363
name	enium ion
def	"OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.369. MS:1000364 fragment ion

Table 371. Term [MS:1000364]
id	MS:1000364
name	fragment ion
def	"OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS]
comment	This term was made obsolete because it was replaced by product ion (MS:1000342).
is_obsolete	true

2.370. MS:1000365 ion?

Table 372. Term [MS:1000365]
id	MS:1000365
name	ion?
def	"OBSOLETE An atomic or molecular species having a net positive or negative electric charge." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.371. MS:1000366 Isotopologue ion

Table 373. Term [MS:1000366]
id	MS:1000366
name	Isotopologue ion
def	"OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.372. MS:1000367 Isotopomeric ion

Table 374. Term [MS:1000367]
id	MS:1000367
name	Isotopomeric ion
def	"OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.373. MS:1000368 metastable ion

Table 375. Term [MS:1000368]
id	MS:1000368
name	metastable ion
def	"OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection." [PSI:MS]
comment	This child of the former purgatory term ion stability type was made obsolete.
is_obsolete	true

2.374. MS:1000369 molecular ion

Table 376. Term [MS:1000369]
id	MS:1000369
name	molecular ion
def	"OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.375. MS:1000370 negative ion

Table 377. Term [MS:1000370]
id	MS:1000370
name	negative ion
def	"OBSOLETE An atomic or molecular species having a net negative electric charge." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.376. MS:1000371 non-classical ion

Table 378. Term [MS:1000371]
id	MS:1000371
name	non-classical ion
def	"OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.377. MS:1000372 onium ion

Table 379. Term [MS:1000372]
id	MS:1000372
name	onium ion
def	"OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.378. MS:1000373 principal ion

Table 380. Term [MS:1000373]
id	MS:1000373
name	principal ion
def	"OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.379. MS:1000374 positive ion

Table 381. Term [MS:1000374]
id	MS:1000374
name	positive ion
def	"OBSOLETE An atomic or molecular species having a net positive electric charge." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.380. MS:1000375 protonated molecule

Table 382. Term [MS:1000375]
id	MS:1000375
name	protonated molecule
def	"OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.381. MS:1000376 radical ion

Table 383. Term [MS:1000376]
id	MS:1000376
name	radical ion
def	"OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.382. MS:1000377 reference ion

Table 384. Term [MS:1000377]
id	MS:1000377
name	reference ion
def	"OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion." [PSI:MS]
comment	This child of the former purgatory term ion chemical type was made obsolete.
is_obsolete	true

2.383. MS:1000378 stable ion

Table 385. Term [MS:1000378]
id	MS:1000378
name	stable ion
def	"OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS]
comment	This child of the former purgatory term ion stability type was made obsolete.
is_obsolete	true

2.384. MS:1000379 unstable ion

Table 386. Term [MS:1000379]
id	MS:1000379
name	unstable ion
def	"OBSOLETE An ion with sufficient energy to dissociate within the ion source." [PSI:MS]
comment	This child of the former purgatory term ion stability type was made obsolete.
is_obsolete	true

2.385. MS:1000380 adiabatic ionization

Table 387. Term [MS:1000380]
id	MS:1000380
name	adiabatic ionization
def	"A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.386. MS:1000381 associative ionization

Table 388. Term [MS:1000381]
id	MS:1000381
name	associative ionization
def	"An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.387. MS:1000382 atmospheric pressure photoionization

Table 389. Term [MS:1000382]
id	MS:1000382
name	atmospheric pressure photoionization
def	"Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS]
is_a	MS:1000240 atmospheric pressure ionization ! atmospheric pressure ionization

2.388. MS:1000383 autodetachment

Table 390. Term [MS:1000383]
id	MS:1000383
name	autodetachment
def	"The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.389. MS:1000384 autoionization

Table 391. Term [MS:1000384]
id	MS:1000384
name	autoionization
def	"The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.390. MS:1000385 charge exchange ionization

Table 392. Term [MS:1000385]
id	MS:1000385
name	charge exchange ionization
def	"The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.391. MS:1000386 chemi-ionization

Table 393. Term [MS:1000386]
id	MS:1000386
name	chemi-ionization
def	"The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.392. MS:1000387 desorption/ionization on silicon

Table 394. Term [MS:1000387]
id	MS:1000387
name	desorption/ionization on silicon
def	"The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS]
is_a	MS:1000247 desorption ionization ! desorption ionization

2.393. MS:1000388 dissociative ionization

Table 395. Term [MS:1000388]
id	MS:1000388
name	dissociative ionization
def	"The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.394. MS:1000389 electron ionization

Table 396. Term [MS:1000389]
id	MS:1000389
name	electron ionization
def	"The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.395. MS:1000390 ion desolvation

Table 397. Term [MS:1000390]
id	MS:1000390
name	ion desolvation
def	"OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.396. MS:1000391 ion-pair formation

Table 398. Term [MS:1000391]
id	MS:1000391
name	ion-pair formation
def	"OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.397. MS:1000392 ionization efficiency

Table 399. Term [MS:1000392]
id	MS:1000392
name	ionization efficiency
def	"The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute

2.398. MS:1000393 laser desorption ionization

Table 400. Term [MS:1000393]
id	MS:1000393
name	laser desorption ionization
def	"The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS]
is_a	MS:1000247 desorption ionization ! desorption ionization

2.399. MS:1000395 liquid secondary ionization

Table 401. Term [MS:1000395]
id	MS:1000395
name	liquid secondary ionization
def	"The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.400. MS:1000396 membrane inlet

Table 402. Term [MS:1000396]
id	MS:1000396
name	membrane inlet
def	"A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS]
is_a	MS:1000007 inlet type ! inlet type

2.401. MS:1000397 microelectrospray

Table 403. Term [MS:1000397]
id	MS:1000397
name	microelectrospray
def	"Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray." [PSI:MS]
is_a	MS:1000073 electrospray ionization ! electrospray ionization

2.402. MS:1000398 nanoelectrospray

Table 404. Term [MS:1000398]
id	MS:1000398
name	nanoelectrospray
def	"Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray." [PSI:MS]
synonym	"nanospray" EXACT []
is_a	MS:1000073 electrospray ionization ! electrospray ionization

2.403. MS:1000399 penning ionization

Table 405. Term [MS:1000399]
id	MS:1000399
name	penning ionization
def	"Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.404. MS:1000400 plasma desorption ionization

Table 406. Term [MS:1000400]
id	MS:1000400
name	plasma desorption ionization
def	"The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.405. MS:1000401 pre-ionization state

Table 407. Term [MS:1000401]
id	MS:1000401
name	pre-ionization state
def	"OBSOLETE An electronic state capable of undergoing auto-Ionization." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.406. MS:1000402 secondary ionization

Table 408. Term [MS:1000402]
id	MS:1000402
name	secondary ionization
def	"The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.407. MS:1000403 soft ionization

Table 409. Term [MS:1000403]
id	MS:1000403
name	soft ionization
def	"The formation of gas-phase ions without extensive fragmentation." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.408. MS:1000404 spark ionization

Table 410. Term [MS:1000404]
id	MS:1000404
name	spark ionization
def	"The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.409. MS:1000405 surface-assisted laser desorption ionization

Table 411. Term [MS:1000405]
id	MS:1000405
name	surface-assisted laser desorption ionization
def	"The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization." [PSI:MS]
is_a	MS:1000247 desorption ionization ! desorption ionization

2.410. MS:1000406 surface ionization

Table 412. Term [MS:1000406]
id	MS:1000406
name	surface ionization
def	"The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.411. MS:1000407 thermal ionization

Table 413. Term [MS:1000407]
id	MS:1000407
name	thermal ionization
def	"The ionization of a neutral species through contact with a high temperature surface." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.412. MS:1000408 vertical ionization

Table 414. Term [MS:1000408]
id	MS:1000408
name	vertical ionization
def	"A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state." [PSI:MS]
is_a	MS:1000008 ionization type ! ionization type

2.413. MS:1000409 association reaction

Table 415. Term [MS:1000409]
id	MS:1000409
name	association reaction
def	"OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.414. MS:1000410 alpha-cleavage

Table 416. Term [MS:1000410]
id	MS:1000410
name	alpha-cleavage
def	"OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.415. MS:1000411 beta-cleavage

Table 417. Term [MS:1000411]
id	MS:1000411
name	beta-cleavage
def	"OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.416. MS:1000412 buffer gas

Table 418. Term [MS:1000412]
id	MS:1000412
name	buffer gas
def	"An inert gas used for collisional deactivation of internally excited ions." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute

2.417. MS:1000413 charge-induced fragmentation

Table 419. Term [MS:1000413]
id	MS:1000413
name	charge-induced fragmentation
def	"OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.418. MS:1000414 charge inversion reaction

Table 420. Term [MS:1000414]
id	MS:1000414
name	charge inversion reaction
def	"OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.419. MS:1000415 charge permutation reaction

Table 421. Term [MS:1000415]
id	MS:1000415
name	charge permutation reaction
def	"OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.420. MS:1000416 charge stripping reaction

Table 422. Term [MS:1000416]
id	MS:1000416
name	charge stripping reaction
def	"OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.421. MS:1000417 charge transfer reaction

Table 423. Term [MS:1000417]
id	MS:1000417
name	charge transfer reaction
def	"OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.422. MS:1000418 collisional excitation

Table 424. Term [MS:1000418]
id	MS:1000418
name	collisional excitation
def	"OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.423. MS:1000419 collision gas

Table 425. Term [MS:1000419]
id	MS:1000419
name	collision gas
def	"An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute

2.424. MS:1000420 heterolytic cleavage

Table 426. Term [MS:1000420]
id	MS:1000420
name	heterolytic cleavage
def	"OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
synonym	"heterolysis" RELATED []
is_obsolete	true

2.425. MS:1000421 high energy collision

Table 427. Term [MS:1000421]
id	MS:1000421
name	high energy collision
def	"OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.426. MS:1000422 beam-type collision-induced dissociation

Table 428. Term [MS:1000422]
id	MS:1000422
name	beam-type collision-induced dissociation
def	"A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS]
synonym	"HCD" EXACT []
is_a	MS:1000133 collision-induced dissociation ! collision-induced dissociation

2.427. MS:1000423 homolytic cleavage

Table 429. Term [MS:1000423]
id	MS:1000423
name	homolytic cleavage
def	"OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
synonym	"homolysis" RELATED []
is_obsolete	true

2.428. MS:1000424 hydrogen/deuterium exchange

Table 430. Term [MS:1000424]
id	MS:1000424
name	hydrogen/deuterium exchange
def	"OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.429. MS:1000425 ion energy loss spectrum

Table 431. Term [MS:1000425]
id	MS:1000425
name	ion energy loss spectrum
def	"OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.430. MS:1000426 ionizing collision

Table 432. Term [MS:1000426]
id	MS:1000426
name	ionizing collision
def	"OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.431. MS:1000427 ion/molecule reaction

Table 433. Term [MS:1000427]
id	MS:1000427
name	ion/molecule reaction
def	"OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.432. MS:1000428 ion/neutral complex

Table 434. Term [MS:1000428]
id	MS:1000428
name	ion/neutral complex
def	"OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.433. MS:1000429 ion/neutral species reaction

Table 435. Term [MS:1000429]
id	MS:1000429
name	ion/neutral species reaction
def	"OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.434. MS:1000430 ion/neutral species exchange reaction

Table 436. Term [MS:1000430]
id	MS:1000430
name	ion/neutral species exchange reaction
def	"OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.435. MS:1000431 kinetic method

Table 437. Term [MS:1000431]
id	MS:1000431
name	kinetic method
def	"OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.436. MS:1000432 low energy collisions

Table 438. Term [MS:1000432]
id	MS:1000432
name	low energy collisions
def	"OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.437. MS:1000433 low-energy collision-induced dissociation

Table 439. Term [MS:1000433]
id	MS:1000433
name	low-energy collision-induced dissociation
def	"A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative." [PSI:MS]
is_a	MS:1000044 dissociation method ! dissociation method

2.438. MS:1000434 McLafferty Rearrangement

Table 440. Term [MS:1000434]
id	MS:1000434
name	McLafferty Rearrangement
def	"OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.439. MS:1000435 photodissociation

Table 441. Term [MS:1000435]
id	MS:1000435
name	photodissociation
def	"A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS]
synonym	"multiphoton dissociation" EXACT []
synonym	"MPD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.440. MS:1000436 partial charge transfer reaction

Table 442. Term [MS:1000436]
id	MS:1000436
name	partial charge transfer reaction
def	"OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.441. MS:1000437 ion reaction

Table 443. Term [MS:1000437]
id	MS:1000437
name	ion reaction
def	"OBSOLETE Chemical transformation involving an ion." [PSI:MS]
comment	This child of the former purgatory term ion was made obsolete.
is_obsolete	true

2.442. MS:1000438 superelastic collision

Table 444. Term [MS:1000438]
id	MS:1000438
name	superelastic collision
def	"OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.443. MS:1000439 surface-induced reaction

Table 445. Term [MS:1000439]
id	MS:1000439
name	surface-induced reaction
def	"OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.444. MS:1000440 unimolecular dissociation

Table 446. Term [MS:1000440]
id	MS:1000440
name	unimolecular dissociation
def	"OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion." [PSI:MS]
comment	This child of the former purgatory term ion reaction was made obsolete.
is_obsolete	true

2.445. MS:1000441 scan

Table 447. Term [MS:1000441]
id	MS:1000441
name	scan
def	"Function or process of the mass spectrometer where it records a spectrum." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.446. MS:1000442 spectrum

Table 448. Term [MS:1000442]
id	MS:1000442
name	spectrum
def	"Representation of intensity values corresponding to a range of measurement space." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.447. MS:1000443 mass analyzer type

Table 449. Term [MS:1000443]
id	MS:1000443
name	mass analyzer type
def	"Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS]
relationship	part_of MS:1000451 mass analyzer ! mass analyzer

2.448. MS:1000444 m/z Separation Method

Table 450. Term [MS:1000444]
id	MS:1000444
name	m/z Separation Method
def	"OBSOLETE Mass/charge separation Method." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.449. MS:1000445 sequential m/z separation method

Table 451. Term [MS:1000445]
id	MS:1000445
name	sequential m/z separation method
def	"OBSOLETE Sequential m/z separation method." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.450. MS:1000446 fast ion bombardment

Table 452. Term [MS:1000446]
id	MS:1000446
name	fast ion bombardment
def	"The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample." [PSI:MS]
synonym	"FIB" EXACT []
is_a	MS:1000008 ionization type ! ionization type

2.451. MS:1000447 LTQ

Table 453. Term [MS:1000447]
id	MS:1000447
name	LTQ
def	"Finnigan LTQ MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.452. MS:1000448 LTQ FT

Table 454. Term [MS:1000448]
id	MS:1000448
name	LTQ FT
def	"Finnigan LTQ FT MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.453. MS:1000449 LTQ Orbitrap

Table 455. Term [MS:1000449]
id	MS:1000449
name	LTQ Orbitrap
def	"Finnigan LTQ Orbitrap MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.454. MS:1000450 LXQ

Table 456. Term [MS:1000450]
id	MS:1000450
name	LXQ
def	"Finnigan LXQ MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.455. MS:1000451 mass analyzer

Table 457. Term [MS:1000451]
id	MS:1000451
name	mass analyzer
def	"Terms used to describe the Analyzer." [PSI:MS]
synonym	"analyzer" EXACT []
relationship	part_of MS:1000463 instrument ! instrument

2.456. MS:1000452 data transformation

Table 458. Term [MS:1000452]
id	MS:1000452
name	data transformation
def	"Terms used to describe types of data processing." [PSI:MS]
synonym	"data processing" EXACT []
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.457. MS:1000453 detector

Table 459. Term [MS:1000453]
id	MS:1000453
name	detector
def	"The device that detects ions." [PSI:MS]
relationship	part_of MS:1000463 instrument ! instrument

2.458. MS:1000454 instrument additional description

Table 460. Term [MS:1000454]
id	MS:1000454
name	instrument additional description
def	"OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.459. MS:1000455 ion selection attribute

Table 461. Term [MS:1000455]
id	MS:1000455
name	ion selection attribute
def	"Ion selection properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000442 spectrum ! spectrum

2.460. MS:1000456 precursor activation

Table 462. Term [MS:1000456]
id	MS:1000456
name	precursor activation
def	"Terms to describe the precursor activation." [PSI:MS]
synonym	"activation" EXACT []
relationship	part_of MS:1000442 spectrum ! spectrum

2.461. MS:1000457 sample

Table 463. Term [MS:1000457]
id	MS:1000457
name	sample
def	"Terms to describe the sample." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.462. MS:1000458 source

Table 464. Term [MS:1000458]
id	MS:1000458
name	source
def	"Terms to describe the source." [PSI:MS]
relationship	part_of MS:1000463 instrument ! instrument

2.463. MS:1000459 spectrum instrument description

Table 465. Term [MS:1000459]
id	MS:1000459
name	spectrum instrument description
def	"OBSOLETE Terms used to describe the spectrum." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.464. MS:1000460 unit

Table 466. Term [MS:1000460]
id	MS:1000460
name	unit
def	"OBSOLETE Terms to describe units." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000).
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information
is_obsolete	true

2.465. MS:1000461 additional description

Table 467. Term [MS:1000461]
id	MS:1000461
name	additional description
def	"OBSOLETE Terms to describe Additional." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.466. MS:1000462 ion optics

Table 468. Term [MS:1000462]
id	MS:1000462
name	ion optics
def	"Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS]
relationship	part_of MS:1000463 instrument ! instrument

2.467. MS:1000463 instrument

Table 469. Term [MS:1000463]
id	MS:1000463
name	instrument
def	"Description of the instrument or the mass spectrometer." [PSI:MS]
synonym	"instrument configuration" EXACT []
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.468. MS:1000464 mass unit

Table 470. Term [MS:1000464]
id	MS:1000464
name	mass unit
def	"OBSOLETE A unit of measurement for mass." [PSI:MS]
comment	This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002).
is_obsolete	true

2.469. MS:1000465 scan polarity

Table 471. Term [MS:1000465]
id	MS:1000465
name	scan polarity
def	"Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS]
relationship	part_of MS:1000441 scan ! scan

2.470. MS:1000466 alternating

Table 472. Term [MS:1000466]
id	MS:1000466
name	alternating
def	"OBSOLETE Alternating." [PSI:MS]
comment	This term was made obsolete because .
is_obsolete	true

2.471. MS:1000467 1200 series LC/MSD SL

Table 473. Term [MS:1000467]
id	MS:1000467
name	1200 series LC/MSD SL
def	"The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.472. MS:1000468 6110 Quadrupole LC/MS

Table 474. Term [MS:1000468]
id	MS:1000468
name	6110 Quadrupole LC/MS
def	"The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.473. MS:1000469 6120A Quadrupole LC/MS

Table 475. Term [MS:1000469]
id	MS:1000469
name	6120A Quadrupole LC/MS
def	"The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.474. MS:1000470 6130 Quadrupole LC/MS

Table 476. Term [MS:1000470]
id	MS:1000470
name	6130 Quadrupole LC/MS
def	"The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.475. MS:1000471 6140 Quadrupole LC/MS

Table 477. Term [MS:1000471]
id	MS:1000471
name	6140 Quadrupole LC/MS
def	"The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.476. MS:1000472 6210 Time-of-Flight LC/MS

Table 478. Term [MS:1000472]
id	MS:1000472
name	6210 Time-of-Flight LC/MS
def	"The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.477. MS:1000473 6310 Ion Trap LC/MS

Table 479. Term [MS:1000473]
id	MS:1000473
name	6310 Ion Trap LC/MS
def	"The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.478. MS:1000474 6320 Ion Trap LC/MS

Table 480. Term [MS:1000474]
id	MS:1000474
name	6320 Ion Trap LC/MS
def	"The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.479. MS:1000475 6330 Ion Trap LC/MS

Table 481. Term [MS:1000475]
id	MS:1000475
name	6330 Ion Trap LC/MS
def	"The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.480. MS:1000476 6340 Ion Trap LC/MS

Table 482. Term [MS:1000476]
id	MS:1000476
name	6340 Ion Trap LC/MS
def	"The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.481. MS:1000477 6410 Triple Quadrupole LC/MS

Table 483. Term [MS:1000477]
id	MS:1000477
name	6410 Triple Quadrupole LC/MS
def	"The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration." [PSI:MS]
synonym	"6410 Triple Quad LC/MS" EXACT []
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.482. MS:1000478 1200 series LC/MSD VL

Table 484. Term [MS:1000478]
id	MS:1000478
name	1200 series LC/MSD VL
def	"The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.483. MS:1000479 purgatory

Table 485. Term [MS:1000479]
id	MS:1000479
name	purgatory
def	"OBSOLETE Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS]
comment	The whole branch purgatory term was made obsolete.
is_obsolete	true

2.484. MS:1000480 mass analyzer attribute

Table 486. Term [MS:1000480]
id	MS:1000480
name	mass analyzer attribute
def	"Analyzer properties that are associated with a value." [PSI:MS]
relationship	part_of MS:1000451 mass analyzer ! mass analyzer

2.485. MS:1000481 detector attribute

Table 487. Term [MS:1000481]
id	MS:1000481
name	detector attribute
def	"Detector attribute recognized as a value." [PSI:MS]
relationship	part_of MS:1000453 detector ! detector

2.486. MS:1000482 source attribute

Table 488. Term [MS:1000482]
id	MS:1000482
name	source attribute
def	"Property of a source device that need a value." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.487. MS:1000483 Thermo Fisher Scientific instrument model

Table 489. Term [MS:1000483]
id	MS:1000483
name	Thermo Fisher Scientific instrument model
def	"Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS]
synonym	"Thermo Scientific" RELATED []
is_a	MS:1000031 instrument model ! instrument model

2.488. MS:1000484 orbitrap

Table 490. Term [MS:1000484]
id	MS:1000484
name	orbitrap
def	"An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS]
is_a	MS:1000443 mass analyzer type ! mass analyzer type

2.489. MS:1000485 nanospray inlet

Table 491. Term [MS:1000485]
id	MS:1000485
name	nanospray inlet
def	"Nanospray Inlet." [PSI:MS]
is_a	MS:1000057 electrospray inlet ! electrospray inlet

2.490. MS:1000486 source potential

Table 492. Term [MS:1000486]
id	MS:1000486
name	source potential
def	"Potential difference at the MS source in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.491. MS:1000487 ion optics attribute

Table 493. Term [MS:1000487]
id	MS:1000487
name	ion optics attribute
def	"Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS]
is_a	MS:1000462 ion optics ! ion optics

2.492. MS:1000488 Hitachi instrument model

Table 494. Term [MS:1000488]
id	MS:1000488
name	Hitachi instrument model
def	"Hitachi instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.493. MS:1000489 Varian instrument model

Table 495. Term [MS:1000489]
id	MS:1000489
name	Varian instrument model
def	"Varian instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.494. MS:1000490 Agilent instrument model

Table 496. Term [MS:1000490]
id	MS:1000490
name	Agilent instrument model
def	"Agilent instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.495. MS:1000491 Dionex instrument model

Table 497. Term [MS:1000491]
id	MS:1000491
name	Dionex instrument model
def	"Dionex instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.496. MS:1000492 Thermo Electron instrument model

Table 498. Term [MS:1000492]
id	MS:1000492
name	Thermo Electron instrument model
def	"Thermo Electron Corporation instrument model." [PSI:MS]
is_a	MS:1000483 Thermo Fisher Scientific instrument model ! Thermo Fisher Scientific instrument model

2.497. MS:1000493 Finnigan MAT instrument model

Table 499. Term [MS:1000493]
id	MS:1000493
name	Finnigan MAT instrument model
def	"Finnigan MAT instrument model." [PSI:MS]
is_a	MS:1000483 Thermo Fisher Scientific instrument model ! Thermo Fisher Scientific instrument model

2.498. MS:1000494 Thermo Scientific instrument model

Table 500. Term [MS:1000494]
id	MS:1000494
name	Thermo Scientific instrument model
def	"Thermo Scientific instrument model." [PSI:MS]
is_a	MS:1000483 Thermo Fisher Scientific instrument model ! Thermo Fisher Scientific instrument model

2.499. MS:1000495 Applied Biosystems instrument model

Table 501. Term [MS:1000495]
id	MS:1000495
name	Applied Biosystems instrument model
def	"Applied Biosystems instrument model." [PSI:MS]
synonym	"ABI" EXACT []
is_a	MS:1000031 instrument model ! instrument model

2.500. MS:1000496 instrument attribute

Table 502. Term [MS:1000496]
id	MS:1000496
name	instrument attribute
def	"Instrument properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000463 instrument ! instrument

2.501. MS:1000497 zoom scan

Table 503. Term [MS:1000497]
id	MS:1000497
name	zoom scan
def	"Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS]
synonym	"enhanced resolution scan" EXACT []
is_a	MS:1000503 scan attribute ! scan attribute

2.502. MS:1000498 full scan

Table 504. Term [MS:1000498]
id	MS:1000498
name	full scan
def	"OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.503. MS:1000499 spectrum attribute

Table 505. Term [MS:1000499]
id	MS:1000499
name	spectrum attribute
def	"Nonphysical characteristic attributed to a spectrum." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum

2.504. MS:1000500 scan window upper limit

Table 506. Term [MS:1000500]
id	MS:1000500
name	scan window upper limit
def	"The lower m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym	"mzRangeStop" RELATED []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000549 selection window attribute ! selection window attribute
relationship	has_units MS:1000040 m/z ! m/z

2.505. MS:1000501 scan window lower limit

Table 507. Term [MS:1000501]
id	MS:1000501
name	scan window lower limit
def	"The upper m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym	"mzRangeStart" RELATED []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000549 selection window attribute ! selection window attribute
relationship	has_units MS:1000040 m/z ! m/z

2.506. MS:1000502 dwell time

Table 508. Term [MS:1000502]
id	MS:1000502
name	dwell time
def	"The time spent gathering data across a peak." [PSI:MS]
synonym	"Scan Duration" RELATED []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.507. MS:1000503 scan attribute

Table 509. Term [MS:1000503]
id	MS:1000503
name	scan attribute
def	"Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000441 scan ! scan

2.508. MS:1000504 base peak m/z

Table 510. Term [MS:1000504]
id	MS:1000504
name	base peak m/z
def	"M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003058 spectrum property ! spectrum property
relationship	has_units MS:1000040 m/z ! m/z

2.509. MS:1000505 base peak intensity

Table 511. Term [MS:1000505]
id	MS:1000505
name	base peak intensity
def	"The intensity of the greatest peak in the mass spectrum." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003058 spectrum property ! spectrum property
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.510. MS:1000506 ion role

Table 512. Term [MS:1000506]
id	MS:1000506
name	ion role
def	"OBSOLETE Ion Role." [PSI:MS]
comment	This child of the former purgatory term ion was made obsolete.
is_obsolete	true

2.511. MS:1000507 ion property

Table 513. Term [MS:1000507]
id	MS:1000507
name	ion property
def	"Nonphysical characteristic attributed to an ion." [PSI:MS]
relationship	part_of MS:1002806 ion ! ion

2.512. MS:1000508 ion chemical type

Table 514. Term [MS:1000508]
id	MS:1000508
name	ion chemical type
def	"OBSOLETE Ion Type." [PSI:MS]
comment	This child of the former purgatory term ion was made obsolete.
is_obsolete	true

2.513. MS:1000509 activation energy

Table 515. Term [MS:1000509]
id	MS:1000509
name	activation energy
def	"Activation Energy." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000266] ! electronvolt

2.514. MS:1000510 precursor activation attribute

Table 516. Term [MS:1000510]
id	MS:1000510
name	precursor activation attribute
def	"Precursor Activation Attribute." [PSI:MS]
relationship	part_of MS:1000456 precursor activation ! precursor activation

2.515. MS:1000511 ms level

Table 517. Term [MS:1000511]
id	MS:1000511
name	ms level
def	"Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.516. MS:1000512 filter string

Table 518. Term [MS:1000512]
id	MS:1000512
name	filter string
def	"A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute

2.517. MS:1000513 binary data array

Table 519. Term [MS:1000513]
id	MS:1000513
name	binary data array
def	"A data array of values." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.518. MS:1000514 m/z array

Table 520. Term [MS:1000514]
id	MS:1000514
name	m/z array
def	"A data array of m/z values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units MS:1000040 m/z ! m/z

2.519. MS:1000515 intensity array

Table 521. Term [MS:1000515]
id	MS:1000515
name	intensity array
def	"A data array of intensity values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.520. MS:1000516 charge array

Table 522. Term [MS:1000516]
id	MS:1000516
name	charge array
def	"A data array of charge values." [PSI:MS]
xref	binary-data-type:MS\:1000519 "32-bit integer"
is_a	MS:1000513 binary data array ! binary data array

2.521. MS:1000517 signal to noise array

Table 523. Term [MS:1000517]
id	MS:1000517
name	signal to noise array
def	"A data array of signal-to-noise values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.522. MS:1000518 binary data type

Table 524. Term [MS:1000518]
id	MS:1000518
name	binary data type
def	"Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.523. MS:1000519 32-bit integer

Table 525. Term [MS:1000519]
id	MS:1000519
name	32-bit integer
def	"Signed 32-bit little-endian integer." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type

2.524. MS:1000520 16-bit float

Table 526. Term [MS:1000520]
id	MS:1000520
name	16-bit float
def	"OBSOLETE Signed 16-bit float." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type
is_obsolete	true

2.525. MS:1000521 32-bit float

Table 527. Term [MS:1000521]
id	MS:1000521
name	32-bit float
def	"32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type

2.526. MS:1000522 64-bit integer

Table 528. Term [MS:1000522]
id	MS:1000522
name	64-bit integer
def	"Signed 64-bit little-endian integer." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type

2.527. MS:1000523 64-bit float

Table 529. Term [MS:1000523]
id	MS:1000523
name	64-bit float
def	"64-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type

2.528. MS:1000524 data file content

Table 530. Term [MS:1000524]
id	MS:1000524
name	data file content
def	"Describes the data content on the file." [PSI:MS]
relationship	part_of MS:1000577 source data file ! source data file

2.529. MS:1000525 spectrum representation

Table 531. Term [MS:1000525]
id	MS:1000525
name	spectrum representation
def	"Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum

2.530. MS:1000526 Waters raw format

Table 532. Term [MS:1000526]
id	MS:1000526
name	Waters raw format
def	"Waters data file format found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.531. MS:1000527 highest observed m/z

Table 533. Term [MS:1000527]
id	MS:1000527
name	highest observed m/z
def	"Highest m/z value observed in the m/z array." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute
is_a	MS:1003058 spectrum property ! spectrum property
relationship	has_units MS:1000040 m/z ! m/z

2.532. MS:1000528 lowest observed m/z

Table 534. Term [MS:1000528]
id	MS:1000528
name	lowest observed m/z
def	"Lowest m/z value observed in the m/z array." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute
is_a	MS:1003058 spectrum property ! spectrum property
relationship	has_units MS:1000040 m/z ! m/z

2.533. MS:1000529 instrument serial number

Table 535. Term [MS:1000529]
id	MS:1000529
name	instrument serial number
def	"Serial Number of the instrument." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000496 instrument attribute ! instrument attribute

2.534. MS:1000530 file format conversion

Table 536. Term [MS:1000530]
id	MS:1000530
name	file format conversion
def	"Conversion of one file format to another." [PSI:MS]
is_a	MS:1000452 data transformation ! data transformation

2.535. MS:1000531 software

Table 537. Term [MS:1000531]
id	MS:1000531
name	software
def	"Software related to the recording or transformation of spectra." [PSI:MS]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.536. MS:1000532 Xcalibur

Table 538. Term [MS:1000532]
id	MS:1000532
name	Xcalibur
def	"Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000693 Thermo Finnigan software ! Thermo Finnigan software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.537. MS:1000533 Bioworks

Table 539. Term [MS:1000533]
id	MS:1000533
name	Bioworks
def	"Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS]
synonym	"Bioworks Browser" RELATED []
is_a	MS:1000693 Thermo Finnigan software ! Thermo Finnigan software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.538. MS:1000534 MassLynx

Table 540. Term [MS:1000534]
id	MS:1000534
name	MassLynx
def	"Micromass software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000694 Waters software ! Waters software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.539. MS:1000535 FlexAnalysis

Table 541. Term [MS:1000535]
id	MS:1000535
name	FlexAnalysis
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.540. MS:1000536 Data Explorer

Table 542. Term [MS:1000536]
id	MS:1000536
name	Data Explorer
def	"Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000691 Applied Biosystems software ! Applied Biosystems software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.541. MS:1000537 4700 Explorer

Table 543. Term [MS:1000537]
id	MS:1000537
name	4700 Explorer
def	"Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000691 Applied Biosystems software ! Applied Biosystems software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.542. MS:1000538 massWolf

Table 544. Term [MS:1000538]
id	MS:1000538
name	massWolf
def	"A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology." [PSI:MS]
synonym	"wolf" EXACT []
is_a	MS:1001457 data processing software ! data processing software

2.543. MS:1000539 Voyager Biospectrometry Workstation System

Table 545. Term [MS:1000539]
id	MS:1000539
name	Voyager Biospectrometry Workstation System
def	"Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS]
is_a	MS:1000691 Applied Biosystems software ! Applied Biosystems software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.544. MS:1000540 FlexControl

Table 546. Term [MS:1000540]
id	MS:1000540
name	FlexControl
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.545. MS:1000541 ReAdW

Table 547. Term [MS:1000541]
id	MS:1000541
name	ReAdW
def	"A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced \"readraw\"." [PSI:MS]
is_a	MS:1001457 data processing software ! data processing software

2.546. MS:1000542 MzStar

Table 548. Term [MS:1000542]
id	MS:1000542
name	MzStar
def	"A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program." [PSI:MS]
is_a	MS:1001457 data processing software ! data processing software

2.547. MS:1000543 data processing action

Table 549. Term [MS:1000543]
id	MS:1000543
name	data processing action
def	"Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS]
is_a	MS:1000452 data transformation ! data transformation

2.548. MS:1000544 Conversion to mzML

Table 550. Term [MS:1000544]
id	MS:1000544
name	Conversion to mzML
def	"Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS]
is_a	MS:1000530 file format conversion ! file format conversion

2.549. MS:1000545 Conversion to mzXML

Table 551. Term [MS:1000545]
id	MS:1000545
name	Conversion to mzXML
def	"Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS]
is_a	MS:1000530 file format conversion ! file format conversion

2.550. MS:1000546 Conversion to mzData

Table 552. Term [MS:1000546]
id	MS:1000546
name	Conversion to mzData
def	"Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS]
is_a	MS:1000530 file format conversion ! file format conversion

2.551. MS:1000547 object attribute

Table 553. Term [MS:1000547]
id	MS:1000547
name	object attribute
def	"Object Attribute." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.552. MS:1000548 sample attribute

Table 554. Term [MS:1000548]
id	MS:1000548
name	sample attribute
def	"Sample properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000457 sample ! sample

2.553. MS:1000549 selection window attribute

Table 555. Term [MS:1000549]
id	MS:1000549
name	selection window attribute
def	"Selection window properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000441 scan ! scan

2.554. MS:1000550 time unit

Table 556. Term [MS:1000550]
id	MS:1000550
name	time unit
def	"OBSOLETE Time Unit." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003).
is_obsolete	true

2.555. MS:1000551 Analyst

Table 557. Term [MS:1000551]
id	MS:1000551
name	Analyst
def	"SCIEX or Applied Biosystems\|MDS SCIEX software for data acquisition." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.556. MS:1000552 maldi spot identifier

Table 558. Term [MS:1000552]
id	MS:1000552
name	maldi spot identifier
def	"OBSOLETE Maldi Spot Identifier." [PSI:MS]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.557. MS:1000553 Trapper

Table 559. Term [MS:1000553]
id	MS:1000553
name	Trapper
def	"A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS]
is_a	MS:1001457 data processing software ! data processing software

2.558. MS:1000554 LCQ Deca

Table 560. Term [MS:1000554]
id	MS:1000554
name	LCQ Deca
def	"ThermoFinnigan LCQ Deca." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.559. MS:1000555 LTQ Orbitrap Discovery

Table 561. Term [MS:1000555]
id	MS:1000555
name	LTQ Orbitrap Discovery
def	"LTQ Orbitrap Discovery." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.560. MS:1000556 LTQ Orbitrap XL

Table 562. Term [MS:1000556]
id	MS:1000556
name	LTQ Orbitrap XL
def	"LTQ Orbitrap XL." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.561. MS:1000557 LTQ FT Ultra

Table 563. Term [MS:1000557]
id	MS:1000557
name	LTQ FT Ultra
def	"LTQ FT Ultra." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.562. MS:1000558 GC Quantum

Table 564. Term [MS:1000558]
id	MS:1000558
name	GC Quantum
def	"GC Quantum." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.563. MS:1000559 spectrum type

Table 565. Term [MS:1000559]
id	MS:1000559
name	spectrum type
def	"Spectrum type." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum

2.564. MS:1000560 mass spectrometer file format

Table 566. Term [MS:1000560]
id	MS:1000560
name	mass spectrometer file format
def	"The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:MS]
is_a	MS:1001459 file format ! file format

2.565. MS:1000561 data file checksum type

Table 567. Term [MS:1000561]
id	MS:1000561
name	data file checksum type
def	"Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS]
relationship	part_of MS:1000577 source data file ! source data file

2.566. MS:1000562 ABI WIFF format

Table 568. Term [MS:1000562]
id	MS:1000562
name	ABI WIFF format
def	"Applied Biosystems WIFF file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.567. MS:1000563 Thermo RAW format

Table 569. Term [MS:1000563]
id	MS:1000563
name	Thermo RAW format
def	"Thermo Scientific RAW file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.568. MS:1000564 PSI mzData format

Table 570. Term [MS:1000564]
id	MS:1000564
name	PSI mzData format
def	"Proteomics Standards Inititative mzData file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.569. MS:1000565 Micromass PKL format

Table 571. Term [MS:1000565]
id	MS:1000565
name	Micromass PKL format
def	"Micromass PKL file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.570. MS:1000566 ISB mzXML format

Table 572. Term [MS:1000566]
id	MS:1000566
name	ISB mzXML format
def	"Institute of Systems Biology mzXML file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.571. MS:1000567 Bruker/Agilent YEP format

Table 573. Term [MS:1000567]
id	MS:1000567
name	Bruker/Agilent YEP format
def	"Bruker/Agilent YEP file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.572. MS:1000568 MD5

Table 574. Term [MS:1000568]
id	MS:1000568
name	MD5
def	"MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000561 data file checksum type ! data file checksum type

2.573. MS:1000569 SHA-1

Table 575. Term [MS:1000569]
id	MS:1000569
name	SHA-1
def	"SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000561 data file checksum type ! data file checksum type

2.574. MS:1000570 spectra combination

Table 576. Term [MS:1000570]
id	MS:1000570
name	spectra combination
def	"Method used to combine the mass spectra." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum

2.575. MS:1000571 sum of spectra

Table 577. Term [MS:1000571]
id	MS:1000571
name	sum of spectra
def	"Spectra Sum." [PSI:MS]
is_a	MS:1000570 spectra combination ! spectra combination

2.576. MS:1000572 binary data compression type

Table 578. Term [MS:1000572]
id	MS:1000572
name	binary data compression type
def	"Compression Type." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.577. MS:1000573 median of spectra

Table 579. Term [MS:1000573]
id	MS:1000573
name	median of spectra
def	"Spectra is combined by calculating the median of the spectra." [PSI:MS]
is_a	MS:1000570 spectra combination ! spectra combination

2.578. MS:1000574 zlib compression

Table 580. Term [MS:1000574]
id	MS:1000574
name	zlib compression
def	"Zlib." [PSI:MS]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.579. MS:1000575 mean of spectra

Table 581. Term [MS:1000575]
id	MS:1000575
name	mean of spectra
def	"Spectra is combined by calculating the mean of the spectra." [PSI:MS]
is_a	MS:1000570 spectra combination ! spectra combination

2.580. MS:1000576 no compression

Table 582. Term [MS:1000576]
id	MS:1000576
name	no compression
def	"No Compression." [PSI:MS]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.581. MS:1000577 source data file

Table 583. Term [MS:1000577]
id	MS:1000577
name	source data file
def	"Data file from which an entity is sourced." [PSI:MS]
synonym	"source file" EXACT []
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.582. MS:1000578 LCQ Fleet

Table 584. Term [MS:1000578]
id	MS:1000578
name	LCQ Fleet
def	"LCQ Fleet." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.583. MS:1000579 MS1 spectrum

Table 585. Term [MS:1000579]
id	MS:1000579
name	MS1 spectrum
def	"Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS]
synonym	"full spectrum" EXACT []
synonym	"Q1 spectrum" EXACT []
synonym	"Q3 spectrum" EXACT []
synonym	"Single-Stage Mass Spectrometry" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.584. MS:1000580 MSn spectrum

Table 586. Term [MS:1000580]
id	MS:1000580
name	MSn spectrum
def	"MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n." [PSI:MS]
synonym	"multiple-stage mass spectrometry spectrum" EXACT []
synonym	"nth generation product ion spectrum" EXACT []
synonym	"product ion spectrum" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.585. MS:1000581 CRM spectrum

Table 587. Term [MS:1000581]
id	MS:1000581
name	CRM spectrum
def	"Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]
is_a	MS:1000294 mass spectrum ! mass spectrum

2.586. MS:1000582 SIM spectrum

Table 588. Term [MS:1000582]
id	MS:1000582
name	SIM spectrum
def	"Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring)." [PSI:MS]
synonym	"MIM spectrum" EXACT []
synonym	"multiple ion monitoring spectrum" EXACT []
synonym	"selected ion monitoring spectrum" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.587. MS:1000583 SRM spectrum

Table 589. Term [MS:1000583]
id	MS:1000583
name	SRM spectrum
def	"Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space." [PSI:MS]
synonym	"MRM spectrum" EXACT []
synonym	"multiple reaction monitoring spectrum" EXACT []
synonym	"selected reaction monitoring spectrum" EXACT []
is_a	MS:1000294 mass spectrum ! mass spectrum

2.588. MS:1000584 mzML format

Table 590. Term [MS:1000584]
id	MS:1000584
name	mzML format
def	"Proteomics Standards Inititative mzML file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.589. MS:1000585 contact attribute

Table 591. Term [MS:1000585]
id	MS:1000585
name	contact attribute
def	"Details about a person or organization to contact in case of concern or discussion about the file." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.590. MS:1000586 contact name

Table 592. Term [MS:1000586]
id	MS:1000586
name	contact name
def	"Name of the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.591. MS:1000587 contact address

Table 593. Term [MS:1000587]
id	MS:1000587
name	contact address
def	"Postal address of the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.592. MS:1000588 contact URL

Table 594. Term [MS:1000588]
id	MS:1000588
name	contact URL
def	"Uniform Resource Locator related to the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.593. MS:1000589 contact email

Table 595. Term [MS:1000589]
id	MS:1000589
name	contact email
def	"Email address of the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.594. MS:1000590 contact affiliation

Table 596. Term [MS:1000590]
id	MS:1000590
name	contact affiliation
def	"Home institution of the contact person." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.595. MS:1000591 MzWiff

Table 597. Term [MS:1000591]
id	MS:1000591
name	MzWiff
def	"A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program." [PSI:MS]
is_a	MS:1001457 data processing software ! data processing software

2.596. MS:1000592 smoothing

Table 598. Term [MS:1000592]
id	MS:1000592
name	smoothing
def	"A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.597. MS:1000593 baseline reduction

Table 599. Term [MS:1000593]
id	MS:1000593
name	baseline reduction
def	"A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.598. MS:1000594 low intensity data point removal

Table 600. Term [MS:1000594]
id	MS:1000594
name	low intensity data point removal
def	"The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS]
synonym	"thresholding" EXACT []
is_a	MS:1001486 data filtering ! data filtering

2.599. MS:1000595 time array

Table 601. Term [MS:1000595]
id	MS:1000595
name	time array
def	"A data array of relative time offset values from a reference time." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.600. MS:1000596 measurement method

Table 602. Term [MS:1000596]
id	MS:1000596
name	measurement method
def	"An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.601. MS:1000597 ion optics type

Table 603. Term [MS:1000597]
id	MS:1000597
name	ion optics type
def	"The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS]
is_a	MS:1000462 ion optics ! ion optics

2.602. MS:1000598 electron transfer dissociation

Table 604. Term [MS:1000598]
id	MS:1000598
name	electron transfer dissociation
def	"A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS]
synonym	"ETD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.603. MS:1000599 pulsed q dissociation

Table 605. Term [MS:1000599]
id	MS:1000599
name	pulsed q dissociation
def	"A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected." [PSI:MS]
synonym	"PQD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.604. MS:1000600 Proteios

Table 606. Term [MS:1000600]
id	MS:1000600
name	Proteios
def	"Database application and analysis platform for proteomics." [PSI:MS, source:http://www.proteios.org]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.605. MS:1000601 ProteinLynx Global Server

Table 607. Term [MS:1000601]
id	MS:1000601
name	ProteinLynx Global Server
def	"Waters software for data analysis." [PSI:MS]
is_a	MS:1000694 Waters software ! Waters software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.606. MS:1000602 Shimadzu MALDI-TOF instrument model

Table 608. Term [MS:1000602]
id	MS:1000602
name	Shimadzu MALDI-TOF instrument model
def	"Shimadzu MALDI-TOF instrument model." [PSI:MS]
is_a	MS:1000124 Shimadzu instrument model ! Shimadzu instrument model

2.607. MS:1000603 Shimadzu Scientific Instruments instrument model

Table 609. Term [MS:1000603]
id	MS:1000603
name	Shimadzu Scientific Instruments instrument model
def	"Shimadzu Scientific Instruments instrument model." [PSI:MS]
is_a	MS:1000124 Shimadzu instrument model ! Shimadzu instrument model

2.608. MS:1000604 LCMS-IT-TOF

Table 610. Term [MS:1000604]
id	MS:1000604
name	LCMS-IT-TOF
def	"Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.609. MS:1000605 LCMS-2010EV

Table 611. Term [MS:1000605]
id	MS:1000605
name	LCMS-2010EV
def	"Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.610. MS:1000606 LCMS-2010A

Table 612. Term [MS:1000606]
id	MS:1000606
name	LCMS-2010A
def	"Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.611. MS:1000607 AXIMA CFR MALDI-TOF

Table 613. Term [MS:1000607]
id	MS:1000607
name	AXIMA CFR MALDI-TOF
def	"Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.612. MS:1000608 AXIMA-QIT

Table 614. Term [MS:1000608]
id	MS:1000608
name	AXIMA-QIT
def	"Shimadzu Biotech AXIMA-QIT MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.613. MS:1000609 AXIMA-CFR plus

Table 615. Term [MS:1000609]
id	MS:1000609
name	AXIMA-CFR plus
def	"Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.614. MS:1000610 AXIMA Performance MALDI-TOF/TOF

Table 616. Term [MS:1000610]
id	MS:1000610
name	AXIMA Performance MALDI-TOF/TOF
def	"Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.615. MS:1000611 AXIMA Confidence MALDI-TOF

Table 617. Term [MS:1000611]
id	MS:1000611
name	AXIMA Confidence MALDI-TOF
def	"Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.616. MS:1000612 AXIMA Assurance Linear MALDI-TOF

Table 618. Term [MS:1000612]
id	MS:1000612
name	AXIMA Assurance Linear MALDI-TOF
def	"Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.617. MS:1000613 DTA format

Table 619. Term [MS:1000613]
id	MS:1000613
name	DTA format
def	"SEQUEST DTA file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.618. MS:1000614 ProteinLynx Global Server mass spectrum XML format

Table 620. Term [MS:1000614]
id	MS:1000614
name	ProteinLynx Global Server mass spectrum XML format
def	"Peak list file format used by ProteinLynx Global Server." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.619. MS:1000615 ProteoWizard software

Table 621. Term [MS:1000615]
id	MS:1000615
name	ProteoWizard software
def	"ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb." [PSI:MS]
synonym	"pwiz" EXACT []
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.620. MS:1000616 preset scan configuration

Table 622. Term [MS:1000616]
id	MS:1000616
name	preset scan configuration
def	"A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute

2.621. MS:1000617 wavelength array

Table 623. Term [MS:1000617]
id	MS:1000617
name	wavelength array
def	"A data array of electromagnetic radiation wavelength values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000018] ! nanometer

2.622. MS:1000618 highest observed wavelength

Table 624. Term [MS:1000618]
id	MS:1000618
name	highest observed wavelength
def	"Highest wavelength observed in an EMR spectrum." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003058 spectrum property ! spectrum property
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute
relationship	has_units [UO:0000018] ! nanometer

2.623. MS:1000619 lowest observed wavelength

Table 625. Term [MS:1000619]
id	MS:1000619
name	lowest observed wavelength
def	"Lowest wavelength observed in an EMR spectrum." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003058 spectrum property ! spectrum property
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute
relationship	has_units [UO:0000018] ! nanometer

2.624. MS:1000620 PDA spectrum

Table 626. Term [MS:1000620]
id	MS:1000620
name	PDA spectrum
def	"OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS]
comment	This term was made obsolete because it was replaced by absorption spectrum (MS:1000806).
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000559 spectrum type ! spectrum type
is_obsolete	true

2.625. MS:1000621 photodiode array detector

Table 627. Term [MS:1000621]
id	MS:1000621
name	photodiode array detector
def	"An array detector used to record spectra in the ultraviolet and visible region of light." [PSI:MS]
synonym	"PDA" EXACT []
is_a	MS:1000345 array detector ! array detector

2.626. MS:1000622 Surveyor PDA

Table 628. Term [MS:1000622]
id	MS:1000622
name	Surveyor PDA
def	"Surveyor PDA." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.627. MS:1000623 Accela PDA

Table 629. Term [MS:1000623]
id	MS:1000623
name	Accela PDA
def	"Accela PDA." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.628. MS:1000624 inductive detector

Table 630. Term [MS:1000624]
id	MS:1000624
name	inductive detector
def	"Inductive detector." [PSI:MS]
synonym	"image current detector" EXACT []
is_a	MS:1000026 detector type ! detector type

2.629. MS:1000625 chromatogram

Table 631. Term [MS:1000625]
id	MS:1000625
name	chromatogram
def	"Representation of a chromatographic separation attribute measurement versus time." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.630. MS:1000626 chromatogram type

Table 632. Term [MS:1000626]
id	MS:1000626
name	chromatogram type
def	"Type of chromatogram measurement being represented." [PSI:MS]
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.631. MS:1000627 selected ion current chromatogram

Table 633. Term [MS:1000627]
id	MS:1000627
name	selected ion current chromatogram
def	"Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS]
synonym	"SIC chromatogram" EXACT []
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram

2.632. MS:1000628 basepeak chromatogram

Table 634. Term [MS:1000628]
id	MS:1000628
name	basepeak chromatogram
def	"Representation of an array of the most intense peaks versus time." [PSI:MS]
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram

2.633. MS:1000629 low intensity threshold

Table 635. Term [MS:1000629]
id	MS:1000629
name	low intensity threshold
def	"Threshold below which some action is taken." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.634. MS:1000630 data processing parameter

Table 636. Term [MS:1000630]
id	MS:1000630
name	data processing parameter
def	"Data processing parameter used in the data processing performed on the data file." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.635. MS:1000631 high intensity threshold

Table 637. Term [MS:1000631]
id	MS:1000631
name	high intensity threshold
def	"Threshold above which some action is taken." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.636. MS:1000632 Q-Tof Premier

Table 638. Term [MS:1000632]
id	MS:1000632
name	Q-Tof Premier
def	"Waters oa-ToF based Q-Tof Premier." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.637. MS:1000633 possible charge state

Table 639. Term [MS:1000633]
id	MS:1000633
name	possible charge state
def	"A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute

2.638. MS:1000634 DSQ

Table 640. Term [MS:1000634]
id	MS:1000634
name	DSQ
def	"ThermoFinnigan DSQ GC-MS." [PSI:MS]
is_a	MS:1000125 Thermo Finnigan instrument model ! Thermo Finnigan instrument model

2.639. MS:1000635 ITQ 700

Table 641. Term [MS:1000635]
id	MS:1000635
name	ITQ 700
def	"Thermo Scientific ITQ 700 GC-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.640. MS:1000636 ITQ 900

Table 642. Term [MS:1000636]
id	MS:1000636
name	ITQ 900
def	"Thermo Scientific ITQ 900 GC-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.641. MS:1000637 ITQ 1100

Table 643. Term [MS:1000637]
id	MS:1000637
name	ITQ 1100
def	"Thermo Scientific ITQ 1100 GC-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.642. MS:1000638 LTQ XL ETD

Table 644. Term [MS:1000638]
id	MS:1000638
name	LTQ XL ETD
def	"Thermo Scientific LTQ XL MS with ETD." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.643. MS:1000639 LTQ Orbitrap XL ETD

Table 645. Term [MS:1000639]
id	MS:1000639
name	LTQ Orbitrap XL ETD
def	"Thermo Scientific LTQ Orbitrap XL MS with ETD." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.644. MS:1000640 DFS

Table 646. Term [MS:1000640]
id	MS:1000640
name	DFS
def	"Thermo Scientific DFS HR GC-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.645. MS:1000641 DSQ II

Table 647. Term [MS:1000641]
id	MS:1000641
name	DSQ II
def	"Thermo Scientific DSQ II GC-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.646. MS:1000642 MALDI LTQ XL

Table 648. Term [MS:1000642]
id	MS:1000642
name	MALDI LTQ XL
def	"Thermo Scientific MALDI LTQ XL MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.647. MS:1000643 MALDI LTQ Orbitrap

Table 649. Term [MS:1000643]
id	MS:1000643
name	MALDI LTQ Orbitrap
def	"Thermo Scientific MALDI LTQ Orbitrap MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.648. MS:1000644 TSQ Quantum Access

Table 650. Term [MS:1000644]
id	MS:1000644
name	TSQ Quantum Access
def	"Thermo Scientific TSQ Quantum Access MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.649. MS:1000645 Element XR

Table 651. Term [MS:1000645]
id	MS:1000645
name	Element XR
def	"Thermo Scientific Element XR HR-ICP-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.650. MS:1000646 Element 2

Table 652. Term [MS:1000646]
id	MS:1000646
name	Element 2
def	"Thermo Scientific Element 2 HR-ICP-MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.651. MS:1000647 Element GD

Table 653. Term [MS:1000647]
id	MS:1000647
name	Element GD
def	"Thermo Scientific Element GD Glow Discharge MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.652. MS:1000648 GC IsoLink

Table 654. Term [MS:1000648]
id	MS:1000648
name	GC IsoLink
def	"Thermo Scientific GC IsoLink Isotope Ratio MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.653. MS:1000649 Exactive

Table 655. Term [MS:1000649]
id	MS:1000649
name	Exactive
def	"Thermo Scientific Exactive MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.654. MS:1000650 Proteome Discoverer

Table 656. Term [MS:1000650]
id	MS:1000650
name	Proteome Discoverer
def	"Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS]
is_a	MS:1000693 Thermo Finnigan software ! Thermo Finnigan software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.655. MS:1000651 3200 QTRAP

Table 657. Term [MS:1000651]
id	MS:1000651
name	3200 QTRAP
def	"SCIEX or Applied Biosystems\|MDS SCIEX QTRAP 3200." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.656. MS:1000652 4800 Plus MALDI TOF/TOF

Table 658. Term [MS:1000652]
id	MS:1000652
name	4800 Plus MALDI TOF/TOF
def	"SCIEX or Applied Biosystems\|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.657. MS:1000653 API 3200

Table 659. Term [MS:1000653]
id	MS:1000653
name	API 3200
def	"SCIEX or Applied Biosystems\|MDS SCIEX API 3200 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.658. MS:1000654 API 5000

Table 660. Term [MS:1000654]
id	MS:1000654
name	API 5000
def	"SCIEX or Applied Biosystems\|MDS SCIEX API 5000 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.659. MS:1000655 QSTAR Elite

Table 661. Term [MS:1000655]
id	MS:1000655
name	QSTAR Elite
def	"SCIEX or Applied Biosystems\|MDS SCIEX QSTAR Elite." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.660. MS:1000656 QSTAR Pulsar

Table 662. Term [MS:1000656]
id	MS:1000656
name	QSTAR Pulsar
def	"Applied Biosystems\|MDS SCIEX QSTAR Pulsar." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.661. MS:1000657 QSTAR XL

Table 663. Term [MS:1000657]
id	MS:1000657
name	QSTAR XL
def	"Applied Biosystems\|MDS SCIEX QSTAR XL." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.662. MS:1000658 4800 Proteomics Analyzer

Table 664. Term [MS:1000658]
id	MS:1000658
name	4800 Proteomics Analyzer
def	"Applied Biosystems\|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS]
is_a	MS:1000495 Applied Biosystems instrument model ! Applied Biosystems instrument model

2.663. MS:1000659 4000 Series Explorer Software

Table 665. Term [MS:1000659]
id	MS:1000659
name	4000 Series Explorer Software
def	"SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.664. MS:1000661 GPS Explorer

Table 666. Term [MS:1000661]
id	MS:1000661
name	GPS Explorer
def	"SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.665. MS:1000662 LightSight Software

Table 667. Term [MS:1000662]
id	MS:1000662
name	LightSight Software
def	"SCIEX or Applied Biosystems\|MDS SCIEX software metabolite identification." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.666. MS:1000663 ProteinPilot Software

Table 668. Term [MS:1000663]
id	MS:1000663
name	ProteinPilot Software
def	"SCIEX or Applied Biosystems\|MDS SCIEX software for protein ID and quant." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.667. MS:1000664 TissueView Software

Table 669. Term [MS:1000664]
id	MS:1000664
name	TissueView Software
def	"Applied Biosystems\|MDS SCIEX software for tissue imaging." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.668. MS:1000665 MarkerView Software

Table 670. Term [MS:1000665]
id	MS:1000665
name	MarkerView Software
def	"Applied Biosystems\|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.669. MS:1000666 MRMPilot Software

Table 671. Term [MS:1000666]
id	MS:1000666
name	MRMPilot Software
def	"Applied Biosystems\|MDS SCIEX software for MRM assay development." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.670. MS:1000667 BioAnalyst

Table 672. Term [MS:1000667]
id	MS:1000667
name	BioAnalyst
def	"Applied Biosystems\|MDS SCIEX software for bio-related data exploration." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.671. MS:1000668 Pro ID

Table 673. Term [MS:1000668]
id	MS:1000668
name	Pro ID
def	"Applied Biosystems\|MDS SCIEX software for protein identification." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.672. MS:1000669 Pro ICAT

Table 674. Term [MS:1000669]
id	MS:1000669
name	Pro ICAT
def	"Applied Biosystems\|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.673. MS:1000670 Pro Quant

Table 675. Term [MS:1000670]
id	MS:1000670
name	Pro Quant
def	"Applied Biosystems\|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.674. MS:1000671 Pro BLAST

Table 676. Term [MS:1000671]
id	MS:1000671
name	Pro BLAST
def	"Applied Biosystems\|MDS SCIEX software for MS-BLAST identification." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.675. MS:1000672 Cliquid

Table 677. Term [MS:1000672]
id	MS:1000672
name	Cliquid
def	"SCIEX Cliquid software for data analysis and quantitation." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software

2.676. MS:1000673 MIDAS Workflow Designer

Table 678. Term [MS:1000673]
id	MS:1000673
name	MIDAS Workflow Designer
def	"Applied Biosystems\|MDS SCIEX software for MRM assay development." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software

2.677. MS:1000674 MultiQuant

Table 679. Term [MS:1000674]
id	MS:1000674
name	MultiQuant
def	"Applied Biosystems\|MDS SCIEX software for MRM-based quantitation." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.678. MS:1000675 6220 Time-of-Flight LC/MS

Table 680. Term [MS:1000675]
id	MS:1000675
name	6220 Time-of-Flight LC/MS
def	"The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.679. MS:1000676 6510 Quadrupole Time-of-Flight LC/MS

Table 681. Term [MS:1000676]
id	MS:1000676
name	6510 Quadrupole Time-of-Flight LC/MS
def	"The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.680. MS:1000677 6520A Quadrupole Time-of-Flight LC/MS

Table 682. Term [MS:1000677]
id	MS:1000677
name	6520A Quadrupole Time-of-Flight LC/MS
def	"The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.681. MS:1000678 MassHunter Data Acquisition

Table 683. Term [MS:1000678]
id	MS:1000678
name	MassHunter Data Acquisition
def	"Software for data acquisition of 6000 series instruments." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001455 acquisition software ! acquisition software

2.682. MS:1000679 MassHunter Easy Access

Table 684. Term [MS:1000679]
id	MS:1000679
name	MassHunter Easy Access
def	"Software for open access data acquisition." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001455 acquisition software ! acquisition software

2.683. MS:1000680 MassHunter Qualitative Analysis

Table 685. Term [MS:1000680]
id	MS:1000680
name	MassHunter Qualitative Analysis
def	"Software for data analysis of data from 6000 series instruments." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.684. MS:1000681 MassHunter Quantitative Analysis

Table 686. Term [MS:1000681]
id	MS:1000681
name	MassHunter Quantitative Analysis
def	"Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.685. MS:1000682 MassHunter Metabolite ID

Table 687. Term [MS:1000682]
id	MS:1000682
name	MassHunter Metabolite ID
def	"Software for identification of metabolites." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.686. MS:1000683 MassHunter BioConfirm

Table 688. Term [MS:1000683]
id	MS:1000683
name	MassHunter BioConfirm
def	"Software for protein characterization." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.687. MS:1000684 Genespring MS

Table 689. Term [MS:1000684]
id	MS:1000684
name	Genespring MS
def	"Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.688. MS:1000685 MassHunter Mass Profiler

Table 690. Term [MS:1000685]
id	MS:1000685
name	MassHunter Mass Profiler
def	"Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.689. MS:1000686 METLIN

Table 691. Term [MS:1000686]
id	MS:1000686
name	METLIN
def	"Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.690. MS:1000687 Spectrum Mill for MassHunter Workstation

Table 692. Term [MS:1000687]
id	MS:1000687
name	Spectrum Mill for MassHunter Workstation
def	"Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.691. MS:1000688 6300 Series Ion Trap Data Analysis Software

Table 693. Term [MS:1000688]
id	MS:1000688
name	6300 Series Ion Trap Data Analysis Software
def	"Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS]
is_a	MS:1000689 Agilent software ! Agilent software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.692. MS:1000689 Agilent software

Table 694. Term [MS:1000689]
id	MS:1000689
name	Agilent software
def	"Agilent software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.693. MS:1000690 SCIEX software

Table 695. Term [MS:1000690]
id	MS:1000690
name	SCIEX software
def	"SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.694. MS:1000691 Applied Biosystems software

Table 696. Term [MS:1000691]
id	MS:1000691
name	Applied Biosystems software
def	"Applied Biosystems\|MDS SCIEX software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.695. MS:1000692 Bruker software

Table 697. Term [MS:1000692]
id	MS:1000692
name	Bruker software
def	"Bruker software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.696. MS:1000693 Thermo Finnigan software

Table 698. Term [MS:1000693]
id	MS:1000693
name	Thermo Finnigan software
def	"Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
synonym	"Bioworks Browser" RELATED []
is_a	MS:1000531 software ! software

2.697. MS:1000694 Waters software

Table 699. Term [MS:1000694]
id	MS:1000694
name	Waters software
def	"Waters software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.698. MS:1000695 apex ultra

Table 700. Term [MS:1000695]
id	MS:1000695
name	apex ultra
def	"Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS]
is_a	MS:1001556 Bruker Daltonics apex series ! Bruker Daltonics apex series

2.699. MS:1000696 autoflex III smartbeam

Table 701. Term [MS:1000696]
id	MS:1000696
name	autoflex III smartbeam
def	"Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.700. MS:1000697 Bruker Daltonics HCT Series

Table 702. Term [MS:1000697]
id	MS:1000697
name	Bruker Daltonics HCT Series
def	"Bruker Daltonics' HCT Series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.701. MS:1000698 HCTultra

Table 703. Term [MS:1000698]
id	MS:1000698
name	HCTultra
def	"Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1000697 Bruker Daltonics HCT Series ! Bruker Daltonics HCT Series

2.702. MS:1000699 HCTultra PTM

Table 704. Term [MS:1000699]
id	MS:1000699
name	HCTultra PTM
def	"Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS]
is_a	MS:1000697 Bruker Daltonics HCT Series ! Bruker Daltonics HCT Series

2.703. MS:1000700 HCTultra ETD II

Table 705. Term [MS:1000700]
id	MS:1000700
name	HCTultra ETD II
def	"Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS]
is_a	MS:1000697 Bruker Daltonics HCT Series ! Bruker Daltonics HCT Series

2.704. MS:1000701 microflex LT

Table 706. Term [MS:1000701]
id	MS:1000701
name	microflex LT
def	"Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.705. MS:1000702 micrOTOF

Table 707. Term [MS:1000702]
id	MS:1000702
name	micrOTOF
def	"Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.706. MS:1000703 micrOTOF-Q

Table 708. Term [MS:1000703]
id	MS:1000703
name	micrOTOF-Q
def	"Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.707. MS:1000704 micrOTOF-Q II

Table 709. Term [MS:1000704]
id	MS:1000704
name	micrOTOF-Q II
def	"Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.708. MS:1000705 ultraflex III TOF/TOF

Table 710. Term [MS:1000705]
id	MS:1000705
name	ultraflex III TOF/TOF
def	"Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.709. MS:1000706 apexControl

Table 711. Term [MS:1000706]
id	MS:1000706
name	apexControl
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.710. MS:1000707 BioTools

Table 712. Term [MS:1000707]
id	MS:1000707
name	BioTools
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.711. MS:1000708 CLINPROT

Table 713. Term [MS:1000708]
id	MS:1000708
name	CLINPROT
def	"Bruker CLINPROT software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.712. MS:1000709 CLINPROT micro

Table 714. Term [MS:1000709]
id	MS:1000709
name	CLINPROT micro
def	"Bruker CLINPROT micro software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.713. MS:1000710 CLINPROT robot

Table 715. Term [MS:1000710]
id	MS:1000710
name	CLINPROT robot
def	"Bruker CLINPROT robot software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.714. MS:1000711 ClinProTools

Table 716. Term [MS:1000711]
id	MS:1000711
name	ClinProTools
def	"Bruker ClinProTools software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.715. MS:1000712 Compass

Table 717. Term [MS:1000712]
id	MS:1000712
name	Compass
def	"Bruker Compass software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.716. MS:1000713 Compass for HCT/esquire

Table 718. Term [MS:1000713]
id	MS:1000713
name	Compass for HCT/esquire
def	"Bruker Compass for HCT/esquire software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.717. MS:1000714 Compass for micrOTOF

Table 719. Term [MS:1000714]
id	MS:1000714
name	Compass for micrOTOF
def	"Bruker Compass for micrOTOF software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.718. MS:1000715 Compass OpenAccess

Table 720. Term [MS:1000715]
id	MS:1000715
name	Compass OpenAccess
def	"Bruker compass OpenAccess software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.719. MS:1000716 Compass Security Pack

Table 721. Term [MS:1000716]
id	MS:1000716
name	Compass Security Pack
def	"Bruker compass Security Pack software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.720. MS:1000717 CompassXport

Table 722. Term [MS:1000717]
id	MS:1000717
name	CompassXport
def	"Bruker stand-alone software for data conversion." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001457 data processing software ! data processing software

2.721. MS:1000718 CompassXtract

Table 723. Term [MS:1000718]
id	MS:1000718
name	CompassXtract
def	"Bruker software library for data access." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001457 data processing software ! data processing software

2.722. MS:1000719 DataAnalysis

Table 724. Term [MS:1000719]
id	MS:1000719
name	DataAnalysis
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.723. MS:1000720 dpControl

Table 725. Term [MS:1000720]
id	MS:1000720
name	dpControl
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.724. MS:1000721 esquireControl

Table 726. Term [MS:1000721]
id	MS:1000721
name	esquireControl
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.725. MS:1000722 flexImaging

Table 727. Term [MS:1000722]
id	MS:1000722
name	flexImaging
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.726. MS:1000723 GENOLINK

Table 728. Term [MS:1000723]
id	MS:1000723
name	GENOLINK
def	"Bruker GENOLINK software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.727. MS:1000724 GenoTools

Table 729. Term [MS:1000724]
id	MS:1000724
name	GenoTools
def	"Bruker GenoTools software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.728. MS:1000725 HCTcontrol

Table 730. Term [MS:1000725]
id	MS:1000725
name	HCTcontrol
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.729. MS:1000726 micrOTOFcontrol

Table 731. Term [MS:1000726]
id	MS:1000726
name	micrOTOFcontrol
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.730. MS:1000727 PolyTools

Table 732. Term [MS:1000727]
id	MS:1000727
name	PolyTools
def	"Bruker PolyTools software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.731. MS:1000728 ProfileAnalysis

Table 733. Term [MS:1000728]
id	MS:1000728
name	ProfileAnalysis
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.732. MS:1000729 PROTEINEER

Table 734. Term [MS:1000729]
id	MS:1000729
name	PROTEINEER
def	"Bruker PROTEINEER software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software

2.733. MS:1000730 PROTEINEER dp

Table 735. Term [MS:1000730]
id	MS:1000730
name	PROTEINEER dp
def	"Bruker PROTEINEER dp software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software

2.734. MS:1000731 PROTEINEER fc

Table 736. Term [MS:1000731]
id	MS:1000731
name	PROTEINEER fc
def	"Bruker PROTEINEER fc software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software

2.735. MS:1000732 PROTEINEER spII

Table 737. Term [MS:1000732]
id	MS:1000732
name	PROTEINEER spII
def	"Bruker PROTEINEER spII software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software

2.736. MS:1000733 PROTEINEER-LC

Table 738. Term [MS:1000733]
id	MS:1000733
name	PROTEINEER-LC
def	"Bruker PROTEINEER-LC software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software

2.737. MS:1000734 ProteinScape

Table 739. Term [MS:1000734]
id	MS:1000734
name	ProteinScape
def	"Bruker ProteinScape software." [PSI:PI]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software

2.738. MS:1000735 PureDisk

Table 740. Term [MS:1000735]
id	MS:1000735
name	PureDisk
def	"BrukerPureDisk software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.739. MS:1000736 QuantAnalysis

Table 741. Term [MS:1000736]
id	MS:1000736
name	QuantAnalysis
def	"Bruker software for data analysis." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.740. MS:1000737 spControl

Table 742. Term [MS:1000737]
id	MS:1000737
name	spControl
def	"Bruker software for data acquisition." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001455 acquisition software ! acquisition software

2.741. MS:1000738 TargetAnalysis

Table 743. Term [MS:1000738]
id	MS:1000738
name	TargetAnalysis
def	"Bruker TargetAnalysis software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.742. MS:1000739 WARP-LC

Table 744. Term [MS:1000739]
id	MS:1000739
name	WARP-LC
def	"Bruker WARP-LC software." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001139 quantitation software name ! quantitation software name

2.743. MS:1000740 parameter file

Table 745. Term [MS:1000740]
id	MS:1000740
name	parameter file
def	"Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.744. MS:1000741 Conversion to dta

Table 746. Term [MS:1000741]
id	MS:1000741
name	Conversion to dta
def	"Conversion to dta format." [PSI:MS]
is_a	MS:1000530 file format conversion ! file format conversion

2.745. MS:1000742 Bioworks SRF format

Table 747. Term [MS:1000742]
id	MS:1000742
name	Bioworks SRF format
def	"Thermo Finnigan SRF file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.746. MS:1000743 TSQ Quantum Ultra AM

Table 748. Term [MS:1000743]
id	MS:1000743
name	TSQ Quantum Ultra AM
def	"Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.747. MS:1000744 selected ion m/z

Table 749. Term [MS:1000744]
id	MS:1000744
name	selected ion m/z
def	"Mass-to-charge ratio of an selected ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	has_units MS:1000040 m/z ! m/z

2.748. MS:1000745 retention time alignment

Table 750. Term [MS:1000745]
id	MS:1000745
name	retention time alignment
def	"The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.749. MS:1000746 high intensity data point removal

Table 751. Term [MS:1000746]
id	MS:1000746
name	high intensity data point removal
def	"The removal of very high intensity data points." [PSI:MS]
is_a	MS:1001486 data filtering ! data filtering

2.750. MS:1000747 completion time

Table 752. Term [MS:1000747]
id	MS:1000747
name	completion time
def	"The time that a data processing action was finished." [PSI:MS]
xref	value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter

2.751. MS:1000748 SSQ 7000

Table 753. Term [MS:1000748]
id	MS:1000748
name	SSQ 7000
def	"ThermoFinnigan SSQ 7000 MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.752. MS:1000749 TSQ 7000

Table 754. Term [MS:1000749]
id	MS:1000749
name	TSQ 7000
def	"ThermoFinnigan TSQ 7000 MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.753. MS:1000750 TSQ

Table 755. Term [MS:1000750]
id	MS:1000750
name	TSQ
def	"ThermoFinnigan TSQ MS." [PSI:MS]
is_a	MS:1000493 Finnigan MAT instrument model ! Finnigan MAT instrument model

2.754. MS:1000751 TSQ Quantum Ultra

Table 756. Term [MS:1000751]
id	MS:1000751
name	TSQ Quantum Ultra
def	"Thermo Scientific TSQ Quantum Ultra." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.755. MS:1000752 TOPP software

Table 757. Term [MS:1000752]
id	MS:1000752
name	TOPP software
def	"TOPP (The OpenMS proteomics pipeline) software." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.756. MS:1000753 BaselineFilter

Table 758. Term [MS:1000753]
id	MS:1000753
name	BaselineFilter
def	"Removes the baseline from profile spectra using a top-hat filter." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.757. MS:1000754 DBExporter

Table 759. Term [MS:1000754]
id	MS:1000754
name	DBExporter
def	"Exports data from an OpenMS database to a file." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.758. MS:1000755 DBImporter

Table 760. Term [MS:1000755]
id	MS:1000755
name	DBImporter
def	"Imports data to an OpenMS database." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.759. MS:1000756 FileConverter

Table 761. Term [MS:1000756]
id	MS:1000756
name	FileConverter
def	"Converts between different MS file formats." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.760. MS:1000757 FileFilter

Table 762. Term [MS:1000757]
id	MS:1000757
name	FileFilter
def	"Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.761. MS:1000758 FileMerger

Table 763. Term [MS:1000758]
id	MS:1000758
name	FileMerger
def	"Merges several MS files into one file." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.762. MS:1000759 InternalCalibration

Table 764. Term [MS:1000759]
id	MS:1000759
name	InternalCalibration
def	"Applies an internal calibration." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.763. MS:1000760 MapAligner

Table 765. Term [MS:1000760]
id	MS:1000760
name	MapAligner
def	"OBSOLETE Corrects retention time distortions between maps." [PSI:MS]
comment	This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch.
is_a	MS:1000752 TOPP software ! TOPP software
is_obsolete	true

2.764. MS:1000761 MapNormalizer

Table 766. Term [MS:1000761]
id	MS:1000761
name	MapNormalizer
def	"Normalizes peak intensities in an MS run." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.765. MS:1000762 NoiseFilter

Table 767. Term [MS:1000762]
id	MS:1000762
name	NoiseFilter
def	"OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS]
comment	This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch.
is_a	MS:1000752 TOPP software ! TOPP software
is_obsolete	true

2.766. MS:1000763 PeakPicker

Table 768. Term [MS:1000763]
id	MS:1000763
name	PeakPicker
def	"OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS]
comment	This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch.
is_a	MS:1000752 TOPP software ! TOPP software
is_obsolete	true

2.767. MS:1000764 Resampler

Table 769. Term [MS:1000764]
id	MS:1000764
name	Resampler
def	"Transforms an LC/MS map into a resampled map or a png image." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.768. MS:1000765 SpectraFilter

Table 770. Term [MS:1000765]
id	MS:1000765
name	SpectraFilter
def	"OBSOLETE Applies a filter to peak spectra." [PSI:MS]
comment	This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch.
is_a	MS:1000752 TOPP software ! TOPP software
is_obsolete	true

2.769. MS:1000766 TOFCalibration

Table 771. Term [MS:1000766]
id	MS:1000766
name	TOFCalibration
def	"Applies time of flight calibration." [PSI:MS]
is_a	MS:1000752 TOPP software ! TOPP software

2.770. MS:1000767 native spectrum identifier format

Table 772. Term [MS:1000767]
id	MS:1000767
name	native spectrum identifier format
def	"Describes how the native spectrum identifiers are formated." [PSI:MS]
synonym	"nativeID format" EXACT []
relationship	part_of MS:1000577 source data file ! source data file

2.771. MS:1000768 Thermo nativeID format

Table 773. Term [MS:1000768]
id	MS:1000768
name	Thermo nativeID format
def	"Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.772. MS:1000769 Waters nativeID format

Table 774. Term [MS:1000769]
id	MS:1000769
name	Waters nativeID format
def	"Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.773. MS:1000770 WIFF nativeID format

Table 775. Term [MS:1000770]
id	MS:1000770
name	WIFF nativeID format
def	"Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.774. MS:1000771 Bruker/Agilent YEP nativeID format

Table 776. Term [MS:1000771]
id	MS:1000771
name	Bruker/Agilent YEP nativeID format
def	"Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.775. MS:1000772 Bruker BAF nativeID format

Table 777. Term [MS:1000772]
id	MS:1000772
name	Bruker BAF nativeID format
def	"Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.776. MS:1000773 Bruker FID nativeID format

Table 778. Term [MS:1000773]
id	MS:1000773
name	Bruker FID nativeID format
def	"Native format defined by file=xsd:IDREF." [PSI:MS]
comment	The nativeID must be the same as the source file ID.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.777. MS:1000774 multiple peak list nativeID format

Table 779. Term [MS:1000774]
id	MS:1000774
name	multiple peak list nativeID format
def	"Native format defined by index=xsd:nonNegativeInteger." [PSI:MS]
comment	Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.778. MS:1000775 single peak list nativeID format

Table 780. Term [MS:1000775]
id	MS:1000775
name	single peak list nativeID format
def	"Native format defined by file=xsd:IDREF." [PSI:MS]
comment	The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.779. MS:1000776 scan number only nativeID format

Table 781. Term [MS:1000776]
id	MS:1000776
name	scan number only nativeID format
def	"Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS]
comment	Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.780. MS:1000777 spectrum identifier nativeID format

Table 782. Term [MS:1000777]
id	MS:1000777
name	spectrum identifier nativeID format
def	"Native format defined by spectrum=xsd:nonNegativeInteger." [PSI:MS]
comment	Used for conversion from mzData. The spectrum id attribute is referenced.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.781. MS:1000778 charge state calculation

Table 783. Term [MS:1000778]
id	MS:1000778
name	charge state calculation
def	"A process that infers the charge state of an MSn spectrum’s precursor(s) by the application of some algorithm." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.782. MS:1000779 below precursor intensity dominance charge state calculation

Table 784. Term [MS:1000779]
id	MS:1000779
name	below precursor intensity dominance charge state calculation
def	"Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS]
is_a	MS:1000778 charge state calculation ! charge state calculation

2.783. MS:1000780 precursor recalculation

Table 785. Term [MS:1000780]
id	MS:1000780
name	precursor recalculation
def	"A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.784. MS:1000781 msPrefix precursor recalculation

Table 786. Term [MS:1000781]
id	MS:1000781
name	msPrefix precursor recalculation
def	"Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS]
is_a	MS:1000780 precursor recalculation ! precursor recalculation

2.785. MS:1000782 Savitzky-Golay smoothing

Table 787. Term [MS:1000782]
id	MS:1000782
name	Savitzky-Golay smoothing
def	"Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques." [PSI:MS]
is_a	MS:1000592 smoothing ! smoothing

2.786. MS:1000783 LOWESS smoothing

Table 788. Term [MS:1000783]
id	MS:1000783
name	LOWESS smoothing
def	"Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible." [PSI:MS]
is_a	MS:1000592 smoothing ! smoothing

2.787. MS:1000784 Gaussian smoothing

Table 789. Term [MS:1000784]
id	MS:1000784
name	Gaussian smoothing
def	"Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS]
synonym	"binomial smoothing" EXACT []
synonym	"Weierstrass transform" EXACT []
is_a	MS:1000592 smoothing ! smoothing

2.788. MS:1000785 moving average smoothing

Table 790. Term [MS:1000785]
id	MS:1000785
name	moving average smoothing
def	"Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect." [PSI:MS]
synonym	"box smoothing" EXACT []
synonym	"boxcar smoothing" EXACT []
synonym	"sliding average smoothing" EXACT []
is_a	MS:1000592 smoothing ! smoothing

2.789. MS:1000786 non-standard data array

Table 791. Term [MS:1000786]
id	MS:1000786
name	non-standard data array
def	"A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added." [PSI:MS]
xref	binary-data-type:MS\:1000519 "32-bit integer"
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000522 "64-bit integer"
xref	binary-data-type:MS\:1000523 "64-bit float"
xref	binary-data-type:MS\:1001479 "null-terminated ASCII string"
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000513 binary data array ! binary data array

2.790. MS:1000787 inclusive low intensity threshold

Table 792. Term [MS:1000787]
id	MS:1000787
name	inclusive low intensity threshold
def	"Threshold at or below which some action is taken." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.791. MS:1000788 inclusive high intensity threshold

Table 793. Term [MS:1000788]
id	MS:1000788
name	inclusive high intensity threshold
def	"Threshold at or above which some action is taken." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100
relationship	has_units [UO:0000269] ! absorbance unit

2.792. MS:1000789 enhanced multiply charged spectrum

Table 794. Term [MS:1000789]
id	MS:1000789
name	enhanced multiply charged spectrum
def	"MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS]
is_a	MS:1000579 MS1 spectrum ! MS1 spectrum

2.793. MS:1000790 time-delayed fragmentation spectrum

Table 795. Term [MS:1000790]
id	MS:1000790
name	time-delayed fragmentation spectrum
def	"MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS]
is_a	MS:1000580 MSn spectrum ! MSn spectrum

2.794. MS:1000791 enhanced resolution scan

Table 796. Term [MS:1000791]
id	MS:1000791
name	enhanced resolution scan
def	"OBSOLETE Scan with enhanced resolution." [PSI:MS]
comment	This term was made obsolete because it was merged with zoom scan (MS:1000497).
is_obsolete	true

2.795. MS:1000792 isolation window attribute

Table 797. Term [MS:1000792]
id	MS:1000792
name	isolation window attribute
def	"Isolation window parameter." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000441 scan ! scan

2.796. MS:1000793 isolation window upper limit

Table 798. Term [MS:1000793]
id	MS:1000793
name	isolation window upper limit
def	"OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS]
comment	This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000792 isolation window attribute ! isolation window attribute
relationship	has_units MS:1000040 m/z ! m/z
is_obsolete	true

2.797. MS:1000794 isolation window lower limit

Table 799. Term [MS:1000794]
id	MS:1000794
name	isolation window lower limit
def	"OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS]
comment	This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000792 isolation window attribute ! isolation window attribute
relationship	has_units MS:1000040 m/z ! m/z
is_obsolete	true

2.798. MS:1000795 no combination

Table 800. Term [MS:1000795]
id	MS:1000795
name	no combination
def	"Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS]
is_a	MS:1000570 spectra combination ! spectra combination

2.799. MS:1000796 spectrum title

Table 801. Term [MS:1000796]
id	MS:1000796
name	spectrum title
def	"Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS]
comment	This is the preferred storage place for the spectrum TITLE from an MGF peak list.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.800. MS:1000797 peak list scans

Table 802. Term [MS:1000797]
id	MS:1000797
name	peak list scans
def	"A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment	This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_a	MS:1003058 spectrum property ! spectrum property

2.801. MS:1000798 peak list raw scans

Table 803. Term [MS:1000798]
id	MS:1000798
name	peak list raw scans
def	"A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment	This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_a	MS:1003058 spectrum property ! spectrum property

2.802. MS:1000799 custom unreleased software tool

Table 804. Term [MS:1000799]
id	MS:1000799
name	custom unreleased software tool
def	"A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000531 software ! software

2.803. MS:1000800 mass resolving power

Table 805. Term [MS:1000800]
id	MS:1000800
name	mass resolving power
def	"The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute

2.804. MS:1000801 area peak picking

Table 806. Term [MS:1000801]
id	MS:1000801
name	area peak picking
def	"Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported." [PSI:MS]
synonym	"sum peak picking" EXACT []
is_a	MS:1000035 peak picking ! peak picking

2.805. MS:1000802 height peak picking

Table 807. Term [MS:1000802]
id	MS:1000802
name	height peak picking
def	"Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported." [PSI:MS]
synonym	"max peak picking" EXACT []
is_a	MS:1000035 peak picking ! peak picking

2.806. MS:1000803 analyzer scan offset

Table 808. Term [MS:1000803]
id	MS:1000803
name	analyzer scan offset
def	"Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units MS:1000040 m/z ! m/z

2.807. MS:1000804 electromagnetic radiation spectrum

Table 809. Term [MS:1000804]
id	MS:1000804
name	electromagnetic radiation spectrum
def	"A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS]
synonym	"EMR spectrum" EXACT []
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000559 spectrum type ! spectrum type

2.808. MS:1000805 emission spectrum

Table 810. Term [MS:1000805]
id	MS:1000805
name	emission spectrum
def	"A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS]
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000559 spectrum type ! spectrum type

2.809. MS:1000806 absorption spectrum

Table 811. Term [MS:1000806]
id	MS:1000806
name	absorption spectrum
def	"A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS]
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000559 spectrum type ! spectrum type

2.810. MS:1000807 Th/s

Table 812. Term [MS:1000807]
id	MS:1000807
name	Th/s
def	"Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS]
is_a	[UO:0000000] ! unit

2.811. MS:1000808 chromatogram attribute

Table 813. Term [MS:1000808]
id	MS:1000808
name	chromatogram attribute
def	"Chromatogram properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.812. MS:1000809 chromatogram title

Table 814. Term [MS:1000809]
id	MS:1000809
name	chromatogram title
def	"A free-form text title describing a chromatogram." [PSI:MS]
comment	This is the preferred storage place for the spectrum title.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000808 chromatogram attribute ! chromatogram attribute

2.813. MS:1000810 ion current chromatogram

Table 815. Term [MS:1000810]
id	MS:1000810
name	ion current chromatogram
def	"Representation of the current of ions versus time." [PSI:MS]
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000626 chromatogram type ! chromatogram type

2.814. MS:1000811 electromagnetic radiation chromatogram

Table 816. Term [MS:1000811]
id	MS:1000811
name	electromagnetic radiation chromatogram
def	"Representation of electromagnetic properties versus time." [PSI:MS]
synonym	"EMR radiation chromatogram" EXACT []
is_a	MS:1000524 data file content ! data file content
is_a	MS:1000626 chromatogram type ! chromatogram type

2.815. MS:1000812 absorption chromatogram

Table 817. Term [MS:1000812]
id	MS:1000812
name	absorption chromatogram
def	"Representation of light absorbed by the sample versus time." [PSI:MS]
is_a	MS:1000811 electromagnetic radiation chromatogram ! electromagnetic radiation chromatogram

2.816. MS:1000813 emission chromatogram

Table 818. Term [MS:1000813]
id	MS:1000813
name	emission chromatogram
def	"Representation of light emitted by the sample versus time." [PSI:MS]
is_a	MS:1000811 electromagnetic radiation chromatogram ! electromagnetic radiation chromatogram

2.817. MS:1000814 counts per second

Table 819. Term [MS:1000814]
id	MS:1000814
name	counts per second
def	"The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS]
is_a	MS:1000043 intensity unit ! intensity unit

2.818. MS:1000815 Bruker BAF format

Table 820. Term [MS:1000815]
id	MS:1000815
name	Bruker BAF format
def	"Bruker BAF raw file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.819. MS:1000816 Bruker U2 format

Table 821. Term [MS:1000816]
id	MS:1000816
name	Bruker U2 format
def	"Bruker HyStar U2 file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.820. MS:1000817 HyStar

Table 822. Term [MS:1000817]
id	MS:1000817
name	HyStar
def	"Bruker software for hyphenated experiments." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software

2.821. MS:1000818 Acquity UPLC PDA

Table 823. Term [MS:1000818]
id	MS:1000818
name	Acquity UPLC PDA
def	"Acquity UPLC Photodiode Array Detector." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model
is_a	MS:1000621 photodiode array detector ! photodiode array detector

2.822. MS:1000819 Acquity UPLC FLR

Table 824. Term [MS:1000819]
id	MS:1000819
name	Acquity UPLC FLR
def	"Acquity UPLC Fluorescence Detector." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model
is_a	MS:1002308 fluorescence detector ! fluorescence detector

2.823. MS:1000820 flow rate array

Table 825. Term [MS:1000820]
id	MS:1000820
name	flow rate array
def	"A data array of flow rate measurements." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000271] ! microliters per minute

2.824. MS:1000821 pressure array

Table 826. Term [MS:1000821]
id	MS:1000821
name	pressure array
def	"A data array of pressure measurements." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000110] ! pascal

2.825. MS:1000822 temperature array

Table 827. Term [MS:1000822]
id	MS:1000822
name	temperature array
def	"A data array of temperature measurements." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000012] ! kelvin

2.826. MS:1000823 Bruker U2 nativeID format

Table 828. Term [MS:1000823]
id	MS:1000823
name	Bruker U2 nativeID format
def	"Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.827. MS:1000824 no nativeID format

Table 829. Term [MS:1000824]
id	MS:1000824
name	no nativeID format
def	"No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.828. MS:1000825 Bruker FID format

Table 830. Term [MS:1000825]
id	MS:1000825
name	Bruker FID format
def	"Bruker FID file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.829. MS:1000826 elution time

Table 831. Term [MS:1000826]
id	MS:1000826
name	elution time
def	"The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.830. MS:1000827 isolation window target m/z

Table 832. Term [MS:1000827]
id	MS:1000827
name	isolation window target m/z
def	"The primary or reference m/z about which the isolation window is defined." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000792 isolation window attribute ! isolation window attribute
relationship	has_units MS:1000040 m/z ! m/z

2.831. MS:1000828 isolation window lower offset

Table 833. Term [MS:1000828]
id	MS:1000828
name	isolation window lower offset
def	"The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000792 isolation window attribute ! isolation window attribute
relationship	has_units MS:1000040 m/z ! m/z

2.832. MS:1000829 isolation window upper offset

Table 834. Term [MS:1000829]
id	MS:1000829
name	isolation window upper offset
def	"The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000792 isolation window attribute ! isolation window attribute
relationship	has_units MS:1000040 m/z ! m/z

2.833. MS:1000831 sample preparation

Table 835. Term [MS:1000831]
id	MS:1000831
name	sample preparation
def	"Properties of the preparation steps which took place before the measurement was performed." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000548 sample attribute ! sample attribute

2.834. MS:1000832 MALDI matrix application

Table 836. Term [MS:1000832]
id	MS:1000832
name	MALDI matrix application
def	"Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS]
relationship	part_of MS:1000831 sample preparation ! sample preparation

2.835. MS:1000833 matrix application type

Table 837. Term [MS:1000833]
id	MS:1000833
name	matrix application type
def	"Describes the technique how the matrix is put on the sample target." [PSI:MS]
relationship	part_of MS:1000832 MALDI matrix application ! MALDI matrix application

2.836. MS:1000834 matrix solution

Table 838. Term [MS:1000834]
id	MS:1000834
name	matrix solution
def	"Describes the chemical solution used as matrix." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000832 MALDI matrix application ! MALDI matrix application

2.837. MS:1000835 matrix solution concentration

Table 839. Term [MS:1000835]
id	MS:1000835
name	matrix solution concentration
def	"Concentration of the chemical solution used as matrix." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000832 MALDI matrix application ! MALDI matrix application
relationship	has_units [UO:0000175] ! gram per liter

2.838. MS:1000836 dried droplet MALDI matrix preparation

Table 840. Term [MS:1000836]
id	MS:1000836
name	dried droplet MALDI matrix preparation
def	"Dried droplet in MALDI matrix preparation." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.839. MS:1000837 printed MALDI matrix preparation

Table 841. Term [MS:1000837]
id	MS:1000837
name	printed MALDI matrix preparation
def	"Printed MALDI matrix preparation." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.840. MS:1000838 sprayed MALDI matrix preparation

Table 842. Term [MS:1000838]
id	MS:1000838
name	sprayed MALDI matrix preparation
def	"Sprayed MALDI matrix preparation." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.841. MS:1000839 precoated MALDI sample plate

Table 843. Term [MS:1000839]
id	MS:1000839
name	precoated MALDI sample plate
def	"Precoated MALDI sample plate." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type
is_a	MS:1001938 sample plate type ! sample plate type

2.842. MS:1000840 laser

Table 844. Term [MS:1000840]
id	MS:1000840
name	laser
def	"Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS]
relationship	part_of MS:1000482 source attribute ! source attribute

2.843. MS:1000841 laser attribute

Table 845. Term [MS:1000841]
id	MS:1000841
name	laser attribute
def	"Laser properties that are associated with a value." [PSI:MS]
relationship	part_of MS:1000840 laser ! laser

2.844. MS:1000842 laser type

Table 846. Term [MS:1000842]
id	MS:1000842
name	laser type
def	"Type of laser used for desorption purpose." [PSI:MS]
relationship	part_of MS:1000840 laser ! laser

2.845. MS:1000843 wavelength

Table 847. Term [MS:1000843]
id	MS:1000843
name	wavelength
def	"OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS]
comment	This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242).
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000018] ! nanometer
is_obsolete	true

2.846. MS:1000844 focus diameter x

Table 848. Term [MS:1000844]
id	MS:1000844
name	focus diameter x
def	"Describes the diameter of the laser beam in x direction." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000017] ! micrometer

2.847. MS:1000845 focus diameter y

Table 849. Term [MS:1000845]
id	MS:1000845
name	focus diameter y
def	"Describes the diameter of the laser beam in y direction." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000017] ! micrometer

2.848. MS:1000846 pulse energy

Table 850. Term [MS:1000846]
id	MS:1000846
name	pulse energy
def	"Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000112] ! joule

2.849. MS:1000847 pulse duration

Table 851. Term [MS:1000847]
id	MS:1000847
name	pulse duration
def	"Describes how long the laser beam was emitted from the laser device." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000150] ! nanosecond

2.850. MS:1000848 attenuation

Table 852. Term [MS:1000848]
id	MS:1000848
name	attenuation
def	"Describes the reduction of the intensity of the laser beam energy." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000187] ! percent

2.851. MS:1000849 impact angle

Table 853. Term [MS:1000849]
id	MS:1000849
name	impact angle
def	"Describes the angle between the laser beam and the sample target." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000841 laser attribute ! laser attribute
relationship	has_units [UO:0000185] ! degree

2.852. MS:1000850 gas laser

Table 854. Term [MS:1000850]
id	MS:1000850
name	gas laser
def	"Laser which is powered by a gaseous medium." [PSI:MS]
is_a	MS:1000842 laser type ! laser type

2.853. MS:1000851 solid-state laser

Table 855. Term [MS:1000851]
id	MS:1000851
name	solid-state laser
def	"Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS]
is_a	MS:1000842 laser type ! laser type

2.854. MS:1000852 dye-laser

Table 856. Term [MS:1000852]
id	MS:1000852
name	dye-laser
def	"Dye lasers use an organic dye as the gain medium." [PSI:MS]
is_a	MS:1000842 laser type ! laser type

2.855. MS:1000853 free electron laser

Table 857. Term [MS:1000853]
id	MS:1000853
name	free electron laser
def	"Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS]
is_a	MS:1000842 laser type ! laser type

2.856. MS:1000854 LTQ XL

Table 858. Term [MS:1000854]
id	MS:1000854
name	LTQ XL
def	"Thermo Scientific LTQ XL MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.857. MS:1000855 LTQ Velos

Table 859. Term [MS:1000855]
id	MS:1000855
name	LTQ Velos
def	"Thermo Scientific LTQ Velos MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.858. MS:1000856 LTQ Velos ETD

Table 860. Term [MS:1000856]
id	MS:1000856
name	LTQ Velos ETD
def	"Thermo Scientific LTQ Velos MS with ETD." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.859. MS:1000857 run attribute

Table 861. Term [MS:1000857]
id	MS:1000857
name	run attribute
def	"Properties of the described run." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute

2.860. MS:1000858 fraction identifier

Table 862. Term [MS:1000858]
id	MS:1000858
name	fraction identifier
def	"Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000857 run attribute ! run attribute

2.861. MS:1000859 molecule

Table 863. Term [MS:1000859]
id	MS:1000859
name	molecule
def	"Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule]
is_a	MS:1000881 molecular entity ! molecular entity

2.862. MS:1000860 peptide

Table 864. Term [MS:1000860]
id	MS:1000860
name	peptide
def	"A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS]
is_a	MS:1000859 molecule ! molecule

2.863. MS:1000861 molecular entity property

Table 865. Term [MS:1000861]
id	MS:1000861
name	molecular entity property
def	"A physical characteristic of a molecular entity." [PSI:MS]
relationship	part_of MS:1000881 molecular entity ! molecular entity

2.864. MS:1000862 isoelectric point

Table 866. Term [MS:1000862]
id	MS:1000862
name	isoelectric point
def	"The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS]
synonym	"pI" EXACT []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000861 molecular entity property ! molecular entity property

2.865. MS:1000863 predicted isoelectric point

Table 867. Term [MS:1000863]
id	MS:1000863
name	predicted isoelectric point
def	"The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS]
synonym	"predicted pI" EXACT []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000862 isoelectric point ! isoelectric point

2.866. MS:1000864 chemical formula

Table 868. Term [MS:1000864]
id	MS:1000864
name	chemical formula
def	"A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846]
is_a	MS:1003033 molecular entity attribute ! molecular entity attribute

2.867. MS:1000865 empirical formula

Table 869. Term [MS:1000865]
id	MS:1000865
name	empirical formula
def	"A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000864 chemical formula ! chemical formula

2.868. MS:1000866 molecular formula

Table 870. Term [MS:1000866]
id	MS:1000866
name	molecular formula
def	"A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000864 chemical formula ! chemical formula

2.869. MS:1000867 structural formula

Table 871. Term [MS:1000867]
id	MS:1000867
name	structural formula
def	"A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000864 chemical formula ! chemical formula

2.870. MS:1000868 SMILES formula

Table 872. Term [MS:1000868]
id	MS:1000868
name	SMILES formula
def	"The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000864 chemical formula ! chemical formula

2.871. MS:1000869 collision gas pressure

Table 873. Term [MS:1000869]
id	MS:1000869
name	collision gas pressure
def	"The gas pressure of the collision gas used for collisional excitation." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000110] ! pascal

2.872. MS:1000870 4000 QTRAP

Table 874. Term [MS:1000870]
id	MS:1000870
name	4000 QTRAP
def	"OBSOLETE SCIEX or Applied Biosystems\|MDS SCIEX QTRAP 4000." [PSI:MS]
comment	This term was obsoleted because was redundant to MS:1000139.
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model
is_obsolete	true

2.873. MS:1000871 SRM software

Table 875. Term [MS:1000871]
id	MS:1000871
name	SRM software
def	"Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS]
is_a	MS:1000531 software ! software

2.874. MS:1000872 MaRiMba

Table 876. Term [MS:1000872]
id	MS:1000872
name	MaRiMba
def	"Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba]
is_a	MS:1000871 SRM software ! SRM software

2.875. MS:1000873 peptide attribute calculation software

Table 877. Term [MS:1000873]
id	MS:1000873
name	peptide attribute calculation software
def	"Software used to predict or calculate numerical attributes of peptides." [PSI:MS]
is_a	MS:1000531 software ! software

2.876. MS:1000874 SSRCalc

Table 878. Term [MS:1000874]
id	MS:1000874
name	SSRCalc
def	"Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence." [http://hs2.proteome.ca/SSRCalc/SSRCalc.html]
is_a	MS:1000873 peptide attribute calculation software ! peptide attribute calculation software

2.877. MS:1000875 declustering potential

Table 879. Term [MS:1000875]
id	MS:1000875
name	declustering potential
def	"Potential difference between the orifice and the skimmer in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.878. MS:1000876 cone voltage

Table 880. Term [MS:1000876]
id	MS:1000876
name	cone voltage
def	"Potential difference between the sampling cone/orifice in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.879. MS:1000877 tube lens voltage

Table 881. Term [MS:1000877]
id	MS:1000877
name	tube lens voltage
def	"Potential difference setting of the tube lens in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.880. MS:1000878 external reference identifier

Table 882. Term [MS:1000878]
id	MS:1000878
name	external reference identifier
def	"An identifier/accession number to an external reference database." [PSI:MS]
is_a	MS:1002840 external reference data ! external reference data

2.881. MS:1000879 PubMed identifier

Table 883. Term [MS:1000879]
id	MS:1000879
name	PubMed identifier
def	"A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.882. MS:1000880 interchannel delay

Table 884. Term [MS:1000880]
id	MS:1000880
name	interchannel delay
def	"The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000010] ! second

2.883. MS:1000881 molecular entity

Table 885. Term [MS:1000881]
id	MS:1000881
name	molecular entity
def	"Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.884. MS:1000882 protein

Table 886. Term [MS:1000882]
id	MS:1000882
name	protein
def	"A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS]
is_a	MS:1000859 molecule ! molecule

2.885. MS:1000883 protein short name

Table 887. Term [MS:1000883]
id	MS:1000883
name	protein short name
def	"A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000884 protein attribute ! protein attribute

2.886. MS:1000884 protein attribute

Table 888. Term [MS:1000884]
id	MS:1000884
name	protein attribute
def	"An nonphysical characterstic attributed to a specific protein." [PSI:MS]
relationship	part_of MS:1000882 protein ! protein
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.887. MS:1000885 protein accession

Table 889. Term [MS:1000885]
id	MS:1000885
name	protein accession
def	"Identifier for a specific protein in a database." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000884 protein attribute ! protein attribute
is_a	MS:1003046 peptide-to-protein mapping attribute ! peptide-to-protein mapping attribute

2.888. MS:1000886 protein name

Table 890. Term [MS:1000886]
id	MS:1000886
name	protein name
def	"A long name describing the function of the protein." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000884 protein attribute ! protein attribute

2.889. MS:1000887 peptide attribute

Table 891. Term [MS:1000887]
id	MS:1000887
name	peptide attribute
def	"Nonphysical characteristic attributed to a peptide." [PSI:MS]
relationship	part_of MS:1000860 peptide ! peptide

2.890. MS:1000888 stripped peptide sequence

Table 892. Term [MS:1000888]
id	MS:1000888
name	stripped peptide sequence
def	"Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003050 peptidoform attribute ! peptidoform attribute

2.891. MS:1000889 peptidoform sequence

Table 893. Term [MS:1000889]
id	MS:1000889
name	peptidoform sequence
def	"Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS]
comment	Make it more general as there are actually many other ways to display a modified peptide sequence.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003050 peptidoform attribute ! peptidoform attribute

2.892. MS:1000890 peptidoform labeling state

Table 894. Term [MS:1000890]
id	MS:1000890
name	peptidoform labeling state
def	"A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS]
is_a	MS:1003050 peptidoform attribute ! peptidoform attribute

2.893. MS:1000891 heavy labeled peptidoform

Table 895. Term [MS:1000891]
id	MS:1000891
name	heavy labeled peptidoform
def	"A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS]
is_a	MS:1000890 peptidoform labeling state ! peptidoform labeling state

2.894. MS:1000892 unlabeled peptidoform

Table 896. Term [MS:1000892]
id	MS:1000892
name	unlabeled peptidoform
def	"A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS]
synonym	"light labeled peptide" EXACT []
is_a	MS:1000890 peptidoform labeling state ! peptidoform labeling state

2.895. MS:1000893 peptidoform group label

Table 897. Term [MS:1000893]
id	MS:1000893
name	peptidoform group label
def	"An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003050 peptidoform attribute ! peptidoform attribute

2.896. MS:1000894 retention time

Table 898. Term [MS:1000894]
id	MS:1000894
name	retention time
def	"A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1003050 peptidoform attribute ! peptidoform attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.897. MS:1000895 local retention time

Table 899. Term [MS:1000895]
id	MS:1000895
name	local retention time
def	"A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000894 retention time ! retention time
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.898. MS:1000896 normalized retention time

Table 900. Term [MS:1000896]
id	MS:1000896
name	normalized retention time
def	"A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000894 retention time ! retention time
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.899. MS:1000897 predicted retention time

Table 901. Term [MS:1000897]
id	MS:1000897
name	predicted retention time
def	"A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000894 retention time ! retention time
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.900. MS:1000898 standard

Table 902. Term [MS:1000898]
id	MS:1000898
name	standard
def	"Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence." [PSI:MS]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.901. MS:1000899 de facto standard

Table 903. Term [MS:1000899]
id	MS:1000899
name	de facto standard
def	"A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard." [PSI:MS]
is_a	MS:1000898 standard ! standard

2.902. MS:1000900 minimum information standard

Table 904. Term [MS:1000900]
id	MS:1000900
name	minimum information standard
def	"A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result." [PSI:MS]
is_a	MS:1000898 standard ! standard

2.903. MS:1000901 retention time normalization standard

Table 905. Term [MS:1000901]
id	MS:1000901
name	retention time normalization standard
def	"A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column." [PSI:MS]
is_a	MS:1000898 standard ! standard

2.904. MS:1000902 H-PINS retention time normalization standard

Table 906. Term [MS:1000902]
id	MS:1000902
name	H-PINS retention time normalization standard
def	"The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281]
is_a	MS:1000901 retention time normalization standard ! retention time normalization standard

2.905. MS:1000903 product ion series ordinal

Table 907. Term [MS:1000903]
id	MS:1000903
name	product ion series ordinal
def	"The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001221 product ion attribute ! product ion attribute

2.906. MS:1000904 product ion m/z delta

Table 908. Term [MS:1000904]
id	MS:1000904
name	product ion m/z delta
def	"The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a	MS:1001221 product ion attribute ! product ion attribute
relationship	has_units MS:1000040 m/z ! m/z

2.907. MS:1000905 percent of base peak times 100

Table 909. Term [MS:1000905]
id	MS:1000905
name	percent of base peak times 100
def	"The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000043 intensity unit ! intensity unit

2.908. MS:1000906 peak intensity rank

Table 910. Term [MS:1000906]
id	MS:1000906
name	peak intensity rank
def	"Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	part_of MS:1000231 peak ! peak

2.909. MS:1000907 peak targeting suitability rank

Table 911. Term [MS:1000907]
id	MS:1000907
name	peak targeting suitability rank
def	"Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	part_of MS:1000231 peak ! peak

2.910. MS:1000908 transition

Table 912. Term [MS:1000908]
id	MS:1000908
name	transition
def	"A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely." [PSI:MS]
synonym	"reaction" EXACT []
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.911. MS:1000909 transition validation method

Table 913. Term [MS:1000909]
id	MS:1000909
name	transition validation method
def	"The strategy used to validate that a transition is effective." [PSI:MS]
relationship	part_of MS:1000908 transition ! transition

2.912. MS:1000910 transition optimized on specified instrument

Table 914. Term [MS:1000910]
id	MS:1000910
name	transition optimized on specified instrument
def	"The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined." [PSI:MS]
is_a	MS:1000909 transition validation method ! transition validation method

2.913. MS:1000911 transition validated with an MS/MS spectrum on specified instrument

Table 915. Term [MS:1000911]
id	MS:1000911
name	transition validated with an MS/MS spectrum on specified instrument
def	"The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term." [PSI:MS]
is_a	MS:1000909 transition validation method ! transition validation method

2.914. MS:1000912 transition purported from an MS/MS spectrum on a different, specified instrument

Table 916. Term [MS:1000912]
id	MS:1000912
name	transition purported from an MS/MS spectrum on a different, specified instrument
def	"The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad)." [PSI:MS]
is_a	MS:1000909 transition validation method ! transition validation method

2.915. MS:1000913 transition predicted by informatic analysis

Table 917. Term [MS:1000913]
id	MS:1000913
name	transition predicted by informatic analysis
def	"The transition has been predicted by informatics software without any direct spectral evidence." [PSI:MS]
is_a	MS:1000909 transition validation method ! transition validation method

2.916. MS:1000914 tab delimited text format

Table 918. Term [MS:1000914]
id	MS:1000914
name	tab delimited text format
def	"A file format that has two or more columns of tabular data where each column is separated by a TAB character." [PSI:MS]
is_a	MS:1001459 file format ! file format
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.917. MS:1000915 retention time window attribute

Table 919. Term [MS:1000915]
id	MS:1000915
name	retention time window attribute
def	"An attribute of a window in time about which a peptide might elute from the column." [PSI:MS]
relationship	part_of MS:1000894 retention time ! retention time

2.918. MS:1000916 retention time window lower offset

Table 920. Term [MS:1000916]
id	MS:1000916
name	retention time window lower offset
def	"The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000915 retention time window attribute ! retention time window attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.919. MS:1000917 retention time window upper offset

Table 921. Term [MS:1000917]
id	MS:1000917
name	retention time window upper offset
def	"The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000915 retention time window attribute ! retention time window attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.920. MS:1000918 target list

Table 922. Term [MS:1000918]
id	MS:1000918
name	target list
def	"A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically." [PSI:MS]
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.921. MS:1000919 target inclusion exclusion priority

Table 923. Term [MS:1000919]
id	MS:1000919
name	target inclusion exclusion priority
def	"A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS]
relationship	part_of MS:1000918 target list ! target list

2.922. MS:1000920 includes supersede excludes

Table 924. Term [MS:1000920]
id	MS:1000920
name	includes supersede excludes
def	"A priority setting specifying that included targets have priority over the excluded targets if there is a conflict." [PSI:MS]
is_a	MS:1000919 target inclusion exclusion priority ! target inclusion exclusion priority

2.923. MS:1000921 excludes supersede includes

Table 925. Term [MS:1000921]
id	MS:1000921
name	excludes supersede includes
def	"A priority setting specifying that excluded targets have priority over the included targets if there is a conflict." [PSI:MS]
is_a	MS:1000919 target inclusion exclusion priority ! target inclusion exclusion priority

2.924. MS:1000922 Skyline

Table 926. Term [MS:1000922]
id	MS:1000922
name	Skyline
def	"Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default]
is_a	MS:1000871 SRM software ! SRM software
is_a	MS:1001139 quantitation software name ! quantitation software name

2.925. MS:1000923 TIQAM

Table 927. Term [MS:1000923]
id	MS:1000923
name	TIQAM
def	"Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/TIQAM/TIQAM.html]
is_a	MS:1000871 SRM software ! SRM software

2.926. MS:1000924 MaRiMba

Table 928. Term [MS:1000924]
id	MS:1000924
name	MaRiMba
def	"OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba]
comment	This term was made obsolete because it was redundant with an existing term (MS:1000872).
is_obsolete	true
replaced_by	MS:1000872

2.927. MS:1000925 ATAQS

Table 929. Term [MS:1000925]
id	MS:1000925
name	ATAQS
def	"Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology." [PSI:MS]
is_a	MS:1000871 SRM software ! SRM software

2.928. MS:1000926 product interpretation rank

Table 930. Term [MS:1000926]
id	MS:1000926
name	product interpretation rank
def	"The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001221 product ion attribute ! product ion attribute

2.929. MS:1000927 ion injection time

Table 931. Term [MS:1000927]
id	MS:1000927
name	ion injection time
def	"The length of time spent filling an ion trapping device." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000028] ! millisecond

2.930. MS:1000928 calibration spectrum

Table 932. Term [MS:1000928]
id	MS:1000928
name	calibration spectrum
def	"A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS]
is_a	MS:1000559 spectrum type ! spectrum type

2.931. MS:1000929 Shimadzu Biotech nativeID format

Table 933. Term [MS:1000929]
id	MS:1000929
name	Shimadzu Biotech nativeID format
def	"Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.932. MS:1000930 Shimadzu Biotech database entity

Table 934. Term [MS:1000930]
id	MS:1000930
name	Shimadzu Biotech database entity
def	"Shimadzu Biotech format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.933. MS:1000931 QTRAP 5500

Table 935. Term [MS:1000931]
id	MS:1000931
name	QTRAP 5500
def	"Applied Biosystems\|MDS SCIEX QTRAP 5500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.934. MS:1000932 TripleTOF 5600

Table 936. Term [MS:1000932]
id	MS:1000932
name	TripleTOF 5600
def	"SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.935. MS:1000933 protein modifications

Table 937. Term [MS:1000933]
id	MS:1000933
name	protein modifications
def	"Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000884 protein attribute ! protein attribute

2.936. MS:1000934 gene name

Table 938. Term [MS:1000934]
id	MS:1000934
name	gene name
def	"Name of the gene from which the protein is translated." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000884 protein attribute ! protein attribute

2.937. MS:1001000 spectrum interpretation

Table 939. Term [MS:1001000]
id	MS:1001000
name	spectrum interpretation
def	"Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.938. MS:1001005 SEQUEST:CleavesAt

Table 940. Term [MS:1001005]
id	MS:1001005
name	SEQUEST:CleavesAt
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.939. MS:1001006 SEQUEST:ViewCV

Table 941. Term [MS:1001006]
id	MS:1001006
name	SEQUEST:ViewCV
def	"SEQUEST View Input Parameters." [PSI:PI]
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.940. MS:1001007 SEQUEST:OutputLines

Table 942. Term [MS:1001007]
id	MS:1001007
name	SEQUEST:OutputLines
def	"Number of peptide results to show." [PSI:MS]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.941. MS:1001009 SEQUEST:DescriptionLines

Table 943. Term [MS:1001009]
id	MS:1001009
name	SEQUEST:DescriptionLines
def	"Number of full protein descriptions to show for top N peptides." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.942. MS:1001010 de novo search

Table 944. Term [MS:1001010]
id	MS:1001010
name	de novo search
def	"A de novo sequencing search (without database)." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.943. MS:1001011 search database details

Table 945. Term [MS:1001011]
id	MS:1001011
name	search database details
def	"Details about the database searched." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.944. MS:1001012 database source

Table 946. Term [MS:1001012]
id	MS:1001012
name	database source
def	"The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.945. MS:1001013 database name

Table 947. Term [MS:1001013]
id	MS:1001013
name	database name
def	"The name of the search database (nr, SwissProt or est_human)." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.946. MS:1001014 database local file path

Table 948. Term [MS:1001014]
id	MS:1001014
name	database local file path
def	"OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine’s point of view." [PSI:PI]
is_a	MS:1001011 search database details ! search database details
is_obsolete	true

2.947. MS:1001015 database original uri

Table 949. Term [MS:1001015]
id	MS:1001015
name	database original uri
def	"URI, from where the search database was originally downloaded." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.948. MS:1001016 database version

Table 950. Term [MS:1001016]
id	MS:1001016
name	database version
def	"Version of the search database. In mzIdentML use the attribute instead." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.949. MS:1001017 database release date

Table 951. Term [MS:1001017]
id	MS:1001017
name	database release date
def	"OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database." [PSI:PI]
is_a	MS:1001011 search database details ! search database details
is_obsolete	true

2.950. MS:1001018 database type

Table 952. Term [MS:1001018]
id	MS:1001018
name	database type
def	"Database containing amino acid or nucleic acid sequences." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.951. MS:1001019 database filtering

Table 953. Term [MS:1001019]
id	MS:1001019
name	database filtering
def	"Was there filtering used on the database." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.952. MS:1001020 DB filter taxonomy

Table 954. Term [MS:1001020]
id	MS:1001020
name	DB filter taxonomy
def	"A taxonomy filter was to the database search." [PSI:PI]
is_a	MS:1001511 Sequence database filter types ! Sequence database filter types

2.953. MS:1001021 DB filter on accession numbers

Table 955. Term [MS:1001021]
id	MS:1001021
name	DB filter on accession numbers
def	"Filtering applied specifically by accession number pattern." [PSI:PI]
is_a	MS:1001511 Sequence database filter types ! Sequence database filter types

2.954. MS:1001022 DB MW filter

Table 956. Term [MS:1001022]
id	MS:1001022
name	DB MW filter
def	"Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI]
is_a	MS:1001511 Sequence database filter types ! Sequence database filter types

2.955. MS:1001023 DB PI filter

Table 957. Term [MS:1001023]
id	MS:1001023
name	DB PI filter
def	"Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI]
is_a	MS:1001511 Sequence database filter types ! Sequence database filter types

2.956. MS:1001024 translation frame

Table 958. Term [MS:1001024]
id	MS:1001024
name	translation frame
def	"The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.957. MS:1001025 translation table

Table 959. Term [MS:1001025]
id	MS:1001025
name	translation table
def	"The translation table used to translate the nucleotides to amino acids." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.958. MS:1001026 SEQUEST:NormalizeXCorrValues

Table 960. Term [MS:1001026]
id	MS:1001026
name	SEQUEST:NormalizeXCorrValues
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.959. MS:1001027 DB filter on sequence pattern

Table 961. Term [MS:1001027]
id	MS:1001027
name	DB filter on sequence pattern
def	"Filtering applied specifically by amino acid sequence pattern." [PSI:PI]
is_a	MS:1001511 Sequence database filter types ! Sequence database filter types

2.960. MS:1001028 SEQUEST:SequenceHeaderFilter

Table 962. Term [MS:1001028]
id	MS:1001028
name	SEQUEST:SequenceHeaderFilter
def	"String in the header of a sequence entry for that entry to be searched." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.961. MS:1001029 number of sequences searched

Table 963. Term [MS:1001029]
id	MS:1001029
name	number of sequences searched
def	"The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.962. MS:1001030 number of peptide seqs compared to each spectrum

Table 964. Term [MS:1001030]
id	MS:1001030
name	number of peptide seqs compared to each spectrum
def	"Number of peptide seqs compared to each spectrum." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.963. MS:1001031 spectral library search

Table 965. Term [MS:1001031]
id	MS:1001031
name	spectral library search
def	"A search using a library of spectra." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.964. MS:1001032 SEQUEST:SequencePartialFilter

Table 966. Term [MS:1001032]
id	MS:1001032
name	SEQUEST:SequencePartialFilter
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.965. MS:1001035 date / time search performed

Table 967. Term [MS:1001035]
id	MS:1001035
name	date / time search performed
def	"OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run." [PSI:PI]
is_a	MS:1001184 search statistics ! search statistics
is_obsolete	true

2.966. MS:1001036 search time taken

Table 968. Term [MS:1001036]
id	MS:1001036
name	search time taken
def	"The time taken to complete the search in seconds." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001184 search statistics ! search statistics

2.967. MS:1001037 SEQUEST:ShowFragmentIons

Table 969. Term [MS:1001037]
id	MS:1001037
name	SEQUEST:ShowFragmentIons
def	"Flag indicating that fragment ions should be shown." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.968. MS:1001038 SEQUEST:Consensus

Table 970. Term [MS:1001038]
id	MS:1001038
name	SEQUEST:Consensus
def	"Specify depth as value of the CVParam." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001006 SEQUEST:ViewCV ! SEQUEST:ViewCV

2.969. MS:1001040 intermediate analysis format

Table 971. Term [MS:1001040]
id	MS:1001040
name	intermediate analysis format
def	"Type of the source file, the mzIdentML was created from." [PSI:PI]
is_a	MS:1001459 file format ! file format

2.970. MS:1001041 SEQUEST:sortCV

Table 972. Term [MS:1001041]
id	MS:1001041
name	SEQUEST:sortCV
def	"SEQUEST View / Sort Input Parameters." [PSI:PI]
is_a	MS:1001006 SEQUEST:ViewCV ! SEQUEST:ViewCV

2.971. MS:1001042 SEQUEST:LimitTo

Table 973. Term [MS:1001042]
id	MS:1001042
name	SEQUEST:LimitTo
def	"Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.972. MS:1001044 cleavage agent details

Table 974. Term [MS:1001044]
id	MS:1001044
name	cleavage agent details
def	"Details of cleavage agent (enzyme)." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.973. MS:1001045 cleavage agent name

Table 975. Term [MS:1001045]
id	MS:1001045
name	cleavage agent name
def	"The name of the cleavage agent." [PSI:PI]
is_a	MS:1001044 cleavage agent details ! cleavage agent details

2.974. MS:1001046 SEQUEST:sort by dCn

Table 976. Term [MS:1001046]
id	MS:1001046
name	SEQUEST:sort by dCn
def	"Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.975. MS:1001047 SEQUEST:sort by dM

Table 977. Term [MS:1001047]
id	MS:1001047
name	SEQUEST:sort by dM
def	"Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.976. MS:1001048 SEQUEST:sort by Ions

Table 978. Term [MS:1001048]
id	MS:1001048
name	SEQUEST:sort by Ions
def	"Sort order of SEQUEST search results given by the ions." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.977. MS:1001049 SEQUEST:sort by MH+

Table 979. Term [MS:1001049]
id	MS:1001049
name	SEQUEST:sort by MH+
def	"Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.978. MS:1001050 SEQUEST:sort by P

Table 980. Term [MS:1001050]
id	MS:1001050
name	SEQUEST:sort by P
def	"Sort order of SEQUEST search results given by the probability." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.979. MS:1001051 multiple enzyme combination rules

Table 981. Term [MS:1001051]
id	MS:1001051
name	multiple enzyme combination rules
def	"OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_obsolete	true

2.980. MS:1001052 SEQUEST:sort by PreviousAminoAcid

Table 982. Term [MS:1001052]
id	MS:1001052
name	SEQUEST:sort by PreviousAminoAcid
def	"Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.981. MS:1001053 SEQUEST:sort by Ref

Table 983. Term [MS:1001053]
id	MS:1001053
name	SEQUEST:sort by Ref
def	"Sort order of SEQUEST search results given by the reference." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.982. MS:1001055 modification parameters

Table 984. Term [MS:1001055]
id	MS:1001055
name	modification parameters
def	"Modification parameters for the search engine run." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.983. MS:1001056 modification specificity rule

Table 985. Term [MS:1001056]
id	MS:1001056
name	modification specificity rule
def	"The specificity rules for the modifications applied by the search engine." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters

2.984. MS:1001057 tolerance on types

Table 986. Term [MS:1001057]
id	MS:1001057
name	tolerance on types
def	"OBSOLETE: Tolerance on types." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters
is_obsolete	true

2.985. MS:1001058 quality estimation by manual validation

Table 987. Term [MS:1001058]
id	MS:1001058
name	quality estimation by manual validation
def	"The quality estimation was done manually." [PSI:PI]
is_a	MS:1001060 quality estimation method details ! quality estimation method details

2.986. MS:1001059 SEQUEST:sort by RSp

Table 988. Term [MS:1001059]
id	MS:1001059
name	SEQUEST:sort by RSp
def	"Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.987. MS:1001060 quality estimation method details

Table 989. Term [MS:1001060]
id	MS:1001060
name	quality estimation method details
def	"Method for quality estimation (manually or with decoy database)." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.988. MS:1001061 neutral loss

Table 990. Term [MS:1001061]
id	MS:1001061
name	neutral loss
def	"OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters
is_obsolete	true
replaced_by	MS:1000336

2.989. MS:1001062 Mascot MGF format

Table 991. Term [MS:1001062]
id	MS:1001062
name	Mascot MGF format
def	"Mascot MGF file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.990. MS:1001065 TODOscoring model

Table 992. Term [MS:1001065]
id	MS:1001065
name	TODOscoring model
def	"OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms." [PSI:PI]
comment	This term was made obsolete and is replaced by the term (MS:1001961).
is_a	MS:1001249 search input details ! search input details
is_obsolete	true
replaced_by	MS:1001961

2.991. MS:1001066 ions series considered in search

Table 993. Term [MS:1001066]
id	MS:1001066
name	ions series considered in search
def	"The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.992. MS:1001068 SEQUEST:sort by Sp

Table 994. Term [MS:1001068]
id	MS:1001068
name	SEQUEST:sort by Sp
def	"Sort order of SEQUEST search results by the Sp score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.993. MS:1001069 SEQUEST:sort by TIC

Table 995. Term [MS:1001069]
id	MS:1001069
name	SEQUEST:sort by TIC
def	"Sort order of SEQUEST search results given by the total ion current." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.994. MS:1001070 SEQUEST:sort by Scan

Table 996. Term [MS:1001070]
id	MS:1001070
name	SEQUEST:sort by Scan
def	"Sort order of SEQUEST search results given by the scan number." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.995. MS:1001071 SEQUEST:sort by Sequence

Table 997. Term [MS:1001071]
id	MS:1001071
name	SEQUEST:sort by Sequence
def	"Sort order of SEQUEST search results given by the sequence." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.996. MS:1001072 SEQUEST:sort by Sf

Table 998. Term [MS:1001072]
id	MS:1001072
name	SEQUEST:sort by Sf
def	"Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.997. MS:1001073 database type amino acid

Table 999. Term [MS:1001073]
id	MS:1001073
name	database type amino acid
def	"Database contains amino acid sequences." [PSI:PI]
is_a	MS:1001018 database type ! database type

2.998. MS:1001079 database type nucleotide

Table 1000. Term [MS:1001079]
id	MS:1001079
name	database type nucleotide
def	"Database contains nucleic acid sequences." [PSI:PI]
is_a	MS:1001018 database type ! database type

2.999. MS:1001080 search type

Table 1001. Term [MS:1001080]
id	MS:1001080
name	search type
def	"Enumeration of type of search value (i.e. from PMF, sequence tag, MS2)." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1000. MS:1001081 pmf search

Table 1002. Term [MS:1001081]
id	MS:1001081
name	pmf search
def	"A peptide mass fingerprint search." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.1001. MS:1001082 tag search

Table 1003. Term [MS:1001082]
id	MS:1001082
name	tag search
def	"A sequence tag search." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.1002. MS:1001083 ms-ms search

Table 1004. Term [MS:1001083]
id	MS:1001083
name	ms-ms search
def	"An MS2 search (with fragment ions)." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.1003. MS:1001084 database nr

Table 1005. Term [MS:1001084]
id	MS:1001084
name	database nr
def	"Non-redundant GenBank sequence database." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1004. MS:1001085 protein-level identification attribute

Table 1006. Term [MS:1001085]
id	MS:1001085
name	protein-level identification attribute
def	"Protein level information." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.1005. MS:1001086 SEQUEST:sort by XCorr

Table 1007. Term [MS:1001086]
id	MS:1001086
name	SEQUEST:sort by XCorr
def	"Sort order of SEQUEST search results by the correlation score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.1006. MS:1001087 SEQUEST:ProcessCV

Table 1008. Term [MS:1001087]
id	MS:1001087
name	SEQUEST:ProcessCV
def	"SEQUEST View / Process Input Parameters." [PSI:PI]
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.1007. MS:1001088 protein description

Table 1009. Term [MS:1001088]
id	MS:1001088
name	protein description
def	"The protein description line from the sequence entry in the source database FASTA file." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute
is_a	MS:1001342 database sequence details ! database sequence details

2.1008. MS:1001089 molecule taxonomy

Table 1010. Term [MS:1001089]
id	MS:1001089
name	molecule taxonomy
def	"The taxonomy of the resultant molecule from the search." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute
is_a	MS:1001342 database sequence details ! database sequence details
is_a	MS:1001512 Sequence database filters ! Sequence database filters

2.1009. MS:1001090 taxonomy nomenclature

Table 1011. Term [MS:1001090]
id	MS:1001090
name	taxonomy nomenclature
def	"OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI]
is_a	MS:1001089 molecule taxonomy ! molecule taxonomy
is_obsolete	true
replaced_by	MS:1001467
replaced_by	MS:1001468
replaced_by	MS:1001469
replaced_by	MS:1001470

2.1010. MS:1001091 NoEnzyme

Table 1012. Term [MS:1001091]
id	MS:1001091
name	NoEnzyme
is_a	MS:1001045 cleavage agent name ! cleavage agent name
comment	This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956).
is_obsolete	true

2.1011. MS:1001092 peptide sequence-level identification statistic

Table 1013. Term [MS:1001092]
id	MS:1001092
name	peptide sequence-level identification statistic
def	"Identification confidence metric for a peptide." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1012. MS:1001093 sequence coverage

Table 1014. Term [MS:1001093]
id	MS:1001093
name	sequence coverage
def	"The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI]
xref	value-type:xsd\:decimal "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1013. MS:1001094 SEQUEST:sort by z

Table 1015. Term [MS:1001094]
id	MS:1001094
name	SEQUEST:sort by z
def	"Sort order of SEQUEST search results given by the charge." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001041 SEQUEST:sortCV ! SEQUEST:sortCV

2.1014. MS:1001095 SEQUEST:ProcessAll

Table 1016. Term [MS:1001095]
id	MS:1001095
name	SEQUEST:ProcessAll
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001087 SEQUEST:ProcessCV ! SEQUEST:ProcessCV

2.1015. MS:1001096 SEQUEST:TopPercentMostIntense

Table 1017. Term [MS:1001096]
id	MS:1001096
name	SEQUEST:TopPercentMostIntense
def	"Specify \"percentage\" as value of the CVParam." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001087 SEQUEST:ProcessCV ! SEQUEST:ProcessCV

2.1016. MS:1001097 distinct peptide sequences

Table 1018. Term [MS:1001097]
id	MS:1001097
name	distinct peptide sequences
def	"This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1017. MS:1001098 confident distinct peptide sequences

Table 1019. Term [MS:1001098]
id	MS:1001098
name	confident distinct peptide sequences
def	"This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1018. MS:1001099 confident peptide qualification

Table 1020. Term [MS:1001099]
id	MS:1001099
name	confident peptide qualification
def	"The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1019. MS:1001100 confident peptide sequence number

Table 1021. Term [MS:1001100]
id	MS:1001100
name	confident peptide sequence number
def	"This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1020. MS:1001101 protein group or subset relationship

Table 1022. Term [MS:1001101]
id	MS:1001101
name	protein group or subset relationship
def	"Protein group or subset relationships." [PSI:PI]
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1021. MS:1001102 SEQUEST:Chromatogram

Table 1023. Term [MS:1001102]
id	MS:1001102
name	SEQUEST:Chromatogram
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001006 SEQUEST:ViewCV ! SEQUEST:ViewCV

2.1022. MS:1001103 SEQUEST:InfoAndLog

Table 1024. Term [MS:1001103]
id	MS:1001103
name	SEQUEST:InfoAndLog
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001006 SEQUEST:ViewCV ! SEQUEST:ViewCV

2.1023. MS:1001104 database UniProtKB/Swiss-Prot

Table 1025. Term [MS:1001104]
id	MS:1001104
name	database UniProtKB/Swiss-Prot
def	"The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI]
is_a	MS:1002126 database UniProtKB ! database UniProtKB

2.1024. MS:1001105 peptide sequence-level identification attribute

Table 1026. Term [MS:1001105]
id	MS:1001105
name	peptide sequence-level identification attribute
def	"Peptide level information." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.1025. MS:1001106 SEQUEST:TopNumber

Table 1027. Term [MS:1001106]
id	MS:1001106
name	SEQUEST:TopNumber
def	"Specify \"number\" as value of the CVParam." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001087 SEQUEST:ProcessCV ! SEQUEST:ProcessCV

2.1026. MS:1001107 data stored in database

Table 1028. Term [MS:1001107]
id	MS:1001107
name	data stored in database
def	"Source file for this mzIdentML was a data set in a database." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1027. MS:1001108 param: a ion

Table 1029. Term [MS:1001108]
id	MS:1001108
name	param: a ion
def	"Parameter information, type of product: a ion with charge on the N-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1028. MS:1001109 SEQUEST:CullTo

Table 1030. Term [MS:1001109]
id	MS:1001109
name	SEQUEST:CullTo
def	"Specify cull string as value of the CVParam." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001087 SEQUEST:ProcessCV ! SEQUEST:ProcessCV

2.1029. MS:1001110 SEQUEST:modeCV

Table 1031. Term [MS:1001110]
id	MS:1001110
name	SEQUEST:modeCV
def	"SEQUEST Mode Input Parameters." [PSI:PI]
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.1030. MS:1001111 SEQUEST:Full

Table 1032. Term [MS:1001111]
id	MS:1001111
name	SEQUEST:Full
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001110 SEQUEST:modeCV ! SEQUEST:modeCV

2.1031. MS:1001112 n-terminal flanking residue

Table 1033. Term [MS:1001112]
id	MS:1001112
name	n-terminal flanking residue
def	"Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003046 peptide-to-protein mapping attribute ! peptide-to-protein mapping attribute
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1032. MS:1001113 c-terminal flanking residue

Table 1034. Term [MS:1001113]
id	MS:1001113
name	c-terminal flanking residue
def	"Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003046 peptide-to-protein mapping attribute ! peptide-to-protein mapping attribute
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1033. MS:1001114 retention time(s)

Table 1035. Term [MS:1001114]
id	MS:1001114
name	retention time(s)
def	"OBSOLETE Retention time of the spectrum from the source file." [PSI:PI]
comment	This term was made obsolete because scan start time (MS:1000016) should be used instead.
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute
is_obsolete	true

2.1034. MS:1001115 scan number(s)

Table 1036. Term [MS:1001115]
id	MS:1001115
name	scan number(s)
def	"OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData." [PSI:PI]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.1035. MS:1001116 single protein identification statistic

Table 1037. Term [MS:1001116]
id	MS:1001116
name	single protein identification statistic
def	"Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI]
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1036. MS:1001117 theoretical mass

Table 1038. Term [MS:1001117]
id	MS:1001117
name	theoretical mass
def	"The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute
relationship	has_units [UO:0000221] ! dalton

2.1037. MS:1001118 param: b ion

Table 1039. Term [MS:1001118]
id	MS:1001118
name	param: b ion
def	"Parameter information, type of product: b ion with charge on the N-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1038. MS:1001119 param: c ion

Table 1040. Term [MS:1001119]
id	MS:1001119
name	param: c ion
def	"Parameter information, type of product: c ion with charge on the N-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1039. MS:1001120 SEQUEST:FormatAndLinks

Table 1041. Term [MS:1001120]
id	MS:1001120
name	SEQUEST:FormatAndLinks
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001110 SEQUEST:modeCV ! SEQUEST:modeCV

2.1040. MS:1001121 number of matched peaks

Table 1042. Term [MS:1001121]
id	MS:1001121
name	number of matched peaks
def	"The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1041. MS:1001122 ions series considered

Table 1043. Term [MS:1001122]
id	MS:1001122
name	ions series considered
def	"The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb)." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1042. MS:1001123 number of peaks used

Table 1044. Term [MS:1001123]
id	MS:1001123
name	number of peaks used
def	"The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don’t." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1043. MS:1001124 number of peaks submitted

Table 1045. Term [MS:1001124]
id	MS:1001124
name	number of peaks submitted
def	"The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1044. MS:1001125 manual validation

Table 1046. Term [MS:1001125]
id	MS:1001125
name	manual validation
def	"Result of quality estimation: decision of a manual validation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.1045. MS:1001126 SEQUEST:Fast

Table 1047. Term [MS:1001126]
id	MS:1001126
name	SEQUEST:Fast
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001110 SEQUEST:modeCV ! SEQUEST:modeCV

2.1046. MS:1001127 peptide sharing details

Table 1048. Term [MS:1001127]
id	MS:1001127
name	peptide sharing details
def	"Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1047. MS:1001128 SEQUEST:selectCV

Table 1049. Term [MS:1001128]
id	MS:1001128
name	SEQUEST:selectCV
def	"SEQUEST Select Input Parameters." [PSI:PI]
is_a	MS:1002096 SEQUEST input parameter ! SEQUEST input parameter

2.1048. MS:1001129 quantification information

Table 1050. Term [MS:1001129]
id	MS:1001129
name	quantification information
def	"Quantification information." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1049. MS:1001130 peptide raw area

Table 1051. Term [MS:1001130]
id	MS:1001130
name	peptide raw area
def	"OBSOLETE Peptide raw area." [PSI:PI]
comment	This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype
is_obsolete	true

2.1050. MS:1001131 error on peptide area

Table 1052. Term [MS:1001131]
id	MS:1001131
name	error on peptide area
def	"Error on peptide area." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1051. MS:1001132 peptide ratio

Table 1053. Term [MS:1001132]
id	MS:1001132
name	peptide ratio
def	"Peptide ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1052. MS:1001133 error on peptide ratio

Table 1054. Term [MS:1001133]
id	MS:1001133
name	error on peptide ratio
def	"Error on peptide ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1053. MS:1001134 protein ratio

Table 1055. Term [MS:1001134]
id	MS:1001134
name	protein ratio
def	"Protein ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1054. MS:1001135 error on protein ratio

Table 1056. Term [MS:1001135]
id	MS:1001135
name	error on protein ratio
def	"Error on protein ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1055. MS:1001136 p-value (protein diff from 1 randomly)

Table 1057. Term [MS:1001136]
id	MS:1001136
name	p-value (protein diff from 1 randomly)
def	"OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
comment	This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype
is_obsolete	true

2.1056. MS:1001137 absolute quantity

Table 1058. Term [MS:1001137]
id	MS:1001137
name	absolute quantity
def	"Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1057. MS:1001138 error on absolute quantity

Table 1059. Term [MS:1001138]
id	MS:1001138
name	error on absolute quantity
def	"Error on absolute quantity." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1058. MS:1001139 quantitation software name

Table 1060. Term [MS:1001139]
id	MS:1001139
name	quantitation software name
def	"Quantitation software name." [PSI:PI]
is_a	MS:1000531 software ! software
is_a	MS:1001129 quantification information ! quantification information

2.1059. MS:1001140 quantitation software version

Table 1061. Term [MS:1001140]
id	MS:1001140
name	quantitation software version
def	"OBSOLETE Quantitation software version." [PSI:PI]
comment	This term was made obsolete because part of mzQuantML schema.
is_a	MS:1001129 quantification information ! quantification information
is_obsolete	true

2.1060. MS:1001141 intensity of precursor ion

Table 1062. Term [MS:1001141]
id	MS:1001141
name	intensity of precursor ion
def	"The intensity of the precursor ion." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1061. MS:1001142 database IPI_human

Table 1063. Term [MS:1001142]
id	MS:1001142
name	database IPI_human
def	"International Protein Index database for Homo sapiens sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1062. MS:1001143 PSM-level search engine specific statistic

Table 1064. Term [MS:1001143]
id	MS:1001143
name	PSM-level search engine specific statistic
def	"Search engine specific peptide spectrum match scores." [PSI:PI]
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic

2.1063. MS:1001144 SEQUEST:SelectDefault

Table 1065. Term [MS:1001144]
id	MS:1001144
name	SEQUEST:SelectDefault
is_a	MS:1001128 SEQUEST:selectCV ! SEQUEST:selectCV

2.1064. MS:1001145 SEQUEST:SelectAdvancedCV

Table 1066. Term [MS:1001145]
id	MS:1001145
name	SEQUEST:SelectAdvancedCV
def	"SEQUEST Select Advanced Input Parameters." [PSI:PI]
is_a	MS:1001128 SEQUEST:selectCV ! SEQUEST:selectCV

2.1065. MS:1001146 param: a ion-NH3 DEPRECATED

Table 1067. Term [MS:1001146]
id	MS:1001146
name	param: a ion-NH3 DEPRECATED
def	"Ion a-NH3 parameter information, type of product: a ion with lost ammonia." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1066. MS:1001147 protein ambiguity group result details

Table 1068. Term [MS:1001147]
id	MS:1001147
name	protein ambiguity group result details
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute
is_a	MS:1001153 search engine specific score ! search engine specific score

2.1067. MS:1001148 param: a ion-H2O DEPRECATED

Table 1069. Term [MS:1001148]
id	MS:1001148
name	param: a ion-H2O DEPRECATED
def	"Ion a-H2O if a significant and fragment includes STED." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1068. MS:1001149 param: b ion-NH3 DEPRECATED

Table 1070. Term [MS:1001149]
id	MS:1001149
name	param: b ion-NH3 DEPRECATED
def	"Ion b-NH3 parameter information, type of product: b ion with lost ammonia." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1069. MS:1001150 param: b ion-H2O DEPRECATED

Table 1071. Term [MS:1001150]
id	MS:1001150
name	param: b ion-H2O DEPRECATED
def	"Ion b-H2O if b significant and fragment includes STED." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1070. MS:1001151 param: y ion-NH3 DEPRECATED

Table 1072. Term [MS:1001151]
id	MS:1001151
name	param: y ion-NH3 DEPRECATED
def	"Ion y-NH3 parameter information, type of product: y ion with lost ammonia." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1071. MS:1001152 param: y ion-H2O DEPRECATED

Table 1073. Term [MS:1001152]
id	MS:1001152
name	param: y ion-H2O DEPRECATED
comment	This term was made obsolete - use MS:1001262 and MS:1002455 instead.
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.1072. MS:1001153 search engine specific score

Table 1074. Term [MS:1001153]
id	MS:1001153
name	search engine specific score
def	"Search engine specific scores." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.1073. MS:1001154 SEQUEST:probability

Table 1075. Term [MS:1001154]
id	MS:1001154
name	SEQUEST:probability
def	"The SEQUEST result 'Probability'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1074. MS:1001155 SEQUEST:xcorr

Table 1076. Term [MS:1001155]
id	MS:1001155
name	SEQUEST:xcorr
def	"The SEQUEST result 'XCorr'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.1075. MS:1001156 SEQUEST:deltacn

Table 1077. Term [MS:1001156]
id	MS:1001156
name	SEQUEST:deltacn
def	"The SEQUEST result 'DeltaCn'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1076. MS:1001157 SEQUEST:sp

Table 1078. Term [MS:1001157]
id	MS:1001157
name	SEQUEST:sp
def	"The SEQUEST result 'Sp' (protein)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1077. MS:1001158 SEQUEST:Uniq

Table 1079. Term [MS:1001158]
id	MS:1001158
name	SEQUEST:Uniq
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1078. MS:1001159 SEQUEST:expectation value

Table 1080. Term [MS:1001159]
id	MS:1001159
name	SEQUEST:expectation value
def	"The SEQUEST result 'Expectation value'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001153 search engine specific score ! search engine specific score

2.1079. MS:1001160 SEQUEST:sf

Table 1081. Term [MS:1001160]
id	MS:1001160
name	SEQUEST:sf
def	"The SEQUEST result 'Sf'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1080. MS:1001161 SEQUEST:matched ions

Table 1082. Term [MS:1001161]
id	MS:1001161
name	SEQUEST:matched ions
def	"The SEQUEST result 'Matched Ions'." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1081. MS:1001162 SEQUEST:total ions

Table 1083. Term [MS:1001162]
id	MS:1001162
name	SEQUEST:total ions
def	"The SEQUEST result 'Total Ions'." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1082. MS:1001163 SEQUEST:consensus score

Table 1084. Term [MS:1001163]
id	MS:1001163
name	SEQUEST:consensus score
def	"The SEQUEST result 'Consensus Score'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001153 search engine specific score ! search engine specific score

2.1083. MS:1001164 Paragon:unused protscore

Table 1085. Term [MS:1001164]
id	MS:1001164
name	Paragon:unused protscore
def	"The Paragon result 'Unused ProtScore'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups

2.1084. MS:1001165 Paragon:total protscore

Table 1086. Term [MS:1001165]
id	MS:1001165
name	Paragon:total protscore
def	"The Paragon result 'Total ProtScore'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups

2.1085. MS:1001166 Paragon:score

Table 1087. Term [MS:1001166]
id	MS:1001166
name	Paragon:score
def	"The Paragon result 'Score'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1086. MS:1001167 Paragon:confidence

Table 1088. Term [MS:1001167]
id	MS:1001167
name	Paragon:confidence
def	"The Paragon result 'Confidence'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1087. MS:1001168 Paragon:expression error factor

Table 1089. Term [MS:1001168]
id	MS:1001168
name	Paragon:expression error factor
def	"The Paragon result 'Expression Error Factor'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1088. MS:1001169 Paragon:expression change p-value

Table 1090. Term [MS:1001169]
id	MS:1001169
name	Paragon:expression change p-value
def	"The Paragon result 'Expression change P-value'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1089. MS:1001170 Paragon:contrib

Table 1091. Term [MS:1001170]
id	MS:1001170
name	Paragon:contrib
def	"The Paragon result 'Contrib'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1090. MS:1001171 Mascot:score

Table 1092. Term [MS:1001171]
id	MS:1001171
name	Mascot:score
def	"The Mascot result 'Score'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1091. MS:1001172 Mascot:expectation value

Table 1093. Term [MS:1001172]
id	MS:1001172
name	Mascot:expectation value
def	"The Mascot result 'expectation value'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1092. MS:1001173 Mascot:matched ions

Table 1094. Term [MS:1001173]
id	MS:1001173
name	Mascot:matched ions
def	"The Mascot result 'Matched ions'." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1093. MS:1001174 Mascot:total ions

Table 1095. Term [MS:1001174]
id	MS:1001174
name	Mascot:total ions
def	"The Mascot result 'Total ions'." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1094. MS:1001175 peptide shared in multiple proteins

Table 1096. Term [MS:1001175]
id	MS:1001175
name	peptide shared in multiple proteins
def	"A peptide matching multiple proteins." [PSI:PI]
is_a	MS:1001127 peptide sharing details ! peptide sharing details

2.1095. MS:1001176 (?⇐[KR])(?\!P)

Table 1097. Term [MS:1001176]
id	MS:1001176
name	(?⇐[KR])(?\!P)
def	"Regular expression for Trypsin." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1096. MS:1001177 number of molecular hypothesis considered

Table 1098. Term [MS:1001177]
id	MS:1001177
name	number of molecular hypothesis considered
def	"Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001184 search statistics ! search statistics

2.1097. MS:1001178 database EST

Table 1099. Term [MS:1001178]
id	MS:1001178
name	database EST
def	"Expressed sequence tag nucleotide sequence database." [PSI:PI]
is_a	MS:1001079 database type nucleotide ! database type nucleotide

2.1098. MS:1001180 Cleavage agent regular expression

Table 1100. Term [MS:1001180]
id	MS:1001180
name	Cleavage agent regular expression
def	"Regular expressions for cleavage enzymes." [PSI:PI]
relationship	part_of MS:1001044 cleavage agent details ! cleavage agent details
is_a	MS:1002479 regular expression ! regular expression

2.1099. MS:1001184 search statistics

Table 1101. Term [MS:1001184]
id	MS:1001184
name	search statistics
def	"The details of the actual run of the search." [PSI:PI]
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.1100. MS:1001189 modification specificity peptide N-term

Table 1102. Term [MS:1001189]
id	MS:1001189
name	modification specificity peptide N-term
def	"As parameter for search engine: apply the modification only at the N-terminus of a peptide." [PSI:PI]
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1101. MS:1001190 modification specificity peptide C-term

Table 1103. Term [MS:1001190]
id	MS:1001190
name	modification specificity peptide C-term
def	"As parameter for search engine: apply the modification only at the C-terminus of a peptide." [PSI:PI]
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1102. MS:1001191 p-value

Table 1104. Term [MS:1001191]
id	MS:1001191
name	p-value
def	"OBSOLETE Quality estimation by p-value." [PSI:PI]
comment	This term was made obsolete because now is split into peptide and protein terms.
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
is_a	MS:1001198 protein identification confidence metric ! protein identification confidence metric
is_obsolete	true

2.1103. MS:1001192 Expect value

Table 1105. Term [MS:1001192]
id	MS:1001192
name	Expect value
def	"Result of quality estimation: Expect value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.1104. MS:1001193 confidence score

Table 1106. Term [MS:1001193]
id	MS:1001193
name	confidence score
def	"Result of quality estimation: confidence score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.1105. MS:1001194 quality estimation with decoy database

Table 1107. Term [MS:1001194]
id	MS:1001194
name	quality estimation with decoy database
def	"Quality estimation by decoy database." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001060 quality estimation method details ! quality estimation method details

2.1106. MS:1001195 decoy DB type reverse

Table 1108. Term [MS:1001195]
id	MS:1001195
name	decoy DB type reverse
def	"Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI]
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1107. MS:1001196 decoy DB type randomized

Table 1109. Term [MS:1001196]
id	MS:1001196
name	decoy DB type randomized
def	"Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI]
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1108. MS:1001197 DB composition target+decoy

Table 1110. Term [MS:1001197]
id	MS:1001197
name	DB composition target+decoy
def	"Decoy database composition: database contains original (target) and decoy entries." [PSI:PI]
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1109. MS:1001198 protein identification confidence metric

Table 1111. Term [MS:1001198]
id	MS:1001198
name	protein identification confidence metric
def	"Identification confidence metric for a protein." [PSI:PI]
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.1110. MS:1001199 Mascot DAT format

Table 1112. Term [MS:1001199]
id	MS:1001199
name	Mascot DAT format
def	"Source file for this mzIdentML was in Mascot DAT file format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1111. MS:1001200 SEQUEST out file format

Table 1113. Term [MS:1001200]
id	MS:1001200
name	SEQUEST out file format
def	"Source file for this mzIdentML was in SEQUEST out file format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1112. MS:1001201 DB MW filter maximum

Table 1114. Term [MS:1001201]
id	MS:1001201
name	DB MW filter maximum
def	"Maximum value of molecular weight filter." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters
relationship	has_units [UO:0000221] ! dalton
relationship	has_units [UO:0000222] ! kilodalton

2.1113. MS:1001202 DB MW filter minimum

Table 1115. Term [MS:1001202]
id	MS:1001202
name	DB MW filter minimum
def	"Minimum value of molecular weight filter." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters
relationship	has_units [UO:0000221] ! dalton
relationship	has_units [UO:0000222] ! kilodalton

2.1114. MS:1001203 DB PI filter maximum

Table 1116. Term [MS:1001203]
id	MS:1001203
name	DB PI filter maximum
def	"Maximum value of isoelectric point filter." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters

2.1115. MS:1001204 DB PI filter minimum

Table 1117. Term [MS:1001204]
id	MS:1001204
name	DB PI filter minimum
def	"Minimum value of isoelectric point filter." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters

2.1116. MS:1001207 Mascot

Table 1118. Term [MS:1001207]
id	MS:1001207
name	Mascot
def	"The name of the Mascot search engine." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1117. MS:1001208 SEQUEST

Table 1119. Term [MS:1001208]
id	MS:1001208
name	SEQUEST
def	"The name of the SEQUEST search engine." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1118. MS:1001209 Phenyx

Table 1120. Term [MS:1001209]
id	MS:1001209
name	Phenyx
def	"The name of the Phenyx search engine." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1119. MS:1001210 mass type settings

Table 1121. Term [MS:1001210]
id	MS:1001210
name	mass type settings
def	"The type of mass difference value to be considered by the search engine (monoisotopic or average)." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1120. MS:1001211 parent mass type mono

Table 1122. Term [MS:1001211]
id	MS:1001211
name	parent mass type mono
def	"Mass type setting for parent mass was monoisotopic." [PSI:PI]
is_a	MS:1001210 mass type settings ! mass type settings

2.1121. MS:1001212 parent mass type average

Table 1123. Term [MS:1001212]
id	MS:1001212
name	parent mass type average
def	"Mass type setting for parent mass was average isotopic." [PSI:PI]
is_a	MS:1001210 mass type settings ! mass type settings

2.1122. MS:1001213 search result details

Table 1124. Term [MS:1001213]
id	MS:1001213
name	search result details
def	"OBSOLETE: Scores and global result characteristics." [PSI:PI]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.1123. MS:1001214 protein-level global FDR

Table 1125. Term [MS:1001214]
id	MS:1001214
name	protein-level global FDR
def	"Estimation of the global false discovery rate of proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002705 protein-level result list statistic ! protein-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1124. MS:1001215 SEQUEST:PeptideSp

Table 1126. Term [MS:1001215]
id	MS:1001215
name	SEQUEST:PeptideSp
def	"The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1125. MS:1001217 SEQUEST:PeptideRankSp

Table 1127. Term [MS:1001217]
id	MS:1001217
name	SEQUEST:PeptideRankSp
def	"The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1126. MS:1001218 SEQUEST:PeptideNumber

Table 1128. Term [MS:1001218]
id	MS:1001218
name	SEQUEST:PeptideNumber
def	"The SEQUEST result '#' in out file (peptide)." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1127. MS:1001219 SEQUEST:PeptideIdnumber

Table 1129. Term [MS:1001219]
id	MS:1001219
name	SEQUEST:PeptideIdnumber
def	"The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1128. MS:1001220 frag: y ion

Table 1130. Term [MS:1001220]
id	MS:1001220
name	frag: y ion
def	"Fragmentation information, type of product: y ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1129. MS:1001221 product ion attribute

Table 1131. Term [MS:1001221]
id	MS:1001221
name	product ion attribute
def	"Fragmentation information like ion types." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.1130. MS:1001222 frag: b ion - H2O

Table 1132. Term [MS:1001222]
id	MS:1001222
name	frag: b ion - H2O
def	"Fragmentation information, type of product: b ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1131. MS:1001223 frag: y ion - H2O

Table 1133. Term [MS:1001223]
id	MS:1001223
name	frag: y ion - H2O
def	"Fragmentation information, type of product: y ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1132. MS:1001224 frag: b ion

Table 1134. Term [MS:1001224]
id	MS:1001224
name	frag: b ion
def	"Fragmentation information, type of product: b ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1133. MS:1001225 product ion m/z

Table 1135. Term [MS:1001225]
id	MS:1001225
name	product ion m/z
def	"The m/z of the product ion." [PSI:PI]
synonym	"fragment ion m/z" EXACT []
is_a	MS:1001221 product ion attribute ! product ion attribute
relationship	has_units MS:1000040 m/z ! m/z

2.1134. MS:1001226 product ion intensity

Table 1136. Term [MS:1001226]
id	MS:1001226
name	product ion intensity
def	"The intensity of a single product ion." [PSI:PI]
synonym	"fragment ion intensity" EXACT []
is_a	MS:1001221 product ion attribute ! product ion attribute
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100

2.1135. MS:1001227 product ion m/z error

Table 1137. Term [MS:1001227]
id	MS:1001227
name	product ion m/z error
def	"The product ion m/z error." [PSI:PI]
is_a	MS:1001221 product ion attribute ! product ion attribute
relationship	has_units MS:1000040 m/z ! m/z
relationship	has_units [UO:0000166] ! parts per notation unit

2.1136. MS:1001228 frag: x ion

Table 1138. Term [MS:1001228]
id	MS:1001228
name	frag: x ion
def	"Fragmentation information, type of product: x ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1137. MS:1001229 frag: a ion

Table 1139. Term [MS:1001229]
id	MS:1001229
name	frag: a ion
def	"Fragmentation information, type of product: a ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1138. MS:1001230 frag: z ion

Table 1140. Term [MS:1001230]
id	MS:1001230
name	frag: z ion
def	"Fragmentation information, type of product: z ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1139. MS:1001231 frag: c ion

Table 1141. Term [MS:1001231]
id	MS:1001231
name	frag: c ion
def	"Fragmentation information, type of product: c ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1140. MS:1001232 frag: b ion - NH3

Table 1142. Term [MS:1001232]
id	MS:1001232
name	frag: b ion - NH3
def	"Ion b-NH3 fragmentation information, type of product: b ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1141. MS:1001233 frag: y ion - NH3

Table 1143. Term [MS:1001233]
id	MS:1001233
name	frag: y ion - NH3
def	"Ion y-NH3 fragmentation information, type of product: y ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1142. MS:1001234 frag: a ion - H2O

Table 1144. Term [MS:1001234]
id	MS:1001234
name	frag: a ion - H2O
def	"Fragmentation information, type of product: a ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1143. MS:1001235 frag: a ion - NH3

Table 1145. Term [MS:1001235]
id	MS:1001235
name	frag: a ion - NH3
def	"Ion a-NH3 fragmentation information, type of product: a ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1144. MS:1001236 frag: d ion

Table 1146. Term [MS:1001236]
id	MS:1001236
name	frag: d ion
def	"Fragmentation information, type of product: d ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1145. MS:1001237 frag: v ion

Table 1147. Term [MS:1001237]
id	MS:1001237
name	frag: v ion
def	"Fragmentation information, type of product: v ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1146. MS:1001238 frag: w ion

Table 1148. Term [MS:1001238]
id	MS:1001238
name	frag: w ion
def	"Fragmentation information, type of product: w ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1147. MS:1001239 frag: immonium ion

Table 1149. Term [MS:1001239]
id	MS:1001239
name	frag: immonium ion
def	"Fragmentation information, type of product: immonium ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1148. MS:1001240 non-identified ion

Table 1150. Term [MS:1001240]
id	MS:1001240
name	non-identified ion
def	"Non-identified ion." [PSI:PI]
is_a	MS:1001221 product ion attribute ! product ion attribute

2.1149. MS:1001241 co-eluting ion

Table 1151. Term [MS:1001241]
id	MS:1001241
name	co-eluting ion
def	"Co-eluting ion." [PSI:PI]
is_a	MS:1001221 product ion attribute ! product ion attribute

2.1150. MS:1001242 SEQUEST out folder

Table 1152. Term [MS:1001242]
id	MS:1001242
name	SEQUEST out folder
def	"Source file for this mzIdentML was a SEQUEST folder with its out files." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1151. MS:1001243 SEQUEST summary

Table 1153. Term [MS:1001243]
id	MS:1001243
name	SEQUEST summary
def	"Source file for this mzIdentML was a SEQUEST summary page (proteins)." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1152. MS:1001245 PerSeptive PKS format

Table 1154. Term [MS:1001245]
id	MS:1001245
name	PerSeptive PKS format
def	"PerSeptive peak list file format." [http://www.matrixscience.com/help/data_file_help.html#PKS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1153. MS:1001246 SCIEX API III format

Table 1155. Term [MS:1001246]
id	MS:1001246
name	SCIEX API III format
def	"PE SCIEX peak list file format." [http://www.matrixscience.com/help/data_file_help.html#API]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1154. MS:1001247 Bruker XML format

Table 1156. Term [MS:1001247]
id	MS:1001247
name	Bruker XML format
def	"Bruker data exchange XML format." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1155. MS:1001249 search input details

Table 1157. Term [MS:1001249]
id	MS:1001249
name	search input details
def	"Details describing the search input." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1156. MS:1001250 local FDR

Table 1158. Term [MS:1001250]
id	MS:1001250
name	local FDR
def	"Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.1157. MS:1001251 Trypsin

Table 1159. Term [MS:1001251]
id	MS:1001251
name	Trypsin
def	"Enzyme trypsin." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001176 (?⇐[KR])(?\!P) ! (?⇐[KR])(?

2.1158. MS:1001252 DB source EBI

Table 1160. Term [MS:1001252]
id	MS:1001252
name	DB source EBI
def	"Database source EBI." [PSI:PI]
is_a	MS:1001012 database source ! database source

2.1159. MS:1001253 DB source NCBI

Table 1161. Term [MS:1001253]
id	MS:1001253
name	DB source NCBI
def	"Database source NCBI." [PSI:PI]
is_a	MS:1001012 database source ! database source

2.1160. MS:1001254 DB source UniProt

Table 1162. Term [MS:1001254]
id	MS:1001254
name	DB source UniProt
def	"Database source UniProt." [PSI:PI]
is_a	MS:1001012 database source ! database source

2.1161. MS:1001255 fragment mass type average

Table 1163. Term [MS:1001255]
id	MS:1001255
name	fragment mass type average
def	"Mass type setting for fragment mass was average isotopic." [PSI:PI]
is_a	MS:1001210 mass type settings ! mass type settings

2.1162. MS:1001256 fragment mass type mono

Table 1164. Term [MS:1001256]
id	MS:1001256
name	fragment mass type mono
def	"Mass type setting for fragment mass was monoisotopic." [PSI:PI]
is_a	MS:1001210 mass type settings ! mass type settings

2.1163. MS:1001257 param: v ion

Table 1165. Term [MS:1001257]
id	MS:1001257
name	param: v ion
def	"Parameter information, type of product: side chain loss v ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1164. MS:1001258 param: d ion

Table 1166. Term [MS:1001258]
id	MS:1001258
name	param: d ion
def	"Parameter information, type of product: side chain loss d ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1165. MS:1001259 param: immonium ion

Table 1167. Term [MS:1001259]
id	MS:1001259
name	param: immonium ion
def	"Parameter information, type of product: immonium ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1166. MS:1001260 param: w ion

Table 1168. Term [MS:1001260]
id	MS:1001260
name	param: w ion
def	"Parameter information, type of product: side chain loss w ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1167. MS:1001261 param: x ion

Table 1169. Term [MS:1001261]
id	MS:1001261
name	param: x ion
def	"Parameter information, type of product: x ion with charge on the C-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1168. MS:1001262 param: y ion

Table 1170. Term [MS:1001262]
id	MS:1001262
name	param: y ion
def	"Parameter information, type of product: y ion with charge on the C-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1169. MS:1001263 param: z ion

Table 1171. Term [MS:1001263]
id	MS:1001263
name	param: z ion
def	"Parameter information, type of product: z ion with charge on the C-terminal side." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1170. MS:1001266 role type

Table 1172. Term [MS:1001266]
id	MS:1001266
name	role type
def	"Role of a Person or Organization." [PSI:PI]
is_a	MS:1000585 contact attribute ! contact attribute

2.1171. MS:1001267 software vendor

Table 1173. Term [MS:1001267]
id	MS:1001267
name	software vendor
def	"Software vendor role." [PSI:PI]
is_a	MS:1001266 role type ! role type

2.1172. MS:1001268 programmer

Table 1174. Term [MS:1001268]
id	MS:1001268
name	programmer
def	"Programmer role." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001266 role type ! role type

2.1173. MS:1001269 instrument vendor

Table 1175. Term [MS:1001269]
id	MS:1001269
name	instrument vendor
def	"Instrument vendor role." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001266 role type ! role type

2.1174. MS:1001270 lab personnel

Table 1176. Term [MS:1001270]
id	MS:1001270
name	lab personnel
def	"Lab personnel role." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001266 role type ! role type

2.1175. MS:1001271 researcher

Table 1177. Term [MS:1001271]
id	MS:1001271
name	researcher
def	"Researcher role." [PSI:PI]
is_a	MS:1001266 role type ! role type

2.1176. MS:1001272 (?⇐R)(?\!P)

Table 1178. Term [MS:1001272]
id	MS:1001272
name	(?⇐R)(?\!P)
def	"Regular expression for Arg-C." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1177. MS:1001273 (?=[BD])

Table 1179. Term [MS:1001273]
id	MS:1001273
name	(?=[BD])
def	"Regular expression for Asp-N." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1178. MS:1001274 (?=[DE])

Table 1180. Term [MS:1001274]
id	MS:1001274
name	(?=[DE])
def	"Regular expression for Asp-N-ambic." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1179. MS:1001275 ProteinScape SearchEvent

Table 1181. Term [MS:1001275]
id	MS:1001275
name	ProteinScape SearchEvent
def	"Source data for this mzIdentML was a ProteinScape SearchEvent." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1180. MS:1001276 ProteinScape Gel

Table 1182. Term [MS:1001276]
id	MS:1001276
name	ProteinScape Gel
def	"Source data for this mzIdentML was a ProteinScape Gel." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1181. MS:1001283 decoy DB accession regexp

Table 1183. Term [MS:1001283]
id	MS:1001283
name	decoy DB accession regexp
def	"Specify the regular expression for decoy accession numbers." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1182. MS:1001284 decoy DB derived from

Table 1184. Term [MS:1001284]
id	MS:1001284
name	decoy DB derived from
def	"OBSOLETE The name of the database, the search database was derived from." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_a	MS:1001450 decoy DB details ! decoy DB details
is_obsolete	true

2.1183. MS:1001285 database IPI_mouse

Table 1185. Term [MS:1001285]
id	MS:1001285
name	database IPI_mouse
def	"International Protein Index database for Mus musculus sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1184. MS:1001286 database IPI_rat

Table 1186. Term [MS:1001286]
id	MS:1001286
name	database IPI_rat
def	"International Protein Index database for Rattus norvegicus sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1185. MS:1001287 database IPI_zebrafish

Table 1187. Term [MS:1001287]
id	MS:1001287
name	database IPI_zebrafish
def	"International Protein Index database for Danio rerio sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1186. MS:1001288 database IPI_chicken

Table 1188. Term [MS:1001288]
id	MS:1001288
name	database IPI_chicken
def	"International Protein Index database for Gallus gallus sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1187. MS:1001289 database IPI_cow

Table 1189. Term [MS:1001289]
id	MS:1001289
name	database IPI_cow
def	"International Protein Index database for Bos taurus sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1188. MS:1001290 database IPI_arabidopsis

Table 1190. Term [MS:1001290]
id	MS:1001290
name	database IPI_arabidopsis
def	"International Protein Index database for Arabidopsis thaliana sequences." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.1189. MS:1001291 decoy DB from nr

Table 1191. Term [MS:1001291]
id	MS:1001291
name	decoy DB from nr
def	"OBSOLETE Decoy database from a non-redundant GenBank sequence database." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1190. MS:1001292 decoy DB from IPI_rat

Table 1192. Term [MS:1001292]
id	MS:1001292
name	decoy DB from IPI_rat
def	"OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1191. MS:1001293 decoy DB from IPI_mouse

Table 1193. Term [MS:1001293]
id	MS:1001293
name	decoy DB from IPI_mouse
def	"OBSOLETE Decoy database from a International Protein Index database for Mus musculus." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1192. MS:1001294 decoy DB from IPI_arabidopsis

Table 1194. Term [MS:1001294]
id	MS:1001294
name	decoy DB from IPI_arabidopsis
def	"OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1193. MS:1001295 decoy DB from EST

Table 1195. Term [MS:1001295]
id	MS:1001295
name	decoy DB from EST
def	"OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1194. MS:1001296 decoy DB from IPI_zebrafish

Table 1196. Term [MS:1001296]
id	MS:1001296
name	decoy DB from IPI_zebrafish
def	"OBSOLETE Decoy database from a International Protein Index database for Danio rerio." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1195. MS:1001297 decoy DB from UniProtKB/Swiss-Prot

Table 1197. Term [MS:1001297]
id	MS:1001297
name	decoy DB from UniProtKB/Swiss-Prot
def	"OBSOLETE Decoy database from a Swiss-Prot protein sequence database." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1196. MS:1001298 decoy DB from IPI_chicken

Table 1198. Term [MS:1001298]
id	MS:1001298
name	decoy DB from IPI_chicken
def	"OBSOLETE Decoy database from a International Protein Index database for Gallus gallus." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1197. MS:1001299 decoy DB from IPI_cow

Table 1199. Term [MS:1001299]
id	MS:1001299
name	decoy DB from IPI_cow
def	"OBSOLETE Decoy database from a International Protein Index database for Bos taurus." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1198. MS:1001300 decoy DB from IPI_human

Table 1200. Term [MS:1001300]
id	MS:1001300
name	decoy DB from IPI_human
def	"OBSOLETE Decoy database from a International Protein Index database for Homo sapiens." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1199. MS:1001301 protein rank

Table 1201. Term [MS:1001301]
id	MS:1001301
name	protein rank
def	"The rank of the protein in a list sorted by the search engine." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001085 protein-level identification attribute ! protein-level identification attribute

2.1200. MS:1001302 search engine specific input parameter

Table 1202. Term [MS:1001302]
id	MS:1001302
name	search engine specific input parameter
def	"Search engine specific input parameters." [PSI:PI]
is_a	MS:1002093 search engine input parameter ! search engine input parameter

2.1201. MS:1001303 Arg-C

Table 1203. Term [MS:1001303]
id	MS:1001303
name	Arg-C
def	"Endoproteinase Arg-C." [PSI:PI]
synonym	"Trypsin/R" EXACT []
synonym	"Clostripain" EXACT []
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001272 (?⇐R)(?\!P) ! (?⇐R)(?

2.1202. MS:1001304 Asp-N

Table 1204. Term [MS:1001304]
id	MS:1001304
name	Asp-N
def	"Endoproteinase Asp-N." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001273 (?=[BD]) ! (?=[BD])

2.1203. MS:1001305 Asp-N_ambic

Table 1205. Term [MS:1001305]
id	MS:1001305
name	Asp-N_ambic
def	"Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001274 (?=[DE]) ! (?=[DE])

2.1204. MS:1001306 Chymotrypsin

Table 1206. Term [MS:1001306]
id	MS:1001306
name	Chymotrypsin
def	"Enzyme chymotrypsin." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001332 (?⇐[FYWL])(?\!P) ! (?⇐[FYWL])(?

2.1205. MS:1001307 CNBr

Table 1207. Term [MS:1001307]
id	MS:1001307
name	CNBr
def	"Cyanogen bromide." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001333 (?⇐M) ! (?⇐M)

2.1206. MS:1001308 Formic_acid

Table 1208. Term [MS:1001308]
id	MS:1001308
name	Formic_acid
def	"Formic acid." [PubChem_Compound:284]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001334 ?⇐D\\|?=D ! ?⇐D\|?=D

2.1207. MS:1001309 Lys-C

Table 1209. Term [MS:1001309]
id	MS:1001309
name	Lys-C
def	"Endoproteinase Lys-C." [PSI:PI]
synonym	"Trypsin/K" EXACT []
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001335 (?⇐K)(?\!P) ! (?⇐K)(?

2.1208. MS:1001310 Lys-C/P

Table 1210. Term [MS:1001310]
id	MS:1001310
name	Lys-C/P
def	"Proteinase Lys-C/P." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001336 (?⇐K) ! (?⇐K)

2.1209. MS:1001311 PepsinA

Table 1211. Term [MS:1001311]
id	MS:1001311
name	PepsinA
def	"PepsinA proteinase." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001337 (?⇐[FL]) ! (?⇐[FL])

2.1210. MS:1001312 TrypChymo

Table 1212. Term [MS:1001312]
id	MS:1001312
name	TrypChymo
def	"Cleavage agent TrypChymo." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001338 (?⇐[FYWLKR])(?\!P) ! (?⇐[FYWLKR])(?

2.1211. MS:1001313 Trypsin/P

Table 1213. Term [MS:1001313]
id	MS:1001313
name	Trypsin/P
def	"Cleavage agent Trypsin/P." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001339 (?⇐[KR]) ! (?⇐[KR])

2.1212. MS:1001314 V8-DE

Table 1214. Term [MS:1001314]
id	MS:1001314
name	V8-DE
def	"Cleavage agent V8-DE." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001340 (?⇐[BDEZ])(?\!P) ! (?⇐[BDEZ])(?

2.1213. MS:1001315 V8-E

Table 1215. Term [MS:1001315]
id	MS:1001315
name	V8-E
def	"Cleavage agent V8-E." [PSI:PI]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001341 (?⇐[EZ])(?\!P) ! (?⇐[EZ])(?

2.1214. MS:1001316 Mascot:SigThreshold

Table 1216. Term [MS:1001316]
id	MS:1001316
name	Mascot:SigThreshold
def	"Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1215. MS:1001317 Mascot:MaxProteinHits

Table 1217. Term [MS:1001317]
id	MS:1001317
name	Mascot:MaxProteinHits
def	"The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1216. MS:1001318 Mascot:ProteinScoringMethod

Table 1218. Term [MS:1001318]
id	MS:1001318
name	Mascot:ProteinScoringMethod
def	"Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1217. MS:1001319 Mascot:MinMSMSThreshold

Table 1219. Term [MS:1001319]
id	MS:1001319
name	Mascot:MinMSMSThreshold
def	"Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1218. MS:1001320 Mascot:ShowHomologousProteinsWithSamePeptides

Table 1220. Term [MS:1001320]
id	MS:1001320
name	Mascot:ShowHomologousProteinsWithSamePeptides
def	"If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1219. MS:1001321 Mascot:ShowHomologousProteinsWithSubsetOfPeptides

Table 1221. Term [MS:1001321]
id	MS:1001321
name	Mascot:ShowHomologousProteinsWithSubsetOfPeptides
def	"If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1220. MS:1001322 Mascot:RequireBoldRed

Table 1222. Term [MS:1001322]
id	MS:1001322
name	Mascot:RequireBoldRed
def	"Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1221. MS:1001323 Mascot:UseUnigeneClustering

Table 1223. Term [MS:1001323]
id	MS:1001323
name	Mascot:UseUnigeneClustering
def	"If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1222. MS:1001324 Mascot:IncludeErrorTolerantMatches

Table 1224. Term [MS:1001324]
id	MS:1001324
name	Mascot:IncludeErrorTolerantMatches
def	"If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1223. MS:1001325 Mascot:ShowDecoyMatches

Table 1225. Term [MS:1001325]
id	MS:1001325
name	Mascot:ShowDecoyMatches
def	"If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1224. MS:1001326 add_others

Table 1226. Term [MS:1001326]
id	MS:1001326
name	add_others
def	"OBSOLETE." [PSI:PI]
comment	This former purgatory term was made obsolete.
is_obsolete	true

2.1225. MS:1001328 OMSSA:evalue

Table 1227. Term [MS:1001328]
id	MS:1001328
name	OMSSA:evalue
def	"OMSSA E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1226. MS:1001329 OMSSA:pvalue

Table 1228. Term [MS:1001329]
id	MS:1001329
name	OMSSA:pvalue
def	"OMSSA p-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1227. MS:1001330 X\!Tandem:expect

Table 1229. Term [MS:1001330]
id	MS:1001330
name	X\!Tandem:expect
def	"The X!Tandem expectation value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1228. MS:1001331 X\!Tandem:hyperscore

Table 1230. Term [MS:1001331]
id	MS:1001331
name	X\!Tandem:hyperscore
def	"The X!Tandem hyperscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1229. MS:1001332 (?⇐[FYWL])(?\!P)

Table 1231. Term [MS:1001332]
id	MS:1001332
name	(?⇐[FYWL])(?\!P)
def	"Regular expression for Chymotrypsin." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1230. MS:1001333 (?⇐M)

Table 1232. Term [MS:1001333]
id	MS:1001333
name	(?⇐M)
def	"Regular expression for CNBr." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1231. MS:1001334 ?⇐D\|?=D

Table 1233. Term [MS:1001334]
id	MS:1001334
name	?⇐D\|?=D
def	"Regular expression for formic acid." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1232. MS:1001335 (?⇐K)(?\!P)

Table 1234. Term [MS:1001335]
id	MS:1001335
name	(?⇐K)(?\!P)
def	"Regular expression for Lys-C." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1233. MS:1001336 (?⇐K)

Table 1235. Term [MS:1001336]
id	MS:1001336
name	(?⇐K)
def	"Regular expression for Lys-C/P." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1234. MS:1001337 (?⇐[FL])

Table 1236. Term [MS:1001337]
id	MS:1001337
name	(?⇐[FL])
def	"Regular expression for PepsinA." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1235. MS:1001338 (?⇐[FYWLKR])(?\!P)

Table 1237. Term [MS:1001338]
id	MS:1001338
name	(?⇐[FYWLKR])(?\!P)
def	"Regular expression for TrypChymo." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1236. MS:1001339 (?⇐[KR])

Table 1238. Term [MS:1001339]
id	MS:1001339
name	(?⇐[KR])
def	"Regular expression for Trypsin/P." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1237. MS:1001340 (?⇐[BDEZ])(?\!P)

Table 1239. Term [MS:1001340]
id	MS:1001340
name	(?⇐[BDEZ])(?\!P)
def	"Regular expression for V8-DE." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1238. MS:1001341 (?⇐[EZ])(?\!P)

Table 1240. Term [MS:1001341]
id	MS:1001341
name	(?⇐[EZ])(?\!P)
def	"Regular expression for V8-E." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1239. MS:1001342 database sequence details

Table 1241. Term [MS:1001342]
id	MS:1001342
name	database sequence details
def	"Details about a single database sequence." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.1240. MS:1001343 NA sequence

Table 1242. Term [MS:1001343]
id	MS:1001343
name	NA sequence
def	"The sequence is a nucleic acid sequence." [PSI:PI]
is_a	MS:1001342 database sequence details ! database sequence details

2.1241. MS:1001344 AA sequence

Table 1243. Term [MS:1001344]
id	MS:1001344
name	AA sequence
def	"The sequence is a amino acid sequence." [PSI:PI]
is_a	MS:1001342 database sequence details ! database sequence details

2.1242. MS:1001345 mass table source

Table 1244. Term [MS:1001345]
id	MS:1001345
name	mass table source
def	"Children of this term specify the source of the mass table used." [PSI:PI]
is_a	MS:1001354 mass table options ! mass table options

2.1243. MS:1001346 AAIndex mass table

Table 1245. Term [MS:1001346]
id	MS:1001346
name	AAIndex mass table
def	"The masses used in the mass table are taken from AAIndex." [PSI:PI]
is_a	MS:1001345 mass table source ! mass table source

2.1244. MS:1001347 database file formats

Table 1246. Term [MS:1001347]
id	MS:1001347
name	database file formats
def	"The children of this term define file formats of the sequence database used." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.1245. MS:1001348 FASTA format

Table 1247. Term [MS:1001348]
id	MS:1001348
name	FASTA format
def	"The sequence database was stored in the FASTA format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1246. MS:1001349 ASN.1

Table 1248. Term [MS:1001349]
id	MS:1001349
name	ASN.1
def	"The sequence database was stored in the Abstract Syntax Notation 1 format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1247. MS:1001350 NCBI .p

Table 1249. Term [MS:1001350]
id	MS:1001350
name	NCBI .p
def	"The sequence database was stored in the NCBI formatdb (.p) format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1248. MS:1001351 clustal aln

Table 1250. Term [MS:1001351]
id	MS:1001351
name	clustal aln
def	"ClustalW ALN (multiple alignment) format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1249. MS:1001352 embl em

Table 1251. Term [MS:1001352]
id	MS:1001352
name	embl em
def	"EMBL entry format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1250. MS:1001353 NBRF PIR

Table 1252. Term [MS:1001353]
id	MS:1001353
name	NBRF PIR
def	"The NBRF PIR was used as format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1251. MS:1001354 mass table options

Table 1253. Term [MS:1001354]
id	MS:1001354
name	mass table options
def	"Root node for options for the mass table used." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1252. MS:1001355 peptide descriptions

Table 1254. Term [MS:1001355]
id	MS:1001355
name	peptide descriptions
def	"Descriptions of peptides." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.1253. MS:1001356 spectrum descriptions

Table 1255. Term [MS:1001356]
id	MS:1001356
name	spectrum descriptions
def	"Descriptions of the input spectra." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1254. MS:1001357 spectrum quality descriptions

Table 1256. Term [MS:1001357]
id	MS:1001357
name	spectrum quality descriptions
def	"Description of the quality of the input spectrum." [PSI:PI]
is_a	MS:1001356 spectrum descriptions ! spectrum descriptions

2.1255. MS:1001358 msmsEval quality

Table 1257. Term [MS:1001358]
id	MS:1001358
name	msmsEval quality
def	"This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001357 spectrum quality descriptions ! spectrum quality descriptions

2.1256. MS:1001359 ambiguous residues

Table 1258. Term [MS:1001359]
id	MS:1001359
name	ambiguous residues
def	"Children of this term describe ambiguous residues." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1257. MS:1001360 alternate single letter codes

Table 1259. Term [MS:1001360]
id	MS:1001360
name	alternate single letter codes
def	"List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001359 ambiguous residues ! ambiguous residues

2.1258. MS:1001361 alternate mass

Table 1260. Term [MS:1001361]
id	MS:1001361
name	alternate mass
def	"List of masses a non-standard letter code is replaced with." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001359 ambiguous residues ! ambiguous residues
relationship	has_units [UO:0000221] ! dalton

2.1259. MS:1001362 number of unmatched peaks

Table 1261. Term [MS:1001362]
id	MS:1001362
name	number of unmatched peaks
def	"The number of unmatched peaks." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1002345 PSM-level attribute ! PSM-level attribute

2.1260. MS:1001363 peptide unique to one protein

Table 1262. Term [MS:1001363]
id	MS:1001363
name	peptide unique to one protein
def	"A peptide matching only one." [PSI:PI]
is_a	MS:1001127 peptide sharing details ! peptide sharing details

2.1261. MS:1001364 peptide sequence-level global FDR

Table 1263. Term [MS:1001364]
id	MS:1001364
name	peptide sequence-level global FDR
def	"Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002703 peptide sequence-level result list statistic ! peptide sequence-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1262. MS:1001365 frag: internal yb ion

Table 1264. Term [MS:1001365]
id	MS:1001365
name	frag: internal yb ion
def	"Fragmentation information, type of product: internal yb ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1263. MS:1001366 frag: internal ya ion

Table 1265. Term [MS:1001366]
id	MS:1001366
name	frag: internal ya ion
def	"Fragmentation information, type of product: internal ya ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1264. MS:1001367 frag: z+1 ion

Table 1266. Term [MS:1001367]
id	MS:1001367
name	frag: z+1 ion
def	"Fragmentation information, type of product: z+1 ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1265. MS:1001368 frag: z+2 ion

Table 1267. Term [MS:1001368]
id	MS:1001368
name	frag: z+2 ion
def	"Fragmentation information, type of product: z+2 ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1266. MS:1001369 text format

Table 1268. Term [MS:1001369]
id	MS:1001369
name	text format
def	"Simple text file format of \"m/z [intensity]\" values for a PMF (or single MS2) search." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1267. MS:1001370 Mascot:homology threshold

Table 1269. Term [MS:1001370]
id	MS:1001370
name	Mascot:homology threshold
def	"The Mascot result 'homology threshold'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1268. MS:1001371 Mascot:identity threshold

Table 1270. Term [MS:1001371]
id	MS:1001371
name	Mascot:identity threshold
def	"The Mascot result 'identity threshold'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1269. MS:1001372 SEQUEST:Sequences

Table 1271. Term [MS:1001372]
id	MS:1001372
name	SEQUEST:Sequences
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1270. MS:1001373 SEQUEST:TIC

Table 1272. Term [MS:1001373]
id	MS:1001373
name	SEQUEST:TIC
def	"SEQUEST total ion current." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1271. MS:1001374 SEQUEST:Sum

Table 1273. Term [MS:1001374]
id	MS:1001374
name	SEQUEST:Sum
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1272. MS:1001375 Phenyx:Instrument Type

Table 1274. Term [MS:1001375]
id	MS:1001375
name	Phenyx:Instrument Type
def	"The instrument type parameter value in Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1273. MS:1001376 Phenyx:Scoring Model

Table 1275. Term [MS:1001376]
id	MS:1001376
name	Phenyx:Scoring Model
def	"The selected scoring model in Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1274. MS:1001377 Phenyx:Default Parent Charge

Table 1276. Term [MS:1001377]
id	MS:1001377
name	Phenyx:Default Parent Charge
def	"The default parent charge value in Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1275. MS:1001378 Phenyx:Trust Parent Charge

Table 1277. Term [MS:1001378]
id	MS:1001378
name	Phenyx:Trust Parent Charge
def	"The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1276. MS:1001379 Phenyx:Turbo

Table 1278. Term [MS:1001379]
id	MS:1001379
name	Phenyx:Turbo
def	"The turbo mode parameter in Phenyx." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1277. MS:1001380 Phenyx:Turbo:ErrorTol

Table 1279. Term [MS:1001380]
id	MS:1001380
name	Phenyx:Turbo:ErrorTol
def	"The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1278. MS:1001381 Phenyx:Turbo:Coverage

Table 1280. Term [MS:1001381]
id	MS:1001381
name	Phenyx:Turbo:Coverage
def	"The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1279. MS:1001382 Phenyx:Turbo:Series

Table 1281. Term [MS:1001382]
id	MS:1001382
name	Phenyx:Turbo:Series
def	"The list of ion series considered in the turbo mode of Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1280. MS:1001383 Phenyx:MinPepLength

Table 1282. Term [MS:1001383]
id	MS:1001383
name	Phenyx:MinPepLength
def	"The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1281. MS:1001384 Phenyx:MinPepzscore

Table 1283. Term [MS:1001384]
id	MS:1001384
name	Phenyx:MinPepzscore
def	"The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1282. MS:1001385 Phenyx:MaxPepPvalue

Table 1284. Term [MS:1001385]
id	MS:1001385
name	Phenyx:MaxPepPvalue
def	"The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1283. MS:1001386 Phenyx:AC Score

Table 1285. Term [MS:1001386]
id	MS:1001386
name	Phenyx:AC Score
def	"The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1284. MS:1001387 Phenyx:Conflict Resolution

Table 1286. Term [MS:1001387]
id	MS:1001387
name	Phenyx:Conflict Resolution
def	"The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002097 Phenyx input parameter ! Phenyx input parameter

2.1285. MS:1001388 Phenyx:AC

Table 1287. Term [MS:1001388]
id	MS:1001388
name	Phenyx:AC
def	"The primary sequence database identifier of a protein in Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1286. MS:1001389 Phenyx:ID

Table 1288. Term [MS:1001389]
id	MS:1001389
name	Phenyx:ID
xref	value-type:xsd\:string "The allowed value-type for this CV term."
def	"A secondary sequence database identifier of a protein in Phenyx." [PSI:PI]
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1287. MS:1001390 Phenyx:Score

Table 1289. Term [MS:1001390]
id	MS:1001390
name	Phenyx:Score
def	"The protein score of a protein match in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1288. MS:1001391 Phenyx:Peptides1

Table 1290. Term [MS:1001391]
id	MS:1001391
name	Phenyx:Peptides1
def	"First number of phenyx result \"#Peptides\"." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1289. MS:1001392 Phenyx:Peptides2

Table 1291. Term [MS:1001392]
id	MS:1001392
name	Phenyx:Peptides2
def	"Second number of phenyx result \"#Peptides\"." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1290. MS:1001393 Phenyx:Auto

Table 1292. Term [MS:1001393]
id	MS:1001393
name	Phenyx:Auto
def	"The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1291. MS:1001394 Phenyx:User

Table 1293. Term [MS:1001394]
id	MS:1001394
name	Phenyx:User
def	"The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1292. MS:1001395 Phenyx:Pepzscore

Table 1294. Term [MS:1001395]
id	MS:1001395
name	Phenyx:Pepzscore
def	"The z-score value of a peptide sequence match in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1293. MS:1001396 Phenyx:PepPvalue

Table 1295. Term [MS:1001396]
id	MS:1001396
name	Phenyx:PepPvalue
def	"The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.1294. MS:1001397 Phenyx:NumberOfMC

Table 1296. Term [MS:1001397]
id	MS:1001397
name	Phenyx:NumberOfMC
def	"The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1295. MS:1001398 Phenyx:Modif

Table 1297. Term [MS:1001398]
id	MS:1001398
name	Phenyx:Modif
def	"The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1296. MS:1001399 OMSSA csv format

Table 1298. Term [MS:1001399]
id	MS:1001399
name	OMSSA csv format
def	"Source file for this mzIdentML was in OMSSA csv file format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1297. MS:1001400 OMSSA xml format

Table 1299. Term [MS:1001400]
id	MS:1001400
name	OMSSA xml format
def	"Source file for this mzIdentML was in OMSSA xml file format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1298. MS:1001401 X\!Tandem xml format

Table 1300. Term [MS:1001401]
id	MS:1001401
name	X\!Tandem xml format
def	"Source file for this mzIdentML was in X!Tandem xml file format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1299. MS:1001405 spectrum identification result details

Table 1301. Term [MS:1001405]
id	MS:1001405
name	spectrum identification result details
def	"This subsection describes terms which can describe details of spectrum identification results." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1300. MS:1001406 param: internal yb ion

Table 1302. Term [MS:1001406]
id	MS:1001406
name	param: internal yb ion
def	"Parameter information, type of product: internal yb ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1301. MS:1001407 param: internal ya ion

Table 1303. Term [MS:1001407]
id	MS:1001407
name	param: internal ya ion
def	"Parameter information, type of product: internal ya ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1302. MS:1001408 param: z+1 ion

Table 1304. Term [MS:1001408]
id	MS:1001408
name	param: z+1 ion
def	"Parameter information, type of product: z+1 ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1303. MS:1001409 param: z+2 ion

Table 1305. Term [MS:1001409]
id	MS:1001409
name	param: z+2 ion
def	"Parameter information, type of product: z+2 ion." [PSI:PI]
is_a	MS:1002473 ion series considered in search ! ion series considered in search

2.1304. MS:1001410 translation start codons

Table 1306. Term [MS:1001410]
id	MS:1001410
name	translation start codons
def	"The translation start codons used to translate the nucleotides to amino acids." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.1305. MS:1001411 search tolerance specification

Table 1307. Term [MS:1001411]
id	MS:1001411
name	search tolerance specification
def	"Specification of the search tolerance." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1306. MS:1001412 search tolerance plus value

Table 1308. Term [MS:1001412]
id	MS:1001412
name	search tolerance plus value
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001411 search tolerance specification ! search tolerance specification
relationship	has_units [UO:0000166] ! parts per notation unit
relationship	has_units [UO:0000169] ! parts per million
relationship	has_units [UO:0000187] ! percent
relationship	has_units [UO:0000221] ! dalton

2.1307. MS:1001413 search tolerance minus value

Table 1309. Term [MS:1001413]
id	MS:1001413
name	search tolerance minus value
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001411 search tolerance specification ! search tolerance specification
relationship	has_units [UO:0000166] ! parts per notation unit
relationship	has_units [UO:0000169] ! parts per million
relationship	has_units [UO:0000187] ! percent
relationship	has_units [UO:0000221] ! dalton

2.1308. MS:1001414 MGF scans

Table 1310. Term [MS:1001414]
id	MS:1001414
name	MGF scans
def	"OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_obsolete	true
replaced_by	MS:1000797

2.1309. MS:1001415 MGF raw scans

Table 1311. Term [MS:1001415]
id	MS:1001415
name	MGF raw scans
def	"OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_obsolete	true
replaced_by	MS:1000798

2.1310. MS:1001416 spectrum title

Table 1312. Term [MS:1001416]
id	MS:1001416
name	spectrum title
def	"OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
is_obsolete	true
replaced_by	MS:1000796

2.1311. MS:1001417 SpectraST:dot

Table 1313. Term [MS:1001417]
id	MS:1001417
name	SpectraST:dot
def	"SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1312. MS:1001418 SpectraST:dot_bias

Table 1314. Term [MS:1001418]
id	MS:1001418
name	SpectraST:dot_bias
def	"SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1313. MS:1001419 SpectraST:discriminant score F

Table 1315. Term [MS:1001419]
id	MS:1001419
name	SpectraST:discriminant score F
def	"SpectraST spectrum score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1314. MS:1001420 SpectraST:delta

Table 1316. Term [MS:1001420]
id	MS:1001420
name	SpectraST:delta
def	"SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1315. MS:1001421 pepXML format

Table 1317. Term [MS:1001421]
id	MS:1001421
name	pepXML format
def	"The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1316. MS:1001422 protXML format

Table 1318. Term [MS:1001422]
id	MS:1001422
name	protXML format
def	"The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1317. MS:1001423 translation table description

Table 1319. Term [MS:1001423]
id	MS:1001423
name	translation table description
def	"A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.1318. MS:1001424 ProteinExtractor:Methodname

Table 1320. Term [MS:1001424]
id	MS:1001424
name	ProteinExtractor:Methodname
def	"Name of the used method in the ProteinExtractor algorithm." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1319. MS:1001425 ProteinExtractor:GenerateNonRedundant

Table 1321. Term [MS:1001425]
id	MS:1001425
name	ProteinExtractor:GenerateNonRedundant
def	"Flag indicating if a non redundant scoring should be generated." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1320. MS:1001426 ProteinExtractor:IncludeIdentified

Table 1322. Term [MS:1001426]
id	MS:1001426
name	ProteinExtractor:IncludeIdentified
def	"Flag indicating if identified proteins should be included." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1321. MS:1001427 ProteinExtractor:MaxNumberOfProteins

Table 1323. Term [MS:1001427]
id	MS:1001427
name	ProteinExtractor:MaxNumberOfProteins
def	"The maximum number of proteins to consider." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1322. MS:1001428 ProteinExtractor:MaxProteinMass

Table 1324. Term [MS:1001428]
id	MS:1001428
name	ProteinExtractor:MaxProteinMass
def	"The maximum considered mass for a protein." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1323. MS:1001429 ProteinExtractor:MinNumberOfPeptides

Table 1325. Term [MS:1001429]
id	MS:1001429
name	ProteinExtractor:MinNumberOfPeptides
def	"The minimum number of proteins to consider." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1324. MS:1001430 ProteinExtractor:UseMascot

Table 1326. Term [MS:1001430]
id	MS:1001430
name	ProteinExtractor:UseMascot
def	"Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1325. MS:1001431 ProteinExtractor:MascotPeptideScoreThreshold

Table 1327. Term [MS:1001431]
id	MS:1001431
name	ProteinExtractor:MascotPeptideScoreThreshold
def	"Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1326. MS:1001432 ProteinExtractor:MascotUniqueScore

Table 1328. Term [MS:1001432]
id	MS:1001432
name	ProteinExtractor:MascotUniqueScore
def	"In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1327. MS:1001433 ProteinExtractor:MascotUseIdentityScore

Table 1329. Term [MS:1001433]
id	MS:1001433
name	ProteinExtractor:MascotUseIdentityScore
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1328. MS:1001434 ProteinExtractor:MascotWeighting

Table 1330. Term [MS:1001434]
id	MS:1001434
name	ProteinExtractor:MascotWeighting
def	"Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1329. MS:1001435 ProteinExtractor:UseSequest

Table 1331. Term [MS:1001435]
id	MS:1001435
name	ProteinExtractor:UseSequest
def	"Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1330. MS:1001436 ProteinExtractor:SequestPeptideScoreThreshold

Table 1332. Term [MS:1001436]
id	MS:1001436
name	ProteinExtractor:SequestPeptideScoreThreshold
def	"Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1331. MS:1001437 ProteinExtractor:SequestUniqueScore

Table 1333. Term [MS:1001437]
id	MS:1001437
name	ProteinExtractor:SequestUniqueScore
def	"In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1332. MS:1001438 ProteinExtractor:SequestWeighting

Table 1334. Term [MS:1001438]
id	MS:1001438
name	ProteinExtractor:SequestWeighting
def	"Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1333. MS:1001439 ProteinExtractor:UseProteinSolver

Table 1335. Term [MS:1001439]
id	MS:1001439
name	ProteinExtractor:UseProteinSolver
def	"Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1334. MS:1001440 ProteinExtractor:ProteinSolverPeptideScoreThreshold

Table 1336. Term [MS:1001440]
id	MS:1001440
name	ProteinExtractor:ProteinSolverPeptideScoreThreshold
def	"Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1335. MS:1001441 ProteinExtractor:ProteinSolverUniqueScore

Table 1337. Term [MS:1001441]
id	MS:1001441
name	ProteinExtractor:ProteinSolverUniqueScore
def	"In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1336. MS:1001442 ProteinExtractor:ProteinSolverWeighting

Table 1338. Term [MS:1001442]
id	MS:1001442
name	ProteinExtractor:ProteinSolverWeighting
def	"Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1337. MS:1001443 ProteinExtractor:UsePhenyx

Table 1339. Term [MS:1001443]
id	MS:1001443
name	ProteinExtractor:UsePhenyx
def	"Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1338. MS:1001444 ProteinExtractor:PhenyxPeptideScoreThreshold

Table 1340. Term [MS:1001444]
id	MS:1001444
name	ProteinExtractor:PhenyxPeptideScoreThreshold
def	"Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1339. MS:1001445 ProteinExtractor:PhenyxUniqueScore

Table 1341. Term [MS:1001445]
id	MS:1001445
name	ProteinExtractor:PhenyxUniqueScore
def	"In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1340. MS:1001446 ProteinExtractor:PhenyxWeighting

Table 1342. Term [MS:1001446]
id	MS:1001446
name	ProteinExtractor:PhenyxWeighting
def	"Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1341. MS:1001447 prot:FDR threshold

Table 1343. Term [MS:1001447]
id	MS:1001447
name	prot:FDR threshold
def	"False-discovery rate threshold for proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002485 protein-level statistical threshold ! protein-level statistical threshold

2.1342. MS:1001448 pep:FDR threshold

Table 1344. Term [MS:1001448]
id	MS:1001448
name	pep:FDR threshold
def	"False-discovery rate threshold for peptides." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002484 peptide-level statistical threshold ! peptide-level statistical threshold

2.1343. MS:1001449 OMSSA e-value threshold

Table 1345. Term [MS:1001449]
id	MS:1001449
name	OMSSA e-value threshold
def	"Threshold for OMSSA e-value for quality estimation." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002099 OMSSA input parameter ! OMSSA input parameter

2.1344. MS:1001450 decoy DB details

Table 1346. Term [MS:1001450]
id	MS:1001450
name	decoy DB details
def	"Details of decoy generation and database structure." [PSI:PI]
is_a	MS:1001011 search database details ! search database details

2.1345. MS:1001451 decoy DB generation algorithm

Table 1347. Term [MS:1001451]
id	MS:1001451
name	decoy DB generation algorithm
def	"Name of algorithm used for decoy generation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1346. MS:1001452 decoy DB type shuffle

Table 1348. Term [MS:1001452]
id	MS:1001452
name	decoy DB type shuffle
def	"Decoy type: Amino acids of protein sequences are used in a random order." [PSI:PI]
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1347. MS:1001453 DB composition only decoy

Table 1349. Term [MS:1001453]
id	MS:1001453
name	DB composition only decoy
def	"Decoy database composition: database contains only decoy entries." [PSI:PI]
is_a	MS:1001450 decoy DB details ! decoy DB details

2.1348. MS:1001454 quality estimation with implicite decoy sequences

Table 1350. Term [MS:1001454]
id	MS:1001454
name	quality estimation with implicite decoy sequences
def	"Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy)." [PSI:PI]
is_a	MS:1001060 quality estimation method details ! quality estimation method details

2.1349. MS:1001455 acquisition software

Table 1351. Term [MS:1001455]
id	MS:1001455
name	acquisition software
def	"Acquisition software." [PSI:MS]
is_a	MS:1000531 software ! software

2.1350. MS:1001456 analysis software

Table 1352. Term [MS:1001456]
id	MS:1001456
name	analysis software
def	"Analysis software." [PSI:MS]
is_a	MS:1000531 software ! software

2.1351. MS:1001457 data processing software

Table 1353. Term [MS:1001457]
id	MS:1001457
name	data processing software
def	"Data processing software." [PSI:MS]
is_a	MS:1000531 software ! software

2.1352. MS:1001458 spectrum generation information

Table 1354. Term [MS:1001458]
id	MS:1001458
name	spectrum generation information
def	"Vocabularies describing the spectrum generation information." [PSI:PI]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.1353. MS:1001459 file format

Table 1355. Term [MS:1001459]
id	MS:1001459
name	file format
def	"Format of data files." [PSI:MS]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.1354. MS:1001460 unknown modification

Table 1356. Term [MS:1001460]
id	MS:1001460
name	unknown modification
def	"This term should be given if the modification was unknown." [PSI:PI]
is_a	MS:1001471 peptide modification details ! peptide modification details

2.1355. MS:1001461 greylag

Table 1357. Term [MS:1001461]
id	MS:1001461
name	greylag
def	"Greylag identification software." [http://greylag.org/]
is_a	MS:1001456 analysis software ! analysis software

2.1356. MS:1001462 PEFF format

Table 1358. Term [MS:1001462]
id	MS:1001462
name	PEFF format
def	"The sequence database was stored in the PEFF (PSI enhanced FastA file) format." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.1357. MS:1001463 Phenyx XML format

Table 1359. Term [MS:1001463]
id	MS:1001463
name	Phenyx XML format
def	"Phenyx open XML file format." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1358. MS:1001464 DTASelect format

Table 1360. Term [MS:1001464]
id	MS:1001464
name	DTASelect format
def	"DTASelect file format." [PMID:12643522, http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1359. MS:1001466 MS2 format

Table 1361. Term [MS:1001466]
id	MS:1001466
name	MS2 format
def	"MS2 file format for MS2 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1360. MS:1001467 taxonomy: NCBI TaxID

Table 1362. Term [MS:1001467]
id	MS:1001467
name	taxonomy: NCBI TaxID
def	"This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001089 molecule taxonomy ! molecule taxonomy

2.1361. MS:1001468 taxonomy: common name

Table 1363. Term [MS:1001468]
id	MS:1001468
name	taxonomy: common name
def	"This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001089 molecule taxonomy ! molecule taxonomy

2.1362. MS:1001469 taxonomy: scientific name

Table 1364. Term [MS:1001469]
id	MS:1001469
name	taxonomy: scientific name
def	"This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001089 molecule taxonomy ! molecule taxonomy

2.1363. MS:1001470 taxonomy: Swiss-Prot ID

Table 1365. Term [MS:1001470]
id	MS:1001470
name	taxonomy: Swiss-Prot ID
def	"This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001089 molecule taxonomy ! molecule taxonomy

2.1364. MS:1001471 peptide modification details

Table 1366. Term [MS:1001471]
id	MS:1001471
name	peptide modification details
def	"The children of this term can be used to describe modifications." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1365. MS:1001472 selected ion monitoring chromatogram

Table 1367. Term [MS:1001472]
id	MS:1001472
name	selected ion monitoring chromatogram
def	"Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS]
synonym	"SIM chromatogram" EXACT []
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram

2.1366. MS:1001473 selected reaction monitoring chromatogram

Table 1368. Term [MS:1001473]
id	MS:1001473
name	selected reaction monitoring chromatogram
def	"Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS]
synonym	"SRM chromatogram" EXACT []
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram

2.1367. MS:1001474 consecutive reaction monitoring chromatogram

Table 1369. Term [MS:1001474]
id	MS:1001474
name	consecutive reaction monitoring chromatogram
def	"OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS]
comment	This term was made obsolete because, by design, it can’t be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way.
synonym	"CRM chromatogram" EXACT []
is_a	MS:1000810 ion current chromatogram ! ion current chromatogram
is_obsolete	true

2.1368. MS:1001475 OMSSA

Table 1370. Term [MS:1001475]
id	MS:1001475
name	OMSSA
def	"Open Mass Spectrometry Search Algorithm was used to analyze the spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1369. MS:1001476 X\!Tandem

Table 1371. Term [MS:1001476]
id	MS:1001476
name	X\!Tandem
def	"X!Tandem was used to analyze the spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1370. MS:1001477 SpectraST

Table 1372. Term [MS:1001477]
id	MS:1001477
name	SpectraST
def	"SpectraST was used to analyze the spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1371. MS:1001478 Mascot Parser

Table 1373. Term [MS:1001478]
id	MS:1001478
name	Mascot Parser
def	"Mascot Parser was used to analyze the spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1372. MS:1001479 null-terminated ASCII string

Table 1374. Term [MS:1001479]
id	MS:1001479
name	null-terminated ASCII string
def	"Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte." [PSI:MS]
is_a	MS:1000518 binary data type ! binary data type

2.1373. MS:1001480 SCIEX TOF/TOF nativeID format

Table 1375. Term [MS:1001480]
id	MS:1001480
name	SCIEX TOF/TOF nativeID format
def	"Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.1374. MS:1001481 SCIEX TOF/TOF database

Table 1376. Term [MS:1001481]
id	MS:1001481
name	SCIEX TOF/TOF database
def	"Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1375. MS:1001482 5800 TOF/TOF

Table 1377. Term [MS:1001482]
id	MS:1001482
name	5800 TOF/TOF
def	"SCIEX 5800 TOF-TOF Analyzer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.1376. MS:1001483 SCIEX TOF/TOF Series Explorer Software

Table 1378. Term [MS:1001483]
id	MS:1001483
name	SCIEX TOF/TOF Series Explorer Software
def	"SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis." [PSI:MS]
is_a	MS:1000690 SCIEX software ! SCIEX software
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1377. MS:1001484 intensity normalization

Table 1379. Term [MS:1001484]
id	MS:1001484
name	intensity normalization
def	"Normalization of data point intensities." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.1378. MS:1001485 m/z calibration

Table 1380. Term [MS:1001485]
id	MS:1001485
name	m/z calibration
def	"Calibration of data point m/z positions." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.1379. MS:1001486 data filtering

Table 1381. Term [MS:1001486]
id	MS:1001486
name	data filtering
def	"Filtering out part of the data." [PSI:MS]
is_a	MS:1000543 data processing action ! data processing action

2.1380. MS:1001487 ProteinExtractor

Table 1382. Term [MS:1001487]
id	MS:1001487
name	ProteinExtractor
def	"An algorithm for protein determination/assembly integrated into Bruker’s ProteinScape." [PSI:MS]
is_a	MS:1000692 Bruker software ! Bruker software
is_a	MS:1001456 analysis software ! analysis software

2.1381. MS:1001488 Mascot Distiller

Table 1383. Term [MS:1001488]
id	MS:1001488
name	Mascot Distiller
def	"Mascot Distiller." [PSI:PI]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software

2.1382. MS:1001489 Mascot Integra

Table 1384. Term [MS:1001489]
id	MS:1001489
name	Mascot Integra
def	"Mascot Integra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1383. MS:1001490 Percolator

Table 1385. Term [MS:1001490]
id	MS:1001490
name	Percolator
def	"Percolator." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1384. MS:1001491 percolator:Q value

Table 1386. Term [MS:1001491]
id	MS:1001491
name	percolator:Q value
def	"Percolator:Q value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1385. MS:1001492 percolator:score

Table 1387. Term [MS:1001492]
id	MS:1001492
name	percolator:score
def	"Percolator:score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1386. MS:1001493 percolator:PEP

Table 1388. Term [MS:1001493]
id	MS:1001493
name	percolator:PEP
def	"Posterior error probability." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1387. MS:1001494 no threshold

Table 1389. Term [MS:1001494]
id	MS:1001494
name	no threshold
def	"In case no threshold was used." [PSI:PI]
is_a	MS:1002482 statistical threshold ! statistical threshold

2.1388. MS:1001495 ProteinScape:SearchResultId

Table 1390. Term [MS:1001495]
id	MS:1001495
name	ProteinScape:SearchResultId
def	"The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1389. MS:1001496 ProteinScape:SearchEventId

Table 1391. Term [MS:1001496]
id	MS:1001496
name	ProteinScape:SearchEventId
def	"The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1390. MS:1001497 ProteinScape:ProfoundProbability

Table 1392. Term [MS:1001497]
id	MS:1001497
name	ProteinScape:ProfoundProbability
def	"The Profound probability score stored by ProteinScape." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1391. MS:1001498 Profound:z value

Table 1393. Term [MS:1001498]
id	MS:1001498
name	Profound:z value
def	"The Profound z value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1392. MS:1001499 Profound:Cluster

Table 1394. Term [MS:1001499]
id	MS:1001499
name	Profound:Cluster
def	"The Profound cluster score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1393. MS:1001500 Profound:ClusterRank

Table 1395. Term [MS:1001500]
id	MS:1001500
name	Profound:ClusterRank
def	"The Profound cluster rank." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1394. MS:1001501 MSFit:Mowse score

Table 1396. Term [MS:1001501]
id	MS:1001501
name	MSFit:Mowse score
def	"The MSFit Mowse score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1395. MS:1001502 Sonar:Score

Table 1397. Term [MS:1001502]
id	MS:1001502
name	Sonar:Score
def	"The Sonar score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1396. MS:1001503 ProteinScape:PFFSolverExp

Table 1398. Term [MS:1001503]
id	MS:1001503
name	ProteinScape:PFFSolverExp
def	"The ProteinSolver exp value stored by ProteinScape." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1397. MS:1001504 ProteinScape:PFFSolverScore

Table 1399. Term [MS:1001504]
id	MS:1001504
name	ProteinScape:PFFSolverScore
def	"The ProteinSolver score stored by ProteinScape." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1398. MS:1001505 ProteinScape:IntensityCoverage

Table 1400. Term [MS:1001505]
id	MS:1001505
name	ProteinScape:IntensityCoverage
def	"The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1399. MS:1001506 ProteinScape:SequestMetaScore

Table 1401. Term [MS:1001506]
id	MS:1001506
name	ProteinScape:SequestMetaScore
def	"The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1400. MS:1001507 ProteinExtractor:Score

Table 1402. Term [MS:1001507]
id	MS:1001507
name	ProteinExtractor:Score
def	"The score calculated by ProteinExtractor." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1401. MS:1001508 Agilent MassHunter nativeID format

Table 1403. Term [MS:1001508]
id	MS:1001508
name	Agilent MassHunter nativeID format
def	"Native format defined by scanId=xsd:nonNegativeInteger." [PSI:PI]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.1402. MS:1001509 Agilent MassHunter format

Table 1404. Term [MS:1001509]
id	MS:1001509
name	Agilent MassHunter format
def	"A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1403. MS:1001510 TSQ Vantage

Table 1405. Term [MS:1001510]
id	MS:1001510
name	TSQ Vantage
def	"TSQ Vantage." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1404. MS:1001511 Sequence database filter types

Table 1406. Term [MS:1001511]
id	MS:1001511
name	Sequence database filter types
def	"Filter types which are used to filter a sequence database." [PSI:PI]
is_a	MS:1001019 database filtering ! database filtering

2.1405. MS:1001512 Sequence database filters

Table 1407. Term [MS:1001512]
id	MS:1001512
name	Sequence database filters
def	"Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search." [PSI:PI]
is_a	MS:1001019 database filtering ! database filtering

2.1406. MS:1001513 DB sequence filter pattern

Table 1408. Term [MS:1001513]
id	MS:1001513
name	DB sequence filter pattern
def	"DB sequence filter pattern." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters

2.1407. MS:1001514 DB accession filter string

Table 1409. Term [MS:1001514]
id	MS:1001514
name	DB accession filter string
def	"DB accession filter string." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001512 Sequence database filters ! Sequence database filters

2.1408. MS:1001515 frag: c ion - H2O

Table 1410. Term [MS:1001515]
id	MS:1001515
name	frag: c ion - H2O
def	"Fragmentation information, type of product: c ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1409. MS:1001516 frag: c ion - NH3

Table 1411. Term [MS:1001516]
id	MS:1001516
name	frag: c ion - NH3
def	"Fragmentation information, type of product: c ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1410. MS:1001517 frag: z ion - H2O

Table 1412. Term [MS:1001517]
id	MS:1001517
name	frag: z ion - H2O
def	"Fragmentation information, type of product: z ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1411. MS:1001518 frag: z ion - NH3

Table 1413. Term [MS:1001518]
id	MS:1001518
name	frag: z ion - NH3
def	"Fragmentation information, type of product: z ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1412. MS:1001519 frag: x ion - H2O

Table 1414. Term [MS:1001519]
id	MS:1001519
name	frag: x ion - H2O
def	"Fragmentation information, type of product: x ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1413. MS:1001520 frag: x ion - NH3

Table 1415. Term [MS:1001520]
id	MS:1001520
name	frag: x ion - NH3
def	"Fragmentation information, type of product: x ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1414. MS:1001521 frag: precursor ion - H2O

Table 1416. Term [MS:1001521]
id	MS:1001521
name	frag: precursor ion - H2O
def	"Fragmentation information, type of product: precursor ion without water." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1415. MS:1001522 frag: precursor ion - NH3

Table 1417. Term [MS:1001522]
id	MS:1001522
name	frag: precursor ion - NH3
def	"Fragmentation information, type of product: precursor ion without ammonia." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1416. MS:1001523 frag: precursor ion

Table 1418. Term [MS:1001523]
id	MS:1001523
name	frag: precursor ion
def	"Fragmentation information, type of product: precursor ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.1417. MS:1001524 fragment neutral loss

Table 1419. Term [MS:1001524]
id	MS:1001524
name	fragment neutral loss
def	"This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details
relationship	has_units [UO:0000221] ! dalton

2.1418. MS:1001525 precursor neutral loss

Table 1420. Term [MS:1001525]
id	MS:1001525
name	precursor neutral loss
def	"This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details
relationship	has_units [UO:0000221] ! dalton

2.1419. MS:1001526 spectrum from database integer nativeID format

Table 1421. Term [MS:1001526]
id	MS:1001526
name	spectrum from database integer nativeID format
def	"Native format defined by databasekey=xsd:long." [PSI:MS]
comment	A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier).
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.1420. MS:1001527 Proteinscape spectra

Table 1422. Term [MS:1001527]
id	MS:1001527
name	Proteinscape spectra
def	"Spectra from Bruker/Protagen Proteinscape database." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1421. MS:1001528 Mascot query number

Table 1423. Term [MS:1001528]
id	MS:1001528
name	Mascot query number
def	"Native format defined by query=xsd:nonNegativeInteger." [PSI:MS]
comment	The spectrum (query) number in a Mascot results file, starting from 1.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.1422. MS:1001529 spectra data details

Table 1424. Term [MS:1001529]
id	MS:1001529
name	spectra data details
def	"Child-terms contain information to map the results back to spectra." [PSI:MS]
is_a	MS:1001249 search input details ! search input details

2.1423. MS:1001530 mzML unique identifier

Table 1425. Term [MS:1001530]
id	MS:1001530
name	mzML unique identifier
def	"Native format defined by mzMLid=xsd:IDREF." [PSI:MS]
comment	A unique identifier of a spectrum stored in an mzML file.
is_a	MS:1001529 spectra data details ! spectra data details

2.1424. MS:1001531 spectrum from ProteinScape database nativeID format

Table 1426. Term [MS:1001531]
id	MS:1001531
name	spectrum from ProteinScape database nativeID format
def	"Native format defined by databasekey=xsd:long." [PSI:MS]
comment	A unique identifier of a spectrum stored in a ProteinScape database.
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format
is_a	MS:1001529 spectra data details ! spectra data details

2.1425. MS:1001532 spectrum from database string nativeID format

Table 1427. Term [MS:1001532]
id	MS:1001532
name	spectrum from database string nativeID format
def	"Native format defined by databasekey=xsd:string." [PSI:MS]
comment	A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier).
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format
is_a	MS:1001529 spectra data details ! spectra data details

2.1426. MS:1001533 Bruker Daltonics esquire series

Table 1428. Term [MS:1001533]
id	MS:1001533
name	Bruker Daltonics esquire series
def	"Bruker Daltonics' esquire series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1427. MS:1001534 Bruker Daltonics flex series

Table 1429. Term [MS:1001534]
id	MS:1001534
name	Bruker Daltonics flex series
def	"Bruker Daltonics' flex series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1428. MS:1001535 Bruker Daltonics BioTOF series

Table 1430. Term [MS:1001535]
id	MS:1001535
name	Bruker Daltonics BioTOF series
def	"Bruker Daltonics' BioTOF series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1429. MS:1001536 Bruker Daltonics micrOTOF series

Table 1431. Term [MS:1001536]
id	MS:1001536
name	Bruker Daltonics micrOTOF series
def	"Bruker Daltonics' micrOTOF series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1430. MS:1001537 BioTOF

Table 1432. Term [MS:1001537]
id	MS:1001537
name	BioTOF
def	"Bruker Daltonics' BioTOF: ESI TOF." [PSI:MS]
is_a	MS:1001535 Bruker Daltonics BioTOF series ! Bruker Daltonics BioTOF series

2.1431. MS:1001538 BioTOF III

Table 1433. Term [MS:1001538]
id	MS:1001538
name	BioTOF III
def	"Bruker Daltonics' BioTOF III: ESI TOF." [PSI:MS]
is_a	MS:1001535 Bruker Daltonics BioTOF series ! Bruker Daltonics BioTOF series

2.1432. MS:1001539 UltroTOF-Q

Table 1434. Term [MS:1001539]
id	MS:1001539
name	UltroTOF-Q
def	"Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional)." [PSI:MS]
is_a	MS:1001535 Bruker Daltonics BioTOF series ! Bruker Daltonics BioTOF series

2.1433. MS:1001540 micrOTOF II

Table 1435. Term [MS:1001540]
id	MS:1001540
name	micrOTOF II
def	"Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.1434. MS:1001541 maXis

Table 1436. Term [MS:1001541]
id	MS:1001541
name	maXis
def	"Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS]
is_a	MS:1001547 Bruker Daltonics maXis series ! Bruker Daltonics maXis series

2.1435. MS:1001542 amaZon ETD

Table 1437. Term [MS:1001542]
id	MS:1001542
name	amaZon ETD
def	"Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR." [PSI:MS]
is_a	MS:1001545 Bruker Daltonics amaZon series ! Bruker Daltonics amaZon series

2.1436. MS:1001543 microflex LRF

Table 1438. Term [MS:1001543]
id	MS:1001543
name	microflex LRF
def	"Bruker Daltonics' microflex LRF: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1437. MS:1001544 ultrafleXtreme

Table 1439. Term [MS:1001544]
id	MS:1001544
name	ultrafleXtreme
def	"Bruker Daltonics' ultrafleXtreme: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1438. MS:1001545 Bruker Daltonics amaZon series

Table 1440. Term [MS:1001545]
id	MS:1001545
name	Bruker Daltonics amaZon series
def	"Bruker Daltonics' amaZon series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1439. MS:1001546 amaZon X

Table 1441. Term [MS:1001546]
id	MS:1001546
name	amaZon X
def	"Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS]
is_a	MS:1001545 Bruker Daltonics amaZon series ! Bruker Daltonics amaZon series

2.1440. MS:1001547 Bruker Daltonics maXis series

Table 1442. Term [MS:1001547]
id	MS:1001547
name	Bruker Daltonics maXis series
def	"Bruker Daltonics' maXis series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1441. MS:1001548 Bruker Daltonics solarix series

Table 1443. Term [MS:1001548]
id	MS:1001548
name	Bruker Daltonics solarix series
def	"Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1442. MS:1001549 solariX

Table 1444. Term [MS:1001549]
id	MS:1001549
name	solariX
def	"Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR." [PSI:MS]
is_a	MS:1001548 Bruker Daltonics solarix series ! Bruker Daltonics solarix series

2.1443. MS:1001550 microflex II

Table 1445. Term [MS:1001550]
id	MS:1001550
name	microflex II
def	"Bruker Daltonics' microflex II: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1444. MS:1001553 autoflex II TOF/TOF

Table 1446. Term [MS:1001553]
id	MS:1001553
name	autoflex II TOF/TOF
def	"Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1445. MS:1001554 autoflex III TOF/TOF smartbeam

Table 1447. Term [MS:1001554]
id	MS:1001554
name	autoflex III TOF/TOF smartbeam
def	"Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1446. MS:1001555 autoflex

Table 1448. Term [MS:1001555]
id	MS:1001555
name	autoflex
def	"Bruker Daltonics' autoflex: MALDI TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.1447. MS:1001556 Bruker Daltonics apex series

Table 1449. Term [MS:1001556]
id	MS:1001556
name	Bruker Daltonics apex series
def	"Bruker Daltonics' apex series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.1448. MS:1001557 Shimadzu Corporation software

Table 1450. Term [MS:1001557]
id	MS:1001557
name	Shimadzu Corporation software
def	"Shimadzu Corporation software." [PSI:MS]
is_a	MS:1000531 software ! software

2.1449. MS:1001558 MALDI Solutions

Table 1451. Term [MS:1001558]
id	MS:1001558
name	MALDI Solutions
def	"Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS]
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software
is_a	MS:1001557 Shimadzu Corporation software ! Shimadzu Corporation software

2.1450. MS:1001559 SCIEX TOF/TOF T2D nativeID format

Table 1452. Term [MS:1001559]
id	MS:1001559
name	SCIEX TOF/TOF T2D nativeID format
def	"Native format defined by file=xsd:IDREF." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.1451. MS:1001560 SCIEX TOF/TOF T2D format

Table 1453. Term [MS:1001560]
id	MS:1001560
name	SCIEX TOF/TOF T2D format
def	"Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1452. MS:1001561 Scaffold

Table 1454. Term [MS:1001561]
id	MS:1001561
name	Scaffold
def	"Scaffold analysis software." [http://www.proteomesoftware.com]
is_a	MS:1001456 analysis software ! analysis software

2.1453. MS:1001562 Scaffold nativeID format

Table 1455. Term [MS:1001562]
id	MS:1001562
name	Scaffold nativeID format
def	"Scaffold native ID format." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.1454. MS:1001563 SEQUEST SQT format

Table 1456. Term [MS:1001563]
id	MS:1001563
name	SEQUEST SQT format
def	"Source file for this mzIdentML was in SEQUEST SQT format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1455. MS:1001564 Discoverer MSF format

Table 1457. Term [MS:1001564]
id	MS:1001564
name	Discoverer MSF format
def	"Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1456. MS:1001565 IdentityE XML format

Table 1458. Term [MS:1001565]
id	MS:1001565
name	IdentityE XML format
def	"Source file for this mzIdentML was in Waters IdentityE XML format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1457. MS:1001566 ProteinLynx XML format

Table 1459. Term [MS:1001566]
id	MS:1001566
name	ProteinLynx XML format
def	"Source file for this mzIdentML was in Waters ProteinLynx XML format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1458. MS:1001567 SpectrumMill directories

Table 1460. Term [MS:1001567]
id	MS:1001567
name	SpectrumMill directories
def	"Source file for this mzIdentML was in Agilent SpectrumMill directory format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1459. MS:1001568 Scaffold:Peptide Probability

Table 1461. Term [MS:1001568]
id	MS:1001568
name	Scaffold:Peptide Probability
def	"Scaffold peptide probability score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1460. MS:1001569 IdentityE Score

Table 1462. Term [MS:1001569]
id	MS:1001569
name	IdentityE Score
def	"Waters IdentityE peptide score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1461. MS:1001570 ProteinLynx:Log Likelihood

Table 1463. Term [MS:1001570]
id	MS:1001570
name	ProteinLynx:Log Likelihood
def	"ProteinLynx log likelihood score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1462. MS:1001571 ProteinLynx:Ladder Score

Table 1464. Term [MS:1001571]
id	MS:1001571
name	ProteinLynx:Ladder Score
def	"Waters ProteinLynx Ladder score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1463. MS:1001572 SpectrumMill:Score

Table 1465. Term [MS:1001572]
id	MS:1001572
name	SpectrumMill:Score
def	"Spectrum mill peptide score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1464. MS:1001573 SpectrumMill:SPI

Table 1466. Term [MS:1001573]
id	MS:1001573
name	SpectrumMill:SPI
def	"SpectrumMill SPI score (%)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1465. MS:1001574 report only spectra assigned to identified proteins

Table 1467. Term [MS:1001574]
id	MS:1001574
name	report only spectra assigned to identified proteins
def	"Flag indicating to report only the spectra assigned to identified proteins." [PSI:PI]
is_a	MS:1001060 quality estimation method details ! quality estimation method details

2.1466. MS:1001575 Scaffold: Minimum Peptide Count

Table 1468. Term [MS:1001575]
id	MS:1001575
name	Scaffold: Minimum Peptide Count
def	"Minimum number of peptides a protein must have to be accepted." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002106 Scaffold input parameter ! Scaffold input parameter

2.1467. MS:1001576 Scaffold: Minimum Protein Probability

Table 1469. Term [MS:1001576]
id	MS:1001576
name	Scaffold: Minimum Protein Probability
def	"Minimum protein probability a protein must have to be accepted." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002106 Scaffold input parameter ! Scaffold input parameter

2.1468. MS:1001577 Scaffold: Minimum Peptide Probability

Table 1470. Term [MS:1001577]
id	MS:1001577
name	Scaffold: Minimum Peptide Probability
def	"Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002106 Scaffold input parameter ! Scaffold input parameter

2.1469. MS:1001578 minimum number of enzymatic termini

Table 1471. Term [MS:1001578]
id	MS:1001578
name	minimum number of enzymatic termini
def	"Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1002094 common search engine input parameter ! common search engine input parameter

2.1470. MS:1001579 Scaffold:Protein Probability

Table 1472. Term [MS:1001579]
id	MS:1001579
name	Scaffold:Protein Probability
def	"Scaffold protein probability score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1471. MS:1001580 SpectrumMill:Discriminant Score

Table 1473. Term [MS:1001580]
id	MS:1001580
name	SpectrumMill:Discriminant Score
def	"Discriminant score from Agilent SpectrumMill software." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1472. MS:1001581 FAIMS compensation voltage

Table 1474. Term [MS:1001581]
id	MS:1001581
name	FAIMS compensation voltage
def	"The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
synonym	"FAIMS CV" EXACT []
is_a	MS:1002892 ion mobility attribute ! ion mobility attribute
relationship	has_units [UO:0000218] ! volt

2.1473. MS:1001582 XCMS

Table 1475. Term [MS:1001582]
id	MS:1001582
name	XCMS
def	"Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1474. MS:1001583 MaxQuant

Table 1476. Term [MS:1001583]
id	MS:1001583
name	MaxQuant
def	"MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software

2.1475. MS:1001584 combined pmf + ms-ms search

Table 1477. Term [MS:1001584]
id	MS:1001584
name	combined pmf + ms-ms search
def	"Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF)." [PSI:MS]
is_a	MS:1001080 search type ! search type

2.1476. MS:1001585 MyriMatch

Table 1478. Term [MS:1001585]
id	MS:1001585
name	MyriMatch
def	"Tabb Lab software for directly comparing peptides in a database to tandem mass spectra." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1477. MS:1001586 DirecTag

Table 1479. Term [MS:1001586]
id	MS:1001586
name	DirecTag
def	"Tabb Lab software for generating sequence tags from tandem mass spectra." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1478. MS:1001587 TagRecon

Table 1480. Term [MS:1001587]
id	MS:1001587
name	TagRecon
def	"Tabb Lab software for reconciling sequence tags to a protein database." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1479. MS:1001588 Pepitome

Table 1481. Term [MS:1001588]
id	MS:1001588
name	Pepitome
def	"Tabb Lab software for spectral library searches on tandem mass spectra." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1480. MS:1001589 MyriMatch:MVH

Table 1482. Term [MS:1001589]
id	MS:1001589
name	MyriMatch:MVH
def	"Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance." [PSI:MS]
synonym	"Pepitome:MVH" EXACT []
synonym	"TagRecon:MVH" EXACT []
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1481. MS:1001590 MyriMatch:mzFidelity

Table 1483. Term [MS:1001590]
id	MS:1001590
name	MyriMatch:mzFidelity
def	"The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution." [PSI:MS]
synonym	"Pepitome:mzFidelity" EXACT []
synonym	"TagRecon:mzFidelity" EXACT []
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1482. MS:1001591 anchor protein

Table 1484. Term [MS:1001591]
id	MS:1001591
name	anchor protein
def	"A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1483. MS:1001592 family member protein

Table 1485. Term [MS:1001592]
id	MS:1001592
name	family member protein
def	"A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1484. MS:1001593 group member with undefined relationship OR ortholog protein

Table 1486. Term [MS:1001593]
id	MS:1001593
name	group member with undefined relationship OR ortholog protein
def	"TO ENDETAIL: a really generic relationship OR ortholog protein." [PSI:MS]
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1485. MS:1001594 sequence same-set protein

Table 1487. Term [MS:1001594]
id	MS:1001594
name	sequence same-set protein
def	"A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1486. MS:1001595 spectrum same-set protein

Table 1488. Term [MS:1001595]
id	MS:1001595
name	spectrum same-set protein
def	"A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1487. MS:1001596 sequence sub-set protein

Table 1489. Term [MS:1001596]
id	MS:1001596
name	sequence sub-set protein
def	"A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1488. MS:1001597 spectrum sub-set protein

Table 1490. Term [MS:1001597]
id	MS:1001597
name	spectrum sub-set protein
def	"A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1489. MS:1001598 sequence subsumable protein

Table 1491. Term [MS:1001598]
id	MS:1001598
name	sequence subsumable protein
def	"A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1490. MS:1001599 spectrum subsumable protein

Table 1492. Term [MS:1001599]
id	MS:1001599
name	spectrum subsumable protein
def	"A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1491. MS:1001600 protein inference confidence category

Table 1493. Term [MS:1001600]
id	MS:1001600
name	protein inference confidence category
def	"Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.1492. MS:1001601 ProteomeDiscoverer:Spectrum Files:Raw File names

Table 1494. Term [MS:1001601]
id	MS:1001601
name	ProteomeDiscoverer:Spectrum Files:Raw File names
def	"OBSOLETE Name and location of the .raw file or files." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1493. MS:1001602 ProteomeDiscoverer:SRF File Selector:SRF File Path

Table 1495. Term [MS:1001602]
id	MS:1001602
name	ProteomeDiscoverer:SRF File Selector:SRF File Path
def	"OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS]
comment	This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1494. MS:1001603 ProteomeDiscoverer:Spectrum Selector:Ionization Source

Table 1496. Term [MS:1001603]
id	MS:1001603
name	ProteomeDiscoverer:Spectrum Selector:Ionization Source
def	"OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1495. MS:1001604 ProteomeDiscoverer:Activation Type

Table 1497. Term [MS:1001604]
id	MS:1001604
name	ProteomeDiscoverer:Activation Type
def	"OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use one of the 'ionization type' terms (MS:1000008) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1496. MS:1001605 ProteomeDiscoverer:Spectrum Selector:Lower RT Limit

Table 1498. Term [MS:1001605]
id	MS:1001605
name	ProteomeDiscoverer:Spectrum Selector:Lower RT Limit
def	"Lower retention-time limit." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1497. MS:1001606 ProteomeDiscoverer:Mass Analyzer

Table 1499. Term [MS:1001606]
id	MS:1001606
name	ProteomeDiscoverer:Mass Analyzer
def	"OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use mass analyzer type (MS:1000443) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1498. MS:1001607 ProteomeDiscoverer:Max Precursor Mass

Table 1500. Term [MS:1001607]
id	MS:1001607
name	ProteomeDiscoverer:Max Precursor Mass
def	"Maximum mass limit of a singly charged precursor ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1499. MS:1001608 ProteomeDiscoverer:Min Precursor Mass

Table 1501. Term [MS:1001608]
id	MS:1001608
name	ProteomeDiscoverer:Min Precursor Mass
def	"Minimum mass limit of a singly charged precursor ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1500. MS:1001609 ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count

Table 1502. Term [MS:1001609]
id	MS:1001609
name	ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
def	"Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1501. MS:1001610 ProteomeDiscoverer:MS Order

Table 1503. Term [MS:1001610]
id	MS:1001610
name	ProteomeDiscoverer:MS Order
def	"OBSOLETE Level of the mass spectrum (MS2 … MS10)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1502. MS:1001611 ProteomeDiscoverer:Polarity Mode

Table 1504. Term [MS:1001611]
id	MS:1001611
name	ProteomeDiscoverer:Polarity Mode
def	"OBSOLETE Polarity mode (positive or negative)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use scan polarity (MS:1000465) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1503. MS:1001612 ProteomeDiscoverer:Spectrum Selector:Precursor Selection

Table 1505. Term [MS:1001612]
id	MS:1001612
name	ProteomeDiscoverer:Spectrum Selector:Precursor Selection
def	"Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1504. MS:1001613 ProteomeDiscoverer:SN Threshold

Table 1506. Term [MS:1001613]
id	MS:1001613
name	ProteomeDiscoverer:SN Threshold
def	"Signal-to-Noise ratio below which peaks are removed." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1505. MS:1001614 ProteomeDiscoverer:Scan Type

Table 1507. Term [MS:1001614]
id	MS:1001614
name	ProteomeDiscoverer:Scan Type
def	"OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1506. MS:1001615 ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold

Table 1508. Term [MS:1001615]
id	MS:1001615
name	ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
def	"Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1507. MS:1001616 ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements

Table 1509. Term [MS:1001616]
id	MS:1001616
name	ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements
def	"Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1508. MS:1001617 ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements

Table 1510. Term [MS:1001617]
id	MS:1001617
name	ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements
def	"Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1509. MS:1001618 ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements

Table 1511. Term [MS:1001618]
id	MS:1001618
name	ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements
def	"Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1510. MS:1001619 ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements

Table 1512. Term [MS:1001619]
id	MS:1001619
name	ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements
def	"Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1511. MS:1001620 ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements

Table 1513. Term [MS:1001620]
id	MS:1001620
name	ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements
def	"Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1512. MS:1001621 ProteomeDiscoverer:Spectrum Selector:Upper RT Limit

Table 1514. Term [MS:1001621]
id	MS:1001621
name	ProteomeDiscoverer:Spectrum Selector:Upper RT Limit
def	"Upper retention-time limit." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1513. MS:1001622 ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset

Table 1515. Term [MS:1001622]
id	MS:1001622
name	ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset
def	"Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1514. MS:1001623 ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass

Table 1516. Term [MS:1001623]
id	MS:1001623
name	ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass
def	"Maximum allowed mass of a neutral loss." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1515. MS:1001624 ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor

Table 1517. Term [MS:1001624]
id	MS:1001624
name	ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor
def	"Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1516. MS:1001625 ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks

Table 1518. Term [MS:1001625]
id	MS:1001625
name	ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks
def	"Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1517. MS:1001626 ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses

Table 1519. Term [MS:1001626]
id	MS:1001626
name	ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses
def	"Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1518. MS:1001627 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones

Table 1520. Term [MS:1001627]
id	MS:1001627
name	ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones
def	"Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1519. MS:1001628 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak

Table 1521. Term [MS:1001628]
id	MS:1001628
name	ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak
def	"Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1520. MS:1001629 ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch

Table 1522. Term [MS:1001629]
id	MS:1001629
name	ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch
def	"Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1521. MS:1001630 ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch

Table 1523. Term [MS:1001630]
id	MS:1001630
name	ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch
def	"Determines whether spectra from different MS order scans can be grouped together." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1522. MS:1001631 ProteomeDiscoverer:Spectrum Grouper:Max RT Difference

Table 1524. Term [MS:1001631]
id	MS:1001631
name	ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
def	"OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use retention time window width (MS:1001907) instead.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1523. MS:1001632 ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion

Table 1525. Term [MS:1001632]
id	MS:1001632
name	ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion
def	"Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1524. MS:1001633 ProteomeDiscoverer:Xtract:Highest Charge

Table 1526. Term [MS:1001633]
id	MS:1001633
name	ProteomeDiscoverer:Xtract:Highest Charge
def	"Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1525. MS:1001634 ProteomeDiscoverer:Xtract:Highest MZ

Table 1527. Term [MS:1001634]
id	MS:1001634
name	ProteomeDiscoverer:Xtract:Highest MZ
def	"OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use scan window upper limit (MS:1000500) instead.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1526. MS:1001635 ProteomeDiscoverer:Xtract:Lowest Charge

Table 1528. Term [MS:1001635]
id	MS:1001635
name	ProteomeDiscoverer:Xtract:Lowest Charge
def	"Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1527. MS:1001636 ProteomeDiscoverer:Xtract:Lowest MZ

Table 1529. Term [MS:1001636]
id	MS:1001636
name	ProteomeDiscoverer:Xtract:Lowest MZ
def	"OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use scan window lower limit (MS:1000501) instead.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1528. MS:1001637 ProteomeDiscoverer:Xtract:Monoisotopic Mass Only

Table 1530. Term [MS:1001637]
id	MS:1001637
name	ProteomeDiscoverer:Xtract:Monoisotopic Mass Only
def	"Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1529. MS:1001638 ProteomeDiscoverer:Xtract:Overlapping Remainder

Table 1531. Term [MS:1001638]
id	MS:1001638
name	ProteomeDiscoverer:Xtract:Overlapping Remainder
def	"Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1530. MS:1001639 ProteomeDiscoverer:Xtract:Required Fitting Accuracy

Table 1532. Term [MS:1001639]
id	MS:1001639
name	ProteomeDiscoverer:Xtract:Required Fitting Accuracy
def	"Accuracy required for a pattern fit to be considered valid." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1531. MS:1001640 ProteomeDiscoverer:Xtract:Resolution At 400

Table 1533. Term [MS:1001640]
id	MS:1001640
name	ProteomeDiscoverer:Xtract:Resolution At 400
def	"Resolution at mass 400." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1532. MS:1001641 ProteomeDiscoverer:Lowest Charge State

Table 1534. Term [MS:1001641]
id	MS:1001641
name	ProteomeDiscoverer:Lowest Charge State
def	"Minimum charge state below which peptides are filtered out." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1533. MS:1001642 ProteomeDiscoverer:Highest Charge State

Table 1535. Term [MS:1001642]
id	MS:1001642
name	ProteomeDiscoverer:Highest Charge State
def	"Maximum charge above which peptides are filtered out." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1534. MS:1001643 ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores

Table 1536. Term [MS:1001643]
id	MS:1001643
name	ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores
def	"Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1535. MS:1001644 ProteomeDiscoverer:Dynamic Modification

Table 1537. Term [MS:1001644]
id	MS:1001644
name	ProteomeDiscoverer:Dynamic Modification
def	"Determine dynamic post-translational modifications (PTMs)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1536. MS:1001645 ProteomeDiscoverer:Static Modification

Table 1538. Term [MS:1001645]
id	MS:1001645
name	ProteomeDiscoverer:Static Modification
def	"Static Modification to all occurrences of a named amino acid." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1537. MS:1001646 ProteomeDiscoverer:Mascot:Decoy Search

Table 1539. Term [MS:1001646]
id	MS:1001646
name	ProteomeDiscoverer:Mascot:Decoy Search
def	"OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use quality estimation with decoy database (MS:1001194) instead.
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1538. MS:1001647 ProteomeDiscoverer:Mascot:Error tolerant Search

Table 1540. Term [MS:1001647]
id	MS:1001647
name	ProteomeDiscoverer:Mascot:Error tolerant Search
def	"Determines whether to search error-tolerant." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1539. MS:1001648 ProteomeDiscoverer:Mascot:Max MGF File Size

Table 1541. Term [MS:1001648]
id	MS:1001648
name	ProteomeDiscoverer:Mascot:Max MGF File Size
def	"Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1540. MS:1001649 ProteomeDiscoverer:Mascot:Mascot Server URL

Table 1542. Term [MS:1001649]
id	MS:1001649
name	ProteomeDiscoverer:Mascot:Mascot Server URL
def	"URL (Uniform resource Locator) of the Mascot server." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1541. MS:1001650 ProteomeDiscoverer:Mascot:Number of attempts to submit the search

Table 1543. Term [MS:1001650]
id	MS:1001650
name	ProteomeDiscoverer:Mascot:Number of attempts to submit the search
def	"Number of attempts to submit the Mascot search." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1542. MS:1001651 ProteomeDiscoverer:Mascot:X Static Modification

Table 1544. Term [MS:1001651]
id	MS:1001651
name	ProteomeDiscoverer:Mascot:X Static Modification
def	"Number of attempts to submit the Mascot search." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1543. MS:1001652 ProteomeDiscoverer:Mascot:User Name

Table 1545. Term [MS:1001652]
id	MS:1001652
name	ProteomeDiscoverer:Mascot:User Name
def	"OBSOLETE Name of the user submitting the Mascot search." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use researcher (MS:1001271) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1544. MS:1001653 ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search

Table 1546. Term [MS:1001653]
id	MS:1001653
name	ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search
def	"Time interval between attempts to submit a search in seconds." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1545. MS:1001654 ProteomeDiscoverer:Enzyme Name

Table 1547. Term [MS:1001654]
id	MS:1001654
name	ProteomeDiscoverer:Enzyme Name
def	"OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use cleavage agent name (MS:1001045) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1546. MS:1001655 ProteomeDiscoverer:Fragment Mass Tolerance

Table 1548. Term [MS:1001655]
id	MS:1001655
name	ProteomeDiscoverer:Fragment Mass Tolerance
def	"OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1547. MS:1001656 Mascot:Instrument

Table 1549. Term [MS:1001656]
id	MS:1001656
name	Mascot:Instrument
def	"Type of instrument used to acquire the data in the raw file." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1548. MS:1001657 ProteomeDiscoverer:Maximum Missed Cleavage Sites

Table 1550. Term [MS:1001657]
id	MS:1001657
name	ProteomeDiscoverer:Maximum Missed Cleavage Sites
def	"Maximum number of missed cleavage sites to consider during the digest." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1549. MS:1001658 ProteomeDiscoverer:Mascot:Peptide CutOff Score

Table 1551. Term [MS:1001658]
id	MS:1001658
name	ProteomeDiscoverer:Mascot:Peptide CutOff Score
def	"Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1550. MS:1001659 ProteomeDiscoverer:Precursor Mass Tolerance

Table 1552. Term [MS:1001659]
id	MS:1001659
name	ProteomeDiscoverer:Precursor Mass Tolerance
def	"OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead.
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1551. MS:1001660 ProteomeDiscoverer:Mascot:Protein CutOff Score

Table 1553. Term [MS:1001660]
id	MS:1001660
name	ProteomeDiscoverer:Mascot:Protein CutOff Score
def	"Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1552. MS:1001661 ProteomeDiscoverer:Protein Database

Table 1554. Term [MS:1001661]
id	MS:1001661
name	ProteomeDiscoverer:Protein Database
def	"OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use database name (MS:1001013) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1553. MS:1001662 ProteomeDiscoverer:Mascot:Protein Relevance Factor

Table 1555. Term [MS:1001662]
id	MS:1001662
name	ProteomeDiscoverer:Mascot:Protein Relevance Factor
def	"Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1554. MS:1001663 ProteomeDiscoverer:Target FDR Relaxed

Table 1556. Term [MS:1001663]
id	MS:1001663
name	ProteomeDiscoverer:Target FDR Relaxed
def	"Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1555. MS:1001664 ProteomeDiscoverer:Target FDR Strict

Table 1557. Term [MS:1001664]
id	MS:1001664
name	ProteomeDiscoverer:Target FDR Strict
def	"Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1556. MS:1001665 ProteomeDiscoverer:Mascot:Taxonomy

Table 1558. Term [MS:1001665]
id	MS:1001665
name	ProteomeDiscoverer:Mascot:Taxonomy
def	"OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use taxonomy: scientific name (MS:1001469) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1557. MS:1001666 ProteomeDiscoverer:Use Average Precursor Mass

Table 1559. Term [MS:1001666]
id	MS:1001666
name	ProteomeDiscoverer:Use Average Precursor Mass
def	"OBSOLETE Use average mass for the precursor." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use parent mass type average (MS:1001212) instead.
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1558. MS:1001667 Mascot:use MudPIT scoring

Table 1560. Term [MS:1001667]
id	MS:1001667
name	Mascot:use MudPIT scoring
def	"OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead.
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter
is_obsolete	true

2.1559. MS:1001668 ProteomeDiscoverer:Absolute XCorr Threshold

Table 1561. Term [MS:1001668]
id	MS:1001668
name	ProteomeDiscoverer:Absolute XCorr Threshold
def	"Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1560. MS:1001669 ProteomeDiscoverer:SEQUEST:Calculate Probability Score

Table 1562. Term [MS:1001669]
id	MS:1001669
name	ProteomeDiscoverer:SEQUEST:Calculate Probability Score
def	"Determines whether to calculate a probability score for every peptide match." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1561. MS:1001670 ProteomeDiscoverer:SEQUEST:CTerminal Modification

Table 1563. Term [MS:1001670]
id	MS:1001670
name	ProteomeDiscoverer:SEQUEST:CTerminal Modification
def	"Dynamic C-terminal modification that is used during the search." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1562. MS:1001671 ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage

Table 1564. Term [MS:1001671]
id	MS:1001671
name	ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage
def	"Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1563. MS:1001672 ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide

Table 1565. Term [MS:1001672]
id	MS:1001672
name	ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide
def	"Maximum number of identical modifications that a single peptide can have." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1564. MS:1001673 ProteomeDiscoverer:Max Modifications Per Peptide

Table 1566. Term [MS:1001673]
id	MS:1001673
name	ProteomeDiscoverer:Max Modifications Per Peptide
def	"Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1565. MS:1001674 ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered

Table 1567. Term [MS:1001674]
id	MS:1001674
name	ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered
def	"Maximum number of peptides that are searched and scored per spectrum." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1566. MS:1001675 ProteomeDiscoverer:Maximum Peptides Output

Table 1568. Term [MS:1001675]
id	MS:1001675
name	ProteomeDiscoverer:Maximum Peptides Output
def	"Maximum number of peptide matches reported per spectrum." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1567. MS:1001676 ProteomeDiscoverer:Maximum Protein References Per Peptide

Table 1569. Term [MS:1001676]
id	MS:1001676
name	ProteomeDiscoverer:Maximum Protein References Per Peptide
def	"Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1568. MS:1001677 ProteomeDiscoverer:SEQUEST:NTerminal Modification

Table 1570. Term [MS:1001677]
id	MS:1001677
name	ProteomeDiscoverer:SEQUEST:NTerminal Modification
def	"Dynamic N-terminal modification that is used during the search." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1569. MS:1001678 ProteomeDiscoverer:Peptide CTerminus

Table 1571. Term [MS:1001678]
id	MS:1001678
name	ProteomeDiscoverer:Peptide CTerminus
def	"Static modification for the C terminal of the peptide used during the search." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1570. MS:1001679 ProteomeDiscoverer:Peptide NTerminus

Table 1572. Term [MS:1001679]
id	MS:1001679
name	ProteomeDiscoverer:Peptide NTerminus
def	"Static modification for the N terminal of the peptide used during the search." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1571. MS:1001680 ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor

Table 1573. Term [MS:1001680]
id	MS:1001680
name	ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor
def	"Specifies a factor to apply to the protein score." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1572. MS:1001681 ProteomeDiscoverer:Protein Relevance Threshold

Table 1574. Term [MS:1001681]
id	MS:1001681
name	ProteomeDiscoverer:Protein Relevance Threshold
def	"Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1573. MS:1001682 ProteomeDiscoverer:Search Against Decoy Database

Table 1575. Term [MS:1001682]
id	MS:1001682
name	ProteomeDiscoverer:Search Against Decoy Database
def	"OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use quality estimation with decoy database (MS:1001194) instead.
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1574. MS:1001683 ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses

Table 1576. Term [MS:1001683]
id	MS:1001683
name	ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses
def	"Use average masses for the fragments." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1575. MS:1001684 ProteomeDiscoverer:Use Neutral Loss a Ions

Table 1577. Term [MS:1001684]
id	MS:1001684
name	ProteomeDiscoverer:Use Neutral Loss a Ions
def	"Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1576. MS:1001685 ProteomeDiscoverer:Use Neutral Loss b Ions

Table 1578. Term [MS:1001685]
id	MS:1001685
name	ProteomeDiscoverer:Use Neutral Loss b Ions
def	"Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1577. MS:1001686 ProteomeDiscoverer:Use Neutral Loss y Ions

Table 1579. Term [MS:1001686]
id	MS:1001686
name	ProteomeDiscoverer:Use Neutral Loss y Ions
def	"Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1578. MS:1001687 ProteomeDiscoverer:Use Neutral Loss z Ions

Table 1580. Term [MS:1001687]
id	MS:1001687
name	ProteomeDiscoverer:Use Neutral Loss z Ions
def	"Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1579. MS:1001688 ProteomeDiscoverer:SEQUEST:Weight of a Ions

Table 1581. Term [MS:1001688]
id	MS:1001688
name	ProteomeDiscoverer:SEQUEST:Weight of a Ions
def	"Uses a ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1580. MS:1001689 ProteomeDiscoverer:SEQUEST:Weight of b Ions

Table 1582. Term [MS:1001689]
id	MS:1001689
name	ProteomeDiscoverer:SEQUEST:Weight of b Ions
def	"Uses b ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1581. MS:1001690 ProteomeDiscoverer:SEQUEST:Weight of c Ions

Table 1583. Term [MS:1001690]
id	MS:1001690
name	ProteomeDiscoverer:SEQUEST:Weight of c Ions
def	"Uses c ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1582. MS:1001691 ProteomeDiscoverer:SEQUEST:Weight of d Ions

Table 1584. Term [MS:1001691]
id	MS:1001691
name	ProteomeDiscoverer:SEQUEST:Weight of d Ions
def	"Uses c ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1583. MS:1001692 ProteomeDiscoverer:SEQUEST:Weight of v Ions

Table 1585. Term [MS:1001692]
id	MS:1001692
name	ProteomeDiscoverer:SEQUEST:Weight of v Ions
def	"Uses c ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1584. MS:1001693 ProteomeDiscoverer:SEQUEST:Weight of w Ions

Table 1586. Term [MS:1001693]
id	MS:1001693
name	ProteomeDiscoverer:SEQUEST:Weight of w Ions
def	"Uses c ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1585. MS:1001694 ProteomeDiscoverer:SEQUEST:Weight of x Ions

Table 1587. Term [MS:1001694]
id	MS:1001694
name	ProteomeDiscoverer:SEQUEST:Weight of x Ions
def	"Uses x ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1586. MS:1001695 ProteomeDiscoverer:SEQUEST:Weight of y Ions

Table 1588. Term [MS:1001695]
id	MS:1001695
name	ProteomeDiscoverer:SEQUEST:Weight of y Ions
def	"Uses y ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1587. MS:1001696 ProteomeDiscoverer:SEQUEST:Weight of z Ions

Table 1589. Term [MS:1001696]
id	MS:1001696
name	ProteomeDiscoverer:SEQUEST:Weight of z Ions
def	"Uses z ions for spectrum matching with this relative factor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1588. MS:1001697 ProteomeDiscoverer:ZCore:Protein Score Cutoff

Table 1590. Term [MS:1001697]
id	MS:1001697
name	ProteomeDiscoverer:ZCore:Protein Score Cutoff
def	"Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1589. MS:1001698 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method

Table 1591. Term [MS:1001698]
id	MS:1001698
name	ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method
def	"Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1590. MS:1001699 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance

Table 1592. Term [MS:1001699]
id	MS:1001699
name	ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance
def	"Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1591. MS:1001700 ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method

Table 1593. Term [MS:1001700]
id	MS:1001700
name	ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method
def	"Quantitation method for isobarically labeled quantitation." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1592. MS:1001701 ProteomeDiscoverer:Spectrum Exporter:Export Format

Table 1594. Term [MS:1001701]
id	MS:1001701
name	ProteomeDiscoverer:Spectrum Exporter:Export Format
def	"OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1593. MS:1001702 ProteomeDiscoverer:Spectrum Exporter:File name

Table 1595. Term [MS:1001702]
id	MS:1001702
name	ProteomeDiscoverer:Spectrum Exporter:File name
def	"Name of the output file that contains the exported data." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1594. MS:1001703 ProteomeDiscoverer:Search Modifications Only For Identified Proteins

Table 1596. Term [MS:1001703]
id	MS:1001703
name	ProteomeDiscoverer:Search Modifications Only For Identified Proteins
def	"Influences the modifications search." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1595. MS:1001704 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1

Table 1597. Term [MS:1001704]
id	MS:1001704
name	ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1
def	"Standard high confidence XCorr parameter for charge = 1." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1596. MS:1001705 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2

Table 1598. Term [MS:1001705]
id	MS:1001705
name	ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2
def	"Standard high confidence XCorr parameter for charge = 2." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1597. MS:1001706 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3

Table 1599. Term [MS:1001706]
id	MS:1001706
name	ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3
def	"Standard high confidence XCorr parameter for charge = 3." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1598. MS:1001707 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4

Table 1600. Term [MS:1001707]
id	MS:1001707
name	ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4
def	"Standard high confidence XCorr parameter for charge >= 4." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1599. MS:1001708 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1

Table 1601. Term [MS:1001708]
id	MS:1001708
name	ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1
def	"Standard medium confidence XCorr parameter for charge = 1." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1600. MS:1001709 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2

Table 1602. Term [MS:1001709]
id	MS:1001709
name	ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2
def	"Standard medium confidence XCorr parameter for charge = 2." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1601. MS:1001710 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3

Table 1603. Term [MS:1001710]
id	MS:1001710
name	ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3
def	"Standard medium confidence XCorr parameter for charge = 3." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1602. MS:1001711 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4

Table 1604. Term [MS:1001711]
id	MS:1001711
name	ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4
def	"Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1603. MS:1001712 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1

Table 1605. Term [MS:1001712]
id	MS:1001712
name	ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
def	"FT high confidence XCorr parameter for charge = 1." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1604. MS:1001713 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2

Table 1606. Term [MS:1001713]
id	MS:1001713
name	ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
def	"FT high confidence XCorr parameter for charge = 2." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1605. MS:1001714 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3

Table 1607. Term [MS:1001714]
id	MS:1001714
name	ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
def	"FT high confidence XCorr parameter for charge = 3." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1606. MS:1001715 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4

Table 1608. Term [MS:1001715]
id	MS:1001715
name	ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
def	"FT high confidence XCorr parameter for charge >= 4." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1607. MS:1001716 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1

Table 1609. Term [MS:1001716]
id	MS:1001716
name	ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
def	"FT medium confidence XCorr parameter for charge = 1." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1608. MS:1001717 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2

Table 1610. Term [MS:1001717]
id	MS:1001717
name	ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
def	"FT medium confidence XCorr parameter for charge = 2." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1609. MS:1001718 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3

Table 1611. Term [MS:1001718]
id	MS:1001718
name	ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
def	"FT medium confidence XCorr parameter for charge = 3." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1610. MS:1001719 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4

Table 1612. Term [MS:1001719]
id	MS:1001719
name	ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
def	"FT medium confidence XCorr parameter for charge >= 4." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1611. MS:1001720 ProteomeDiscoverer:1. Dynamic Modification

Table 1613. Term [MS:1001720]
id	MS:1001720
name	ProteomeDiscoverer:1. Dynamic Modification
def	"OBSOLETE ProteomeDiscoverer’s 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1612. MS:1001721 ProteomeDiscoverer:2. Dynamic Modification

Table 1614. Term [MS:1001721]
id	MS:1001721
name	ProteomeDiscoverer:2. Dynamic Modification
def	"OBSOLETE ProteomeDiscoverer’s 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1613. MS:1001722 ProteomeDiscoverer:3. Dynamic Modification

Table 1615. Term [MS:1001722]
id	MS:1001722
name	ProteomeDiscoverer:3. Dynamic Modification
def	"OBSOLETE ProteomeDiscoverer’s 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1614. MS:1001723 ProteomeDiscoverer:4. Dynamic Modification

Table 1616. Term [MS:1001723]
id	MS:1001723
name	ProteomeDiscoverer:4. Dynamic Modification
def	"OBSOLETE ProteomeDiscoverer’s 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1615. MS:1001724 ProteomeDiscoverer:Static Modification for X

Table 1617. Term [MS:1001724]
id	MS:1001724
name	ProteomeDiscoverer:Static Modification for X
def	"Static Modification for X." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1616. MS:1001725 ProteomeDiscoverer:Initial minimal peptide probability

Table 1618. Term [MS:1001725]
id	MS:1001725
name	ProteomeDiscoverer:Initial minimal peptide probability
def	"Minimal initial peptide probability to contribute to analysis." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1617. MS:1001726 ProteomeDiscoverer:Minimal peptide probability

Table 1619. Term [MS:1001726]
id	MS:1001726
name	ProteomeDiscoverer:Minimal peptide probability
def	"Minimum adjusted peptide probability contributing to protein probability." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1618. MS:1001727 ProteomeDiscoverer:Minimal peptide weight

Table 1620. Term [MS:1001727]
id	MS:1001727
name	ProteomeDiscoverer:Minimal peptide weight
def	"Minimum peptide weight contributing to protein probability." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1619. MS:1001728 ProteomeDiscoverer:Number of input1 spectra

Table 1621. Term [MS:1001728]
id	MS:1001728
name	ProteomeDiscoverer:Number of input1 spectra
def	"Number of spectra from 1+ precursor ions." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1620. MS:1001729 ProteomeDiscoverer:Number of input2 spectra

Table 1622. Term [MS:1001729]
id	MS:1001729
name	ProteomeDiscoverer:Number of input2 spectra
def	"Number of spectra from 2+ precursor ions." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1621. MS:1001730 ProteomeDiscoverer:Number of input3 spectra

Table 1623. Term [MS:1001730]
id	MS:1001730
name	ProteomeDiscoverer:Number of input3 spectra
def	"Number of spectra from 3+ precursor ions." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1622. MS:1001731 ProteomeDiscoverer:Number of input4 spectra

Table 1624. Term [MS:1001731]
id	MS:1001731
name	ProteomeDiscoverer:Number of input4 spectra
def	"Number of spectra from 4+ precursor ions." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1623. MS:1001732 ProteomeDiscoverer:Number of input5 spectra

Table 1625. Term [MS:1001732]
id	MS:1001732
name	ProteomeDiscoverer:Number of input5 spectra
def	"Number of spectra from 5+ precursor ions." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1624. MS:1001733 ProteomeDiscoverer:Number of predicted correct proteins

Table 1626. Term [MS:1001733]
id	MS:1001733
name	ProteomeDiscoverer:Number of predicted correct proteins
def	"Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1625. MS:1001734 ProteomeDiscoverer:Organism

Table 1627. Term [MS:1001734]
id	MS:1001734
name	ProteomeDiscoverer:Organism
def	"OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use taxonomy: scientific name (MS:1001469) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1626. MS:1001735 ProteomeDiscoverer:Reference Database

Table 1628. Term [MS:1001735]
id	MS:1001735
name	ProteomeDiscoverer:Reference Database
def	"OBSOLETE Full path database name." [PSI:MS]
comment	This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1627. MS:1001736 ProteomeDiscoverer:Residue substitution list

Table 1629. Term [MS:1001736]
id	MS:1001736
name	ProteomeDiscoverer:Residue substitution list
def	"Residues considered equivalent when comparing peptides." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1628. MS:1001737 ProteomeDiscoverer:Source file extension

Table 1630. Term [MS:1001737]
id	MS:1001737
name	ProteomeDiscoverer:Source file extension
def	"OBSOLETE File type (if not pepXML)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use mass spectrometer file format (MS:1000560) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1629. MS:1001738 ProteomeDiscoverer:Source Files

Table 1631. Term [MS:1001738]
id	MS:1001738
name	ProteomeDiscoverer:Source Files
def	"OBSOLETE Input pepXML files." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use pepXML file (MS:1001421) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1630. MS:1001739 ProteomeDiscoverer:Source Files old

Table 1632. Term [MS:1001739]
id	MS:1001739
name	ProteomeDiscoverer:Source Files old
def	"OBSOLETE Input pepXML files (old)." [PSI:MS]
comment	This term was made obsolete because it’s recommended to use pepXML file (MS:1001421) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1631. MS:1001740 ProteomeDiscoverer:WinCyg reference database

Table 1633. Term [MS:1001740]
id	MS:1001740
name	ProteomeDiscoverer:WinCyg reference database
def	"Windows full path for database." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1632. MS:1001741 ProteomeDiscoverer:WinCyg source files

Table 1634. Term [MS:1001741]
id	MS:1001741
name	ProteomeDiscoverer:WinCyg source files
def	"Windows pepXML file names." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1633. MS:1001742 LTQ Orbitrap Velos

Table 1635. Term [MS:1001742]
id	MS:1001742
name	LTQ Orbitrap Velos
def	"Finnigan LTQ Orbitrap Velos MS." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1634. MS:1001743 ProteomeDiscoverer:Mascot:Weight of A Ions

Table 1636. Term [MS:1001743]
id	MS:1001743
name	ProteomeDiscoverer:Mascot:Weight of A Ions
def	"Determines if to use A ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1635. MS:1001744 ProteomeDiscoverer:Mascot:Weight of B Ions

Table 1637. Term [MS:1001744]
id	MS:1001744
name	ProteomeDiscoverer:Mascot:Weight of B Ions
def	"Determines if to use B ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1636. MS:1001745 ProteomeDiscoverer:Mascot:Weight of C Ions

Table 1638. Term [MS:1001745]
id	MS:1001745
name	ProteomeDiscoverer:Mascot:Weight of C Ions
def	"Determines if to use C ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1637. MS:1001746 ProteomeDiscoverer:Mascot:Weight of D Ions

Table 1639. Term [MS:1001746]
id	MS:1001746
name	ProteomeDiscoverer:Mascot:Weight of D Ions
def	"Determines if to use D ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1638. MS:1001747 ProteomeDiscoverer:Mascot:Weight of V Ions

Table 1640. Term [MS:1001747]
id	MS:1001747
name	ProteomeDiscoverer:Mascot:Weight of V Ions
def	"Determines if to use V ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1639. MS:1001748 ProteomeDiscoverer:Mascot:Weight of W Ions

Table 1641. Term [MS:1001748]
id	MS:1001748
name	ProteomeDiscoverer:Mascot:Weight of W Ions
def	"Determines if to use W ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1640. MS:1001749 ProteomeDiscoverer:Mascot:Weight of X Ions

Table 1642. Term [MS:1001749]
id	MS:1001749
name	ProteomeDiscoverer:Mascot:Weight of X Ions
def	"Determines if to use X ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1641. MS:1001750 ProteomeDiscoverer:Mascot:Weight of Y Ions

Table 1643. Term [MS:1001750]
id	MS:1001750
name	ProteomeDiscoverer:Mascot:Weight of Y Ions
def	"Determines if to use Y ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1642. MS:1001751 ProteomeDiscoverer:Mascot:Weight of Z Ions

Table 1644. Term [MS:1001751]
id	MS:1001751
name	ProteomeDiscoverer:Mascot:Weight of Z Ions
def	"Determines if to use z ions for spectrum matching." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1643. MS:1001752 ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation

Table 1645. Term [MS:1001752]
id	MS:1001752
name	ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation
def	"Determines if to use precursor reevaluation." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1644. MS:1001753 ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly

Table 1646. Term [MS:1001753]
id	MS:1001753
name	ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly
def	"Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1645. MS:1001754 ProteomeDiscoverer:Mascot:Please Do not Touch this

Table 1647. Term [MS:1001754]
id	MS:1001754
name	ProteomeDiscoverer:Mascot:Please Do not Touch this
def	"Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1646. MS:1001755 contact phone number

Table 1648. Term [MS:1001755]
id	MS:1001755
name	contact phone number
def	"Phone number of the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.1647. MS:1001756 contact fax number

Table 1649. Term [MS:1001756]
id	MS:1001756
name	contact fax number
def	"Fax number for the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.1648. MS:1001757 contact toll-free phone number

Table 1650. Term [MS:1001757]
id	MS:1001757
name	contact toll-free phone number
def	"Toll-free phone number of the contact person or organization." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000585 contact attribute ! contact attribute

2.1649. MS:1001758 Mascot:SigThresholdType

Table 1651. Term [MS:1001758]
id	MS:1001758
name	Mascot:SigThresholdType
def	"Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1650. MS:1001759 Mascot:ProteinGrouping

Table 1652. Term [MS:1001759]
id	MS:1001759
name	Mascot:ProteinGrouping
def	"Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam’s razor' or 'family clustering')." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1651. MS:1001760 Percolator:features

Table 1653. Term [MS:1001760]
id	MS:1001760
name	Percolator:features
def	"List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002107 Percolator input parameter ! Percolator input parameter

2.1652. MS:1001761 ACQUITY UPLC

Table 1654. Term [MS:1001761]
id	MS:1001761
name	ACQUITY UPLC
def	"Waters LC-system ACQUITY UPLC." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1653. MS:1001762 ACQUITY UPLC H-Class

Table 1655. Term [MS:1001762]
id	MS:1001762
name	ACQUITY UPLC H-Class
def	"Waters LC-system ACQUITY UPLC H-Class." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1654. MS:1001763 ACQUITY UPLC H-Class Bio

Table 1656. Term [MS:1001763]
id	MS:1001763
name	ACQUITY UPLC H-Class Bio
def	"Waters LC-system ACQUITY UPLC H-Class Bio." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1655. MS:1001764 ACQUITY UPLC I-Class

Table 1657. Term [MS:1001764]
id	MS:1001764
name	ACQUITY UPLC I-Class
def	"Waters LC-system ACQUITY UPLC I-Class." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1656. MS:1001765 ACQUITY UPLC Systems with 2D Technology

Table 1658. Term [MS:1001765]
id	MS:1001765
name	ACQUITY UPLC Systems with 2D Technology
def	"Waters LC-system ACQUITY UPLC Systems with 2D Technology." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1657. MS:1001766 nanoACQUITY UPLC

Table 1659. Term [MS:1001766]
id	MS:1001766
name	nanoACQUITY UPLC
def	"Waters LC-system nanoACQUITY UPLC." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1658. MS:1001767 nanoACQUITY UPLC System with 1D Technology

Table 1660. Term [MS:1001767]
id	MS:1001767
name	nanoACQUITY UPLC System with 1D Technology
def	"Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1659. MS:1001768 nanoACQUITY UPLC with HDX Technology

Table 1661. Term [MS:1001768]
id	MS:1001768
name	nanoACQUITY UPLC with HDX Technology
def	"Waters LC-system nanoACQUITY UPLC with HDX Technology." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1660. MS:1001769 TRIZAIC UPLC nanoTile

Table 1662. Term [MS:1001769]
id	MS:1001769
name	TRIZAIC UPLC nanoTile
def	"Waters LC-system TRIZAIC UPLC nanoTile." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1661. MS:1001770 GCT Premier

Table 1663. Term [MS:1001770]
id	MS:1001770
name	GCT Premier
def	"Waters oa-ToF based GCT Premier." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1662. MS:1001771 MALDI Synapt G2 HDMS

Table 1664. Term [MS:1001771]
id	MS:1001771
name	MALDI Synapt G2 HDMS
def	"Waters oa-ToF based MALDI Synapt G2 HDMS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1663. MS:1001772 MALDI Synapt G2 MS

Table 1665. Term [MS:1001772]
id	MS:1001772
name	MALDI Synapt G2 MS
def	"Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1664. MS:1001773 MALDI Synapt G2-S HDMS

Table 1666. Term [MS:1001773]
id	MS:1001773
name	MALDI Synapt G2-S HDMS
def	"Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1665. MS:1001774 MALDI Synapt G2-S MS

Table 1667. Term [MS:1001774]
id	MS:1001774
name	MALDI Synapt G2-S MS
def	"Waters oa-ToF based MALDI Synapt G2-S MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1666. MS:1001775 MALDI Synapt HDMS

Table 1668. Term [MS:1001775]
id	MS:1001775
name	MALDI Synapt HDMS
def	"Waters oa-ToF based MALDI Synapt HDMS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1667. MS:1001776 MALDI Synapt MS

Table 1669. Term [MS:1001776]
id	MS:1001776
name	MALDI Synapt MS
def	"Waters oa-ToF based MALDI Synapt MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1668. MS:1001777 Synapt G2 HDMS

Table 1670. Term [MS:1001777]
id	MS:1001777
name	Synapt G2 HDMS
def	"Waters oa-ToF based Synapt G2 HDMS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1669. MS:1001778 Synapt G2 MS

Table 1671. Term [MS:1001778]
id	MS:1001778
name	Synapt G2 MS
def	"Waters oa-ToF based Synapt G2 MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1670. MS:1001779 Synapt G2-S HDMS

Table 1672. Term [MS:1001779]
id	MS:1001779
name	Synapt G2-S HDMS
def	"Waters oa-ToF based Synapt G2-S HDMS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1671. MS:1001780 Synapt G2-S MS

Table 1673. Term [MS:1001780]
id	MS:1001780
name	Synapt G2-S MS
def	"Waters oa-ToF based Synapt G2-S MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1672. MS:1001781 Synapt HDMS

Table 1674. Term [MS:1001781]
id	MS:1001781
name	Synapt HDMS
def	"Waters oa-ToF based Synapt HDMS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1673. MS:1001782 Synapt MS

Table 1675. Term [MS:1001782]
id	MS:1001782
name	Synapt MS
def	"Waters oa-ToF based Synapt MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1674. MS:1001783 Xevo G2 Q-Tof

Table 1676. Term [MS:1001783]
id	MS:1001783
name	Xevo G2 Q-Tof
def	"Waters oa-ToF based Xevo G2 Q-Tof." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1675. MS:1001784 Xevo G2 Tof

Table 1677. Term [MS:1001784]
id	MS:1001784
name	Xevo G2 Tof
def	"Waters oa-ToF based Xevo G2 Tof." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1676. MS:1001785 Xevo Q-Tof

Table 1678. Term [MS:1001785]
id	MS:1001785
name	Xevo Q-Tof
def	"Waters oa-ToF based Xevo Q-Tof." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1677. MS:1001786 3100

Table 1679. Term [MS:1001786]
id	MS:1001786
name	3100
def	"Waters quadrupole based 3100." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1678. MS:1001787 Acquity SQD

Table 1680. Term [MS:1001787]
id	MS:1001787
name	Acquity SQD
def	"Waters quadrupole based Acquity SQD." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1679. MS:1001788 Acquity TQD

Table 1681. Term [MS:1001788]
id	MS:1001788
name	Acquity TQD
def	"Waters quadrupole based Acquity TQD." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1680. MS:1001789 Quattro micro GC

Table 1682. Term [MS:1001789]
id	MS:1001789
name	Quattro micro GC
def	"Waters (triple) quadrupole based Quattro micro GC." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1681. MS:1001790 Xevo TQ MS

Table 1683. Term [MS:1001790]
id	MS:1001790
name	Xevo TQ MS
def	"Waters quadrupole based Xevo TQ MS." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1682. MS:1001791 Xevo TQD

Table 1684. Term [MS:1001791]
id	MS:1001791
name	Xevo TQD
def	"Waters quadrupole based Xevo TQD." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1683. MS:1001792 Xevo TQ-S

Table 1685. Term [MS:1001792]
id	MS:1001792
name	Xevo TQ-S
def	"Waters quadrupole based Xevo TQ-S." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.1684. MS:1001793 Mascot:PreferredTaxonomy

Table 1686. Term [MS:1001793]
id	MS:1001793
name	Mascot:PreferredTaxonomy
def	"NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1685. MS:1001795 Empower

Table 1687. Term [MS:1001795]
id	MS:1001795
name	Empower
def	"Waters Empower software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]
is_a	MS:1000694 Waters software ! Waters software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1686. MS:1001796 UNIFY

Table 1688. Term [MS:1001796]
id	MS:1001796
name	UNIFY
def	"Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]
is_a	MS:1000694 Waters software ! Waters software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1687. MS:1001797 travelling wave ion mobility mass spectrometer

Table 1689. Term [MS:1001797]
id	MS:1001797
name	travelling wave ion mobility mass spectrometer
def	"OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
comment	This child of the former purgatory term ion mobility spectrometry was made obsolete.
synonym	"TWIMS" EXACT []
is_obsolete	true

2.1688. MS:1001798 LECO software

Table 1690. Term [MS:1001798]
id	MS:1001798
name	LECO software
def	"LECO software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.1689. MS:1001799 ChromaTOF software

Table 1691. Term [MS:1001799]
id	MS:1001799
name	ChromaTOF software
def	"Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS]
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software
is_a	MS:1001798 LECO software ! LECO software

2.1690. MS:1001800 LECO instrument model

Table 1692. Term [MS:1001800]
id	MS:1001800
name	LECO instrument model
def	"LECO instrument model." [PSI:MS]
is_a	MS:1000031 instrument model ! instrument model

2.1691. MS:1001801 Pegasus HRT

Table 1693. Term [MS:1001801]
id	MS:1001801
name	Pegasus HRT
def	"LECO high resolution time-of-flight GC mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.1692. MS:1001802 Citius HRT

Table 1694. Term [MS:1001802]
id	MS:1001802
name	Citius HRT
def	"LECO high resolution time-of-flight LC mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.1693. MS:1001803 Pegasus

Table 1695. Term [MS:1001803]
id	MS:1001803
name	Pegasus
def	"LECO GC time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.1694. MS:1001804 TruTOF

Table 1696. Term [MS:1001804]
id	MS:1001804
name	TruTOF
def	"LECO bench-top GC time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.1695. MS:1001805 quantification datatype

Table 1697. Term [MS:1001805]
id	MS:1001805
name	quantification datatype
def	"The data type of the value reported in a QuantLayer." [PSI:MS]
is_a	MS:1001129 quantification information ! quantification information

2.1696. MS:1001806 quantification object attribute

Table 1698. Term [MS:1001806]
id	MS:1001806
name	quantification object attribute
def	"Attributes describing the details of an object relevant for reporting quantification workflows or values." [PSI:MS]
is_a	MS:1001129 quantification information ! quantification information

2.1697. MS:1001807 study variable attribute

Table 1699. Term [MS:1001807]
id	MS:1001807
name	study variable attribute
def	"Attribute describing a study variable." [PSI:MS]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1698. MS:1001808 technical replicate

Table 1700. Term [MS:1001808]
id	MS:1001808
name	technical replicate
def	"The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1699. MS:1001809 biological replicate

Table 1701. Term [MS:1001809]
id	MS:1001809
name	biological replicate
def	"The study variable is 'biological replicate'. This means, the run was generated from another individual or sample." [PSI:MS]
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1700. MS:1001810 experimental condition 'case'

Table 1702. Term [MS:1001810]
id	MS:1001810
name	experimental condition 'case'
def	"The experimental condition is 'case' in contrast to 'control'." [PSI:MS]
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1701. MS:1001811 experimental condition 'control'

Table 1703. Term [MS:1001811]
id	MS:1001811
name	experimental condition 'control'
def	"The experimental condition is 'control' in contrast to 'case'." [PSI:MS]
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1702. MS:1001812 experimental condition 'disease'

Table 1704. Term [MS:1001812]
id	MS:1001812
name	experimental condition 'disease'
def	"The experimental condition is 'disease' in contrast to 'healthy'." [PSI:MS]
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1703. MS:1001813 experimental condition 'healthy'

Table 1705. Term [MS:1001813]
id	MS:1001813
name	experimental condition 'healthy'
def	"The experimental condition is 'healthy' in contrast to 'disease'." [PSI:MS]
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1704. MS:1001814 generic experimental condition

Table 1706. Term [MS:1001814]
id	MS:1001814
name	generic experimental condition
def	"The experimental condition is given in the value of this term." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1705. MS:1001815 time series, time point X

Table 1707. Term [MS:1001815]
id	MS:1001815
name	time series, time point X
def	"The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1706. MS:1001816 dilution series, concentration X

Table 1708. Term [MS:1001816]
id	MS:1001816
name	dilution series, concentration X
def	"The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001807 study variable attribute ! study variable attribute

2.1707. MS:1001817 raw file attribute

Table 1709. Term [MS:1001817]
id	MS:1001817
name	raw file attribute
def	"Attribute describing a raw file." [PSI:MS]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1708. MS:1001818 one sample run

Table 1710. Term [MS:1001818]
id	MS:1001818
name	one sample run
def	"The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free)." [PSI:MS]
is_a	MS:1001817 raw file attribute ! raw file attribute

2.1709. MS:1001819 two sample run

Table 1711. Term [MS:1001819]
id	MS:1001819
name	two sample run
def	"The raw file contains the run of two samples (e.g. SILAC, metabolic labelling)." [PSI:MS]
is_a	MS:1001817 raw file attribute ! raw file attribute

2.1710. MS:1001820 three sample run

Table 1712. Term [MS:1001820]
id	MS:1001820
name	three sample run
def	"The raw file contains the run of three samples (e.g. 3-plex SILAC)." [PSI:MS]
is_a	MS:1001817 raw file attribute ! raw file attribute

2.1711. MS:1001821 four sample run

Table 1713. Term [MS:1001821]
id	MS:1001821
name	four sample run
def	"The raw file contains the run of four samples (e.g. 4-plex iTraq)." [PSI:MS]
is_a	MS:1001817 raw file attribute ! raw file attribute

2.1712. MS:1001822 eight sample run

Table 1714. Term [MS:1001822]
id	MS:1001822
name	eight sample run
def	"The raw file contains the run of eight samples (e.g. 8-plex iTraq)." [PSI:MS]
is_a	MS:1001817 raw file attribute ! raw file attribute

2.1713. MS:1001823 raw files group attribute

Table 1715. Term [MS:1001823]
id	MS:1001823
name	raw files group attribute
def	"Attribute describing, how raw files build a raw file group." [PSI:MS]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1714. MS:1001824 merge of runs of 1D gel bands

Table 1716. Term [MS:1001824]
id	MS:1001824
name	merge of runs of 1D gel bands
def	"Attribute describing, how raw files build a raw file group." [PSI:MS]
is_a	MS:1001823 raw files group attribute ! raw files group attribute

2.1715. MS:1001825 feature list attribute

Table 1717. Term [MS:1001825]
id	MS:1001825
name	feature list attribute
def	"Attribute describing a feature list." [PSI:MS]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1716. MS:1001826 mass trace reporting: rectangles

Table 1718. Term [MS:1001826]
id	MS:1001826
name	mass trace reporting: rectangles
def	"The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given." [PSI:MS]
is_a	MS:1001825 feature list attribute ! feature list attribute

2.1717. MS:1001827 mass trace reporting: polygons

Table 1719. Term [MS:1001827]
id	MS:1001827
name	mass trace reporting: polygons
def	"The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, … , RT_i, MZ_i, … , RT_n, MZ_n), where the line (RT_n, MZ_n)→(RT_1, MZ_1) is implicit." [PSI:MS]
is_a	MS:1001825 feature list attribute ! feature list attribute

2.1718. MS:1001828 feature attribute

Table 1720. Term [MS:1001828]
id	MS:1001828
name	feature attribute
def	"Attribute describing a feature." [PSI:MS]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1719. MS:1001829 SRM transition ID

Table 1721. Term [MS:1001829]
id	MS:1001829
name	SRM transition ID
def	"Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001828 feature attribute ! feature attribute

2.1720. MS:1001830 Progenesis LC-MS

Table 1722. Term [MS:1001830]
id	MS:1001830
name	Progenesis LC-MS
def	"Software from Nonlinear Dynamics for LC-MS label-free workflow." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.1721. MS:1001831 SILACAnalyzer

Table 1723. Term [MS:1001831]
id	MS:1001831
name	SILACAnalyzer
def	"Software for SILAC workflow." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1000752 TOPP software ! TOPP software

2.1722. MS:1001832 quantitation software comment or customizations

Table 1724. Term [MS:1001832]
id	MS:1001832
name	quantitation software comment or customizations
def	"Quantitation software comment or any customizations to the default setup of the software." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001129 quantification information ! quantification information

2.1723. MS:1001833 quantitation analysis summary

Table 1725. Term [MS:1001833]
id	MS:1001833
name	quantitation analysis summary
def	"The overall workflow of this quantitation report." [PSI:PI]
is_a	MS:1001129 quantification information ! quantification information

2.1724. MS:1001834 LC-MS label-free quantitation analysis

Table 1726. Term [MS:1001834]
id	MS:1001834
name	LC-MS label-free quantitation analysis
def	"LC-MS label-free workflow (RT m/z map)." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1725. MS:1001835 SILAC quantitation analysis

Table 1727. Term [MS:1001835]
id	MS:1001835
name	SILAC quantitation analysis
def	"SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1726. MS:1001836 spectral counting quantitation analysis

Table 1728. Term [MS:1001836]
id	MS:1001836
name	spectral counting quantitation analysis
def	"Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant)." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1727. MS:1001837 iTRAQ quantitation analysis

Table 1729. Term [MS:1001837]
id	MS:1001837
name	iTRAQ quantitation analysis
def	"Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.1728. MS:1001838 SRM quantitation analysis

Table 1730. Term [MS:1001838]
id	MS:1001838
name	SRM quantitation analysis
def	"Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair)." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1729. MS:1001839 metabolic labeling 14N / 15N quantitation analysis

Table 1731. Term [MS:1001839]
id	MS:1001839
name	metabolic labeling 14N / 15N quantitation analysis
def	"Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1730. MS:1001840 LC-MS feature intensity

Table 1732. Term [MS:1001840]
id	MS:1001840
name	LC-MS feature intensity
def	"Maximum peak intensity of the LC-MS feature." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1731. MS:1001841 LC-MS feature volume

Table 1733. Term [MS:1001841]
id	MS:1001841
name	LC-MS feature volume
def	"Real (intensity times area) volume of the LC-MS feature." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1732. MS:1001842 sequence-level spectral count

Table 1734. Term [MS:1001842]
id	MS:1001842
name	sequence-level spectral count
def	"The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1733. MS:1001843 MS1 feature maximum intensity

Table 1735. Term [MS:1001843]
id	MS:1001843
name	MS1 feature maximum intensity
def	"Maximum intensity of MS1 feature." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1734. MS:1001844 MS1 feature area

Table 1736. Term [MS:1001844]
id	MS:1001844
name	MS1 feature area
def	"Area of MS1 feature." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1735. MS:1001845 peak area

Table 1737. Term [MS:1001845]
id	MS:1001845
name	peak area
def	"OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI]
comment	This term was made obsolete because it was a duplication of MS:1001844.
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype
is_obsolete	true

2.1736. MS:1001846 isotopic pattern area

Table 1738. Term [MS:1001846]
id	MS:1001846
name	isotopic pattern area
def	"Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1737. MS:1001847 reporter ion intensity

Table 1739. Term [MS:1001847]
id	MS:1001847
name	reporter ion intensity
def	"Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1738. MS:1001848 simple ratio of two values

Table 1740. Term [MS:1001848]
id	MS:1001848
name	simple ratio of two values
def	"Simple ratio of two values (enumerator and denominator)." [PSI:PI]
is_a	MS:1002066 ratio calculation method ! ratio calculation method

2.1739. MS:1001849 sum of MatchedFeature values

Table 1741. Term [MS:1001849]
id	MS:1001849
name	sum of MatchedFeature values
def	"OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI]
comment	This term was made obsolete because the concept MatchedFeature was dropped.
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype
is_obsolete	true

2.1740. MS:1001850 normalized peptide value

Table 1742. Term [MS:1001850]
id	MS:1001850
name	normalized peptide value
def	"Normalized peptide value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1741. MS:1001851 protein value: sum of peptide values

Table 1743. Term [MS:1001851]
id	MS:1001851
name	protein value: sum of peptide values
def	"Protein quantification value calculated as sum of peptide values." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1742. MS:1001852 normalized protein value

Table 1744. Term [MS:1001852]
id	MS:1001852
name	normalized protein value
def	"Normalized protein value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1743. MS:1001853 max fold change

Table 1745. Term [MS:1001853]
id	MS:1001853
name	max fold change
def	"Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1744. MS:1001854 ANOVA p-value

Table 1746. Term [MS:1001854]
id	MS:1001854
name	ANOVA p-value
def	"Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002072 p-value ! p-value

2.1745. MS:1001855 t-test p-value

Table 1747. Term [MS:1001855]
id	MS:1001855
name	t-test p-value
def	"P-value of t-Test of two groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002072 p-value ! p-value

2.1746. MS:1001856 reporter ion raw value

Table 1748. Term [MS:1001856]
id	MS:1001856
name	reporter ion raw value
def	"Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1747. MS:1001857 reporter ion normalized value

Table 1749. Term [MS:1001857]
id	MS:1001857
name	reporter ion normalized value
def	"Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1748. MS:1001858 XIC area

Table 1750. Term [MS:1001858]
id	MS:1001858
name	XIC area
def	"Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1749. MS:1001859 normalized XIC area

Table 1751. Term [MS:1001859]
id	MS:1001859
name	normalized XIC area
def	"Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1750. MS:1001860 protein value: mean of peptide ratios

Table 1752. Term [MS:1001860]
id	MS:1001860
name	protein value: mean of peptide ratios
def	"Protein quantification value calculated as mean of peptide ratios." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1751. MS:1001861 quantification data processing

Table 1753. Term [MS:1001861]
id	MS:1001861
name	quantification data processing
def	"Terms used to describe types of quantification data processing." [PSI:MS]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.1752. MS:1001862 normalization to mean of sum of all proteins

Table 1754. Term [MS:1001862]
id	MS:1001862
name	normalization to mean of sum of all proteins
def	"Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting)." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1753. MS:1001863 quantile normalization, proteins

Table 1755. Term [MS:1001863]
id	MS:1001863
name	quantile normalization, proteins
def	"Normalization of protein values to approach the same distribution." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1754. MS:1001864 quantile normalization, peptides

Table 1756. Term [MS:1001864]
id	MS:1001864
name	quantile normalization, peptides
def	"Normalization of peptide values to approach the same distribution." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1755. MS:1001865 Progenesis automatic alignment

Table 1757. Term [MS:1001865]
id	MS:1001865
name	Progenesis automatic alignment
def	"Automatic RT alignment of Progenesis software." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1756. MS:1001866 Progenesis manual alignment

Table 1758. Term [MS:1001866]
id	MS:1001866
name	Progenesis manual alignment
def	"RT alignment of Progenesis software using automatic and manual vectors." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1757. MS:1001867 Progenesis normalization

Table 1759. Term [MS:1001867]
id	MS:1001867
name	Progenesis normalization
def	"Normalization as performed by Progenesis LC-MS." [PSI:MS]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1758. MS:1001868 distinct peptide-level q-value

Table 1760. Term [MS:1001868]
id	MS:1001868
name	distinct peptide-level q-value
def	"Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002484 peptide-level statistical threshold ! peptide-level statistical threshold
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1759. MS:1001869 protein-level q-value

Table 1761. Term [MS:1001869]
id	MS:1001869
name	protein-level q-value
def	"Estimation of the q-value for proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1760. MS:1001870 peptide sequence-level p-value

Table 1762. Term [MS:1001870]
id	MS:1001870
name	peptide sequence-level p-value
def	"Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1761. MS:1001871 protein-level p-value

Table 1763. Term [MS:1001871]
id	MS:1001871
name	protein-level p-value
def	"Estimation of the p-value for proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1762. MS:1001872 peptide sequence-level e-value

Table 1764. Term [MS:1001872]
id	MS:1001872
name	peptide sequence-level e-value
def	"Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.1763. MS:1001873 protein-level e-value

Table 1765. Term [MS:1001873]
id	MS:1001873
name	protein-level e-value
def	"Estimation of the e-value for proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.1764. MS:1001874 FDRScore

Table 1766. Term [MS:1001874]
id	MS:1001874
name	FDRScore
def	"OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293]
comment	This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374).
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
is_obsolete	true

2.1765. MS:1001875 modification motif

Table 1767. Term [MS:1001875]
id	MS:1001875
name	modification motif
def	"The regular expression describing the sequence motif for a modification." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1766. MS:1001876 modification probability

Table 1768. Term [MS:1001876]
id	MS:1001876
name	modification probability
def	"The a priori probability of a modification." [PSI:PI]
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1767. MS:1001877 ChromaTOF HRT software

Table 1769. Term [MS:1001877]
id	MS:1001877
name	ChromaTOF HRT software
def	"Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS]
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software
is_a	MS:1001798 LECO software ! LECO software

2.1768. MS:1001878 MALDI Solutions Microbial Identification

Table 1770. Term [MS:1001878]
id	MS:1001878
name	MALDI Solutions Microbial Identification
def	"Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS]
is_a	MS:1001558 MALDI Solutions ! MALDI Solutions

2.1769. MS:1001879 offset voltage

Table 1771. Term [MS:1001879]
id	MS:1001879
name	offset voltage
def	"The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.1770. MS:1001880 in-source collision-induced dissociation

Table 1772. Term [MS:1001880]
id	MS:1001880
name	in-source collision-induced dissociation
def	"The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum." [PSI:MS]
is_a	MS:1000044 dissociation method ! dissociation method

2.1771. MS:1001881 mz5 format

Table 1773. Term [MS:1001881]
id	MS:1001881
name	mz5 format
def	"mz5 file format, modelled after mzML." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.1772. MS:1001882 transition validation attribute

Table 1774. Term [MS:1001882]
id	MS:1001882
name	transition validation attribute
def	"Attributes of the quality of a transition that affect its selection as appropriate." [PSI:MS]
relationship	part_of MS:1000908 transition ! transition

2.1773. MS:1001883 coefficient of variation

Table 1775. Term [MS:1001883]
id	MS:1001883
name	coefficient of variation
def	"Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1001882 transition validation attribute ! transition validation attribute

2.1774. MS:1001884 signal-to-noise ratio

Table 1776. Term [MS:1001884]
id	MS:1001884
name	signal-to-noise ratio
def	"Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1001882 transition validation attribute ! transition validation attribute

2.1775. MS:1001885 command-line parameters

Table 1777. Term [MS:1001885]
id	MS:1001885
name	command-line parameters
def	"Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter

2.1776. MS:1001886 SQID

Table 1778. Term [MS:1001886]
id	MS:1001886
name	SQID
def	"Software for data analysis of peptides and proteins." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1777. MS:1001887 SQID:score

Table 1779. Term [MS:1001887]
id	MS:1001887
name	SQID:score
def	"The SQID result 'Score'." [PSI:PI]
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1778. MS:1001888 SQID:deltaScore

Table 1780. Term [MS:1001888]
id	MS:1001888
name	SQID:deltaScore
def	"The SQID result 'deltaScore'." [PSI:PI]
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1779. MS:1001889 SQID:protein score

Table 1781. Term [MS:1001889]
id	MS:1001889
name	SQID:protein score
def	"The SQID result 'protein score'." [PSI:PI]
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1780. MS:1001890 Progenesis:protein normalised abundance

Table 1782. Term [MS:1001890]
id	MS:1001890
name	Progenesis:protein normalised abundance
def	"The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1781. MS:1001891 Progenesis:peptide normalised abundance

Table 1783. Term [MS:1001891]
id	MS:1001891
name	Progenesis:peptide normalised abundance
def	"The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1782. MS:1001892 Progenesis:protein raw abundance

Table 1784. Term [MS:1001892]
id	MS:1001892
name	Progenesis:protein raw abundance
def	"The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1783. MS:1001893 Progenesis:peptide raw abundance

Table 1785. Term [MS:1001893]
id	MS:1001893
name	Progenesis:peptide raw abundance
def	"The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1784. MS:1001894 Progenesis:confidence score

Table 1786. Term [MS:1001894]
id	MS:1001894
name	Progenesis:confidence score
def	"The data type confidence score produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1785. MS:1001895 Progenesis:peptide count

Table 1787. Term [MS:1001895]
id	MS:1001895
name	Progenesis:peptide count
def	"The data type peptide count produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1786. MS:1001896 Progenesis:feature intensity

Table 1788. Term [MS:1001896]
id	MS:1001896
name	Progenesis:feature intensity
def	"The data type feature intensity produced by Progenesis LC-MS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1787. MS:1001897 MaxQuant:peptide counts (unique)

Table 1789. Term [MS:1001897]
id	MS:1001897
name	MaxQuant:peptide counts (unique)
def	"The data type peptide counts (unique) produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1788. MS:1001898 MaxQuant:peptide counts (all)

Table 1790. Term [MS:1001898]
id	MS:1001898
name	MaxQuant:peptide counts (all)
def	"The data type peptide counts (all) produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1789. MS:1001899 MaxQuant:peptide counts (razor+unique)

Table 1791. Term [MS:1001899]
id	MS:1001899
name	MaxQuant:peptide counts (razor+unique)
def	"The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1790. MS:1001900 MaxQuant:sequence length

Table 1792. Term [MS:1001900]
id	MS:1001900
name	MaxQuant:sequence length
def	"The data type sequence length produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1791. MS:1001901 MaxQuant:PEP

Table 1793. Term [MS:1001901]
id	MS:1001901
name	MaxQuant:PEP
def	"The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1792. MS:1001902 MaxQuant:LFQ intensity

Table 1794. Term [MS:1001902]
id	MS:1001902
name	MaxQuant:LFQ intensity
def	"The data type LFQ intensity produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1793. MS:1001903 MaxQuant:feature intensity

Table 1795. Term [MS:1001903]
id	MS:1001903
name	MaxQuant:feature intensity
def	"The data type feature intensity produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.1794. MS:1001904 MaxQuant:MS/MS count

Table 1796. Term [MS:1001904]
id	MS:1001904
name	MaxQuant:MS/MS count
def	"The data type MS2 count produced by MaxQuant." [PSI:MS]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1795. MS:1001905 emPAI value

Table 1797. Term [MS:1001905]
id	MS:1001905
name	emPAI value
def	"The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1796. MS:1001906 APEX value

Table 1798. Term [MS:1001906]
id	MS:1001906
name	APEX value
def	"The APEX value of protein abundance, produced from the APEX software." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1797. MS:1001907 retention time window width

Table 1799. Term [MS:1001907]
id	MS:1001907
name	retention time window width
def	"The full width of a retention time window for a chromatographic peak." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000915 retention time window attribute ! retention time window attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.1798. MS:1001908 ISQ

Table 1800. Term [MS:1001908]
id	MS:1001908
name	ISQ
def	"Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1799. MS:1001909 Velos Plus

Table 1801. Term [MS:1001909]
id	MS:1001909
name	Velos Plus
def	"Thermo Scientific second generation Velos." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1800. MS:1001910 LTQ Orbitrap Elite

Table 1802. Term [MS:1001910]
id	MS:1001910
name	LTQ Orbitrap Elite
def	"Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1801. MS:1001911 Q Exactive

Table 1803. Term [MS:1001911]
id	MS:1001911
name	Q Exactive
def	"Thermo Scientific Q Exactive." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.1802. MS:1001912 PinPoint

Table 1804. Term [MS:1001912]
id	MS:1001912
name	PinPoint
def	"Thermo Scientific PinPoint SRM analysis software." [PSI:MS]
is_a	MS:1000693 Thermo Finnigan software ! Thermo Finnigan software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1803. MS:1001913 S-lens voltage

Table 1805. Term [MS:1001913]
id	MS:1001913
name	S-lens voltage
def	"Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000218] ! volt

2.1804. MS:1001914 pymzML

Table 1806. Term [MS:1001914]
id	MS:1001914
name	pymzML
def	"Python module to interface mzML Data." [PSI:MS]
is_a	MS:1001457 data processing software ! data processing software

2.1805. MS:1001915 leukocyte elastase

Table 1807. Term [MS:1001915]
id	MS:1001915
name	leukocyte elastase
def	"Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001957 (?⇐[ALIV])(?!P) ! (?⇐[ALIV])(?

2.1806. MS:1001916 proline endopeptidase

Table 1808. Term [MS:1001916]
id	MS:1001916
name	proline endopeptidase
def	"Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001958 (?⇐[HKR]P)(?!P) ! (?⇐[HKR]P)(?

2.1807. MS:1001917 glutamyl endopeptidase

Table 1809. Term [MS:1001917]
id	MS:1001917
name	glutamyl endopeptidase
def	"Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [BRENDA:3.4.21.19]
synonym	"staphylococcal protease" EXACT []
synonym	"Glu-C" EXACT []
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001959 (?⇐[^E]E) ! (?⇐[^E]E)

2.1808. MS:1001918 2-iodobenzoate

Table 1810. Term [MS:1001918]
id	MS:1001918
name	2-iodobenzoate
def	"Chemical iodobenzoate. Cleaves after W." [PubChem_Compound:4739928]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001960 (?⇐W) ! (?⇐W)

2.1809. MS:1001919 ProteomeXchange accession number

Table 1811. Term [MS:1001919]
id	MS:1001919
name	ProteomeXchange accession number
def	"Main identifier of a ProteomeXchange dataset." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1810. MS:1001921 ProteomeXchange accession number version number

Table 1812. Term [MS:1001921]
id	MS:1001921
name	ProteomeXchange accession number version number
def	"Version number of a ProteomeXchange accession number." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1811. MS:1001922 Digital Object Identifier (DOI)

Table 1813. Term [MS:1001922]
id	MS:1001922
name	Digital Object Identifier (DOI)
def	"DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
synonym	"doi" EXACT []
is_a	MS:1000878 external reference identifier ! external reference identifier
relationship	has_regexp MS:1002480 regular expression for a digital object identifier (DOI) ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?

2.1812. MS:1001923 external reference keyword

Table 1814. Term [MS:1001923]
id	MS:1001923
name	external reference keyword
def	"Free text attribute that can enrich the information about an entity." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002840 external reference data ! external reference data

2.1813. MS:1001924 journal article keyword

Table 1815. Term [MS:1001924]
id	MS:1001924
name	journal article keyword
def	"Keyword present in a scientific publication." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001923 external reference keyword ! external reference keyword

2.1814. MS:1001925 submitter keyword

Table 1816. Term [MS:1001925]
id	MS:1001925
name	submitter keyword
def	"Keyword assigned by the data submitter." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001923 external reference keyword ! external reference keyword

2.1815. MS:1001926 curator keyword

Table 1817. Term [MS:1001926]
id	MS:1001926
name	curator keyword
def	"Keyword assigned by a data curator." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001923 external reference keyword ! external reference keyword

2.1816. MS:1001927 Tranche file hash

Table 1818. Term [MS:1001927]
id	MS:1001927
name	Tranche file hash
def	"Hash assigned by the Tranche resource to an individual file." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1817. MS:1001928 Tranche project hash

Table 1819. Term [MS:1001928]
id	MS:1001928
name	Tranche project hash
def	"Hash assigned by the Tranche resource to a whole project." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1818. MS:1001929 PRIDE experiment URI

Table 1820. Term [MS:1001929]
id	MS:1001929
name	PRIDE experiment URI
def	"URI that allows the access to one experiment in the PRIDE database." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1819. MS:1001930 PRIDE project URI

Table 1821. Term [MS:1001930]
id	MS:1001930
name	PRIDE project URI
def	"URI that allows the access to one project in the PRIDE database." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1820. MS:1001931 source interface

Table 1822. Term [MS:1001931]
id	MS:1001931
name	source interface
def	"The source interface." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.1821. MS:1001932 source interface model

Table 1823. Term [MS:1001932]
id	MS:1001932
name	source interface model
def	"The source interface model." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001931 source interface ! source interface

2.1822. MS:1001933 source sprayer

Table 1824. Term [MS:1001933]
id	MS:1001933
name	source sprayer
def	"The source sprayer." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1000458 source ! source

2.1823. MS:1001934 source sprayer type

Table 1825. Term [MS:1001934]
id	MS:1001934
name	source sprayer type
def	"The source sprayer type." [PSI:MS]
relationship	part_of MS:1001933 source sprayer ! source sprayer

2.1824. MS:1001935 source sprayer manufacturer

Table 1826. Term [MS:1001935]
id	MS:1001935
name	source sprayer manufacturer
def	"The source sprayer manufacturer." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001933 source sprayer ! source sprayer

2.1825. MS:1001936 source sprayer model

Table 1827. Term [MS:1001936]
id	MS:1001936
name	source sprayer model
def	"The source sprayer model." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001933 source sprayer ! source sprayer

2.1826. MS:1001937 sample plate

Table 1828. Term [MS:1001937]
id	MS:1001937
name	sample plate
def	"Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.1827. MS:1001938 sample plate type

Table 1829. Term [MS:1001938]
id	MS:1001938
name	sample plate type
def	"The sample plate type." [PSI:MS]
relationship	part_of MS:1001937 sample plate ! sample plate

2.1828. MS:1001939 stainless steel plate

Table 1830. Term [MS:1001939]
id	MS:1001939
name	stainless steel plate
def	"Stainless steel plate." [PSI:MS]
is_a	MS:1001938 sample plate type ! sample plate type

2.1829. MS:1001940 coated glass plate

Table 1831. Term [MS:1001940]
id	MS:1001940
name	coated glass plate
def	"Coated glass plate." [PSI:MS]
is_a	MS:1001938 sample plate type ! sample plate type

2.1830. MS:1001941 electrospray supply type

Table 1832. Term [MS:1001941]
id	MS:1001941
name	electrospray supply type
def	"Whether the sprayer is fed or is loaded with sample once." [PSI:MS]
relationship	part_of MS:1000458 source ! source

2.1831. MS:1001942 static supply electrospray

Table 1833. Term [MS:1001942]
id	MS:1001942
name	static supply electrospray
def	"The sprayer is loaded with sample once." [PSI:MS]
is_a	MS:1001941 electrospray supply type ! electrospray supply type

2.1832. MS:1001943 fed supply electrospray

Table 1834. Term [MS:1001943]
id	MS:1001943
name	fed supply electrospray
def	"The sprayer is continuously fed with sample." [PSI:MS]
is_a	MS:1001941 electrospray supply type ! electrospray supply type

2.1833. MS:1001944 Collision cell exit potential

Table 1835. Term [MS:1001944]
id	MS:1001944
name	Collision cell exit potential
def	"Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000218] ! volt
synonym	"CXP" EXACT []

2.1834. MS:1001945 Pegasus 4D

Table 1836. Term [MS:1001945]
id	MS:1001945
name	Pegasus 4D
def	"LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.1835. MS:1001946 PEAKS Studio

Table 1837. Term [MS:1001946]
id	MS:1001946
name	PEAKS Studio
def	"PEAKS Studio software for data analysis." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1836. MS:1001947 PEAKS Online

Table 1838. Term [MS:1001947]
id	MS:1001947
name	PEAKS Online
def	"PEAKS Online software for high throughput data analysis." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1837. MS:1001948 PEAKS Node

Table 1839. Term [MS:1001948]
id	MS:1001948
name	PEAKS Node
def	"PEAKS Node software for high throughput data analysis." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.1838. MS:1001949 BSI software

Table 1840. Term [MS:1001949]
id	MS:1001949
name	BSI software
def	"Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.1839. MS:1001950 PEAKS:peptideScore

Table 1841. Term [MS:1001950]
id	MS:1001950
name	PEAKS:peptideScore
def	"The PEAKS peptide '-10lgP Score'." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1840. MS:1001951 PEAKS:proteinScore

Table 1842. Term [MS:1001951]
id	MS:1001951
name	PEAKS:proteinScore
def	"The PEAKS protein '-10lgP Score'." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1841. MS:1001952 ZCore:probScore

Table 1843. Term [MS:1001952]
id	MS:1001952
name	ZCore:probScore
def	"The ZCore probability score." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1842. MS:1001953 source interface manufacturer

Table 1844. Term [MS:1001953]
id	MS:1001953
name	source interface manufacturer
def	"The source interface manufacturer." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001931 source interface ! source interface

2.1843. MS:1001954 acquisition parameter

Table 1845. Term [MS:1001954]
id	MS:1001954
name	acquisition parameter
def	"Parameters used in the mass spectrometry acquisition." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.1844. MS:1001955 no cleavage

Table 1846. Term [MS:1001955]
id	MS:1001955
name	no cleavage
def	"No cleavage." [PSI:MS]
is_a	MS:1001045 cleavage agent name ! cleavage agent name

2.1845. MS:1001956 unspecific cleavage

Table 1847. Term [MS:1001956]
id	MS:1001956
name	unspecific cleavage
def	"Unspecific cleavage." [PSI:MS]
is_a	MS:1001045 cleavage agent name ! cleavage agent name

2.1846. MS:1001957 (?⇐[ALIV])(?!P)

Table 1848. Term [MS:1001957]
id	MS:1001957
name	(?⇐[ALIV])(?!P)
def	"Regular expression for leukocyte elastase." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1847. MS:1001958 (?⇐[HKR]P)(?!P)

Table 1849. Term [MS:1001958]
id	MS:1001958
name	(?⇐[HKR]P)(?!P)
def	"Regular expression for proline endopeptidase." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1848. MS:1001959 (?⇐[^E]E)

Table 1850. Term [MS:1001959]
id	MS:1001959
name	(?⇐[^E]E)
def	"Regular expression for glutamyl endopeptidase." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1849. MS:1001960 (?⇐W)

Table 1851. Term [MS:1001960]
id	MS:1001960
name	(?⇐W)
def	"Regular expression for 2-iodobenzoate." [PSI:PI]
is_a	MS:1001180 Cleavage agent regular expression ! Cleavage agent regular expression

2.1850. MS:1001961 peptide spectrum match scoring algorithm

Table 1852. Term [MS:1001961]
id	MS:1001961
name	peptide spectrum match scoring algorithm
def	"Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	part_of MS:1001458 spectrum generation information ! spectrum generation information

2.1851. MS:1001962 Mascot:C13 counts

Table 1853. Term [MS:1001962]
id	MS:1001962
name	Mascot:C13 counts
def	"C13 peaks to use in peak detection." [PSI:MS]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.1852. MS:1001963 ProteinExtractor:Weighting

Table 1854. Term [MS:1001963]
id	MS:1001963
name	ProteinExtractor:Weighting
def	"Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002098 ProteinExtractor input parameter ! ProteinExtractor input parameter

2.1853. MS:1001964 ProteinScape:second round Mascot

Table 1855. Term [MS:1001964]
id	MS:1001964
name	ProteinScape:second round Mascot
def	"Flag indicating a second round search with Mascot." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002100 ProteinScape input parameter ! ProteinScape input parameter

2.1854. MS:1001965 ProteinScape:second round Phenyx

Table 1856. Term [MS:1001965]
id	MS:1001965
name	ProteinScape:second round Phenyx
def	"Flag indicating a second round search with Phenyx." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002100 ProteinScape input parameter ! ProteinScape input parameter

2.1855. MS:1001966 product ion mobility

Table 1857. Term [MS:1001966]
id	MS:1001966
name	product ion mobility
def	"The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry." [PSI:MS]
is_a	MS:1001221 product ion attribute ! product ion attribute

2.1856. MS:1001967 product ion drift time

Table 1858. Term [MS:1001967]
id	MS:1001967
name	product ion drift time
def	"OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002222 SRM transition attribute ! SRM transition attribute
relationship	has_units [UO:0000028] ! millisecond
comment	This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476).
is_obsolete	true

2.1857. MS:1001968 PTM localization PSM-level statistic

Table 1859. Term [MS:1001968]
id	MS:1001968
name	PTM localization PSM-level statistic
def	"Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level." [PSI:MS]
is_a	MS:1002689 PTM localization single result statistic ! PTM localization single result statistic

2.1858. MS:1001969 phosphoRS score

Table 1860. Term [MS:1001969]
id	MS:1001969
name	phosphoRS score
def	"phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1859. MS:1001970 phosphoRS sequence probability

Table 1861. Term [MS:1001970]
id	MS:1001970
name	phosphoRS sequence probability
def	"Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1860. MS:1001971 phosphoRS site probability

Table 1862. Term [MS:1001971]
id	MS:1001971
name	phosphoRS site probability
def	"Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1861. MS:1001972 PTM scoring algorithm version

Table 1863. Term [MS:1001972]
id	MS:1001972
name	PTM scoring algorithm version
def	"Version of the post-translational modification scoring algorithm." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details

2.1862. MS:1001973 DeBunker

Table 1864. Term [MS:1001973]
id	MS:1001973
name	DeBunker
def	"DeBunker software." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1863. MS:1001974 DeBunker:score

Table 1865. Term [MS:1001974]
id	MS:1001974
name	DeBunker:score
def	"Score specific to DeBunker." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1864. MS:1001975 delta m/z

Table 1866. Term [MS:1001975]
id	MS:1001975
name	delta m/z
def	"The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS]
synonym	"m/z difference" EXACT []
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
relationship	has_units [UO:0000166] ! parts per notation unit
relationship	has_units [UO:0000187] ! percent
relationship	has_units [UO:0000221] ! dalton

2.1865. MS:1001976 delta M

Table 1867. Term [MS:1001976]
id	MS:1001976
name	delta M
def	"The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS]
synonym	"mass difference" EXACT []
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details
relationship	has_units [UO:0000166] ! parts per notation unit
relationship	has_units [UO:0000187] ! percent
relationship	has_units [UO:0000221] ! dalton

2.1866. MS:1001977 MSQuant

Table 1868. Term [MS:1001977]
id	MS:1001977
name	MSQuant
def	"MSQuant software." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1867. MS:1001978 MSQuant:PTM-score

Table 1869. Term [MS:1001978]
id	MS:1001978
name	MSQuant:PTM-score
def	"The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1868. MS:1001979 MaxQuant:PTM Score

Table 1870. Term [MS:1001979]
id	MS:1001979
name	MaxQuant:PTM Score
def	"The PTM score from MaxQuant software." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1869. MS:1001980 MaxQuant:Phospho (STY) Probabilities

Table 1871. Term [MS:1001980]
id	MS:1001980
name	MaxQuant:Phospho (STY) Probabilities
def	"The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1870. MS:1001981 MaxQuant:Phospho (STY) Score Diffs

Table 1872. Term [MS:1001981]
id	MS:1001981
name	MaxQuant:Phospho (STY) Score Diffs
def	"The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic

2.1871. MS:1001982 MaxQuant:P-site localization probability

Table 1873. Term [MS:1001982]
id	MS:1001982
name	MaxQuant:P-site localization probability
def	"The P-site localization probability value from MaxQuant software." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1872. MS:1001983 MaxQuant:PTM Delta Score

Table 1874. Term [MS:1001983]
id	MS:1001983
name	MaxQuant:PTM Delta Score
def	"The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1873. MS:1001984 Ascore software

Table 1875. Term [MS:1001984]
id	MS:1001984
name	Ascore software
def	"Ascore software." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.1874. MS:1001985 Ascore

Table 1876. Term [MS:1001985]
id	MS:1001985
name	Ascore
def	"A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1875. MS:1001986 H-Score

Table 1877. Term [MS:1001986]
id	MS:1001986
name	H-Score
def	"H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.1876. MS:1001987 vacuum drying MALDI sample preparation

Table 1878. Term [MS:1001987]
id	MS:1001987
name	vacuum drying MALDI sample preparation
def	"Vacuum-drying MALDI sample preparation crystallization method." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.1877. MS:1001988 crushed crystal MALDI sample preparation

Table 1879. Term [MS:1001988]
id	MS:1001988
name	crushed crystal MALDI sample preparation
def	"Crushed-crystal MALDI sample preparation method." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.1878. MS:1001989 fast evaporation MALDI sample preparation

Table 1880. Term [MS:1001989]
id	MS:1001989
name	fast evaporation MALDI sample preparation
def	"Fast-evaporation MALDI sample preparation method." [DOI:10.1021/ac00091a044]
is_a	MS:1000833 matrix application type ! matrix application type

2.1879. MS:1001990 overlayer MALDI sample preparation

Table 1881. Term [MS:1001990]
id	MS:1001990
name	overlayer MALDI sample preparation
def	"Overlayer method combining features of the crushed-crystal method and the fast-evaporation method." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.1880. MS:1001991 sandwich MALDI sample preparation

Table 1882. Term [MS:1001991]
id	MS:1001991
name	sandwich MALDI sample preparation
def	"Sandwich MALDI sample preparation method." [DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4]
is_a	MS:1000833 matrix application type ! matrix application type

2.1881. MS:1001992 spin coating MALDI sample preparation

Table 1883. Term [MS:1001992]
id	MS:1001992
name	spin coating MALDI sample preparation
def	"Spin coating MALDI sample preparation method." [DOI:10.1021/cc0500710, PMID:16283807]
is_a	MS:1000833 matrix application type ! matrix application type

2.1882. MS:1001993 quick and dirty MALDI sample preparation

Table 1884. Term [MS:1001993]
id	MS:1001993
name	quick and dirty MALDI sample preparation
def	"Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling." [PSI:MS]
is_a	MS:1000833 matrix application type ! matrix application type

2.1883. MS:1001994 top hat baseline reduction

Table 1885. Term [MS:1001994]
id	MS:1001994
name	top hat baseline reduction
def	"Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'." [PSI:MS]
is_a	MS:1000593 baseline reduction ! baseline reduction

2.1884. MS:1001995 convex hull baseline reduction

Table 1886. Term [MS:1001995]
id	MS:1001995
name	convex hull baseline reduction
def	"Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures." [PSI:MS]
is_a	MS:1000593 baseline reduction ! baseline reduction

2.1885. MS:1001996 median baseline reduction

Table 1887. Term [MS:1001996]
id	MS:1001996
name	median baseline reduction
def	"The spectrum that will be baseline subtracted is divided into a number of segments." [PSI:MS]
is_a	MS:1000593 baseline reduction ! baseline reduction

2.1886. MS:1001997 wavelet transformation smoothing

Table 1888. Term [MS:1001997]
id	MS:1001997
name	wavelet transformation smoothing
def	"The random noise is removed by using the undecimated wavelet transform." [DOI:10.1093/bioinformatics/btl355, PMID:16820428]
is_a	MS:1000592 smoothing ! smoothing

2.1887. MS:1001998 sophisticated numerical annotation procedure

Table 1889. Term [MS:1001998]
id	MS:1001998
name	sophisticated numerical annotation procedure
def	"It searches for known patterns in the measured spectrum." [DOI:10.1021/ac951158i, PMID:21619291]
synonym	"SNAP" EXACT []
is_a	MS:1000801 area peak picking ! area peak picking

2.1888. MS:1001999 area normalization

Table 1890. Term [MS:1001999]
id	MS:1001999
name	area normalization
def	"Normalization of areas below the curves." [PSI:MS]
is_a	MS:1001484 intensity normalization ! intensity normalization

2.1889. MS:1002000 LIFT

Table 1891. Term [MS:1002000]
id	MS:1002000
name	LIFT
def	"A Bruker’s proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID." [DOI:10.1007/s00216-003-2057-0 , PMID:12830354]
is_a	MS:1000044 dissociation method ! dissociation method

2.1890. MS:1002001 MS1 label-based raw feature quantitation

Table 1892. Term [MS:1002001]
id	MS:1002001
name	MS1 label-based raw feature quantitation
def	"MS1 label-based raw feature quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002018 MS1 label-based analysis ! MS1 label-based analysis

2.1891. MS:1002002 MS1 label-based peptide level quantitation

Table 1893. Term [MS:1002002]
id	MS:1002002
name	MS1 label-based peptide level quantitation
def	"MS1 label-based peptide level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002018 MS1 label-based analysis ! MS1 label-based analysis

2.1892. MS:1002003 MS1 label-based protein level quantitation

Table 1894. Term [MS:1002003]
id	MS:1002003
name	MS1 label-based protein level quantitation
def	"MS1 label-based protein level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002018 MS1 label-based analysis ! MS1 label-based analysis

2.1893. MS:1002004 MS1 label-based proteingroup level quantitation

Table 1895. Term [MS:1002004]
id	MS:1002004
name	MS1 label-based proteingroup level quantitation
def	"MS1 label-based proteingroup level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002018 MS1 label-based analysis ! MS1 label-based analysis

2.1894. MS:1002005 iRT retention time normalization standard

Table 1896. Term [MS:1002005]
id	MS:1002005
name	iRT retention time normalization standard
def	"A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys." [DOI:10.1002/pmic.201100463, http://www.biognosys.ch/products/rt-kit.html]
is_a	MS:1000901 retention time normalization standard ! retention time normalization standard

2.1895. MS:1002006 SRM transition type

Table 1897. Term [MS:1002006]
id	MS:1002006
name	SRM transition type
def	"The type of the transitions, e.g. target or decoy." [PSI:MS]
synonym	"MRM transition type" EXACT []
relationship	part_of MS:1000908 transition ! transition

2.1896. MS:1002007 target SRM transition

Table 1898. Term [MS:1002007]
id	MS:1002007
name	target SRM transition
def	"A transition used to target a specific compound that may be in the sample." [PSI:MS]
synonym	"target MRM transition" EXACT []
is_a	MS:1002006 SRM transition type ! SRM transition type

2.1897. MS:1002008 decoy SRM transition

Table 1899. Term [MS:1002008]
id	MS:1002008
name	decoy SRM transition
def	"A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows." [PSI:MS]
synonym	"decoy MRM transition" EXACT []
is_a	MS:1002006 SRM transition type ! SRM transition type

2.1898. MS:1002009 isobaric label quantitation analysis

Table 1900. Term [MS:1002009]
id	MS:1002009
name	isobaric label quantitation analysis
def	"Quantitation analysis using an isobaric labelling workflow." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1899. MS:1002010 TMT quantitation analysis

Table 1901. Term [MS:1002010]
id	MS:1002010
name	TMT quantitation analysis
def	"Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.1900. MS:1002011 desorption electrospray ionization

Table 1902. Term [MS:1002011]
id	MS:1002011
name	desorption electrospray ionization
def	"Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure." [DOI:10.1126/science.1104404, PMID:15486296]
synonym	"DESI" EXACT []
is_a	MS:1000240 atmospheric pressure ionization ! atmospheric pressure ionization

2.1901. MS:1002012 Mascot:PTM site assignment confidence

Table 1903. Term [MS:1002012]
id	MS:1002012
name	Mascot:PTM site assignment confidence
def	"Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_units [UO:0000187] ! percent

2.1902. MS:1002013 collision energy ramp start

Table 1904. Term [MS:1002013]
id	MS:1002013
name	collision energy ramp start
def	"Collision energy at the start of the collision energy ramp." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000045 collision energy ! collision energy
relationship	has_units [UO:0000266] ! electronvolt

2.1903. MS:1002014 collision energy ramp end

Table 1905. Term [MS:1002014]
id	MS:1002014
name	collision energy ramp end
def	"Collision energy at the end of the collision energy ramp." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000045 collision energy ! collision energy
relationship	has_units [UO:0000266] ! electronvolt

2.1904. MS:1002015 spectral count peptide level quantitation

Table 1906. Term [MS:1002015]
id	MS:1002015
name	spectral count peptide level quantitation
def	"Spectral count peptide level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001836 spectral counting quantitation analysis ! spectral counting quantitation analysis

2.1905. MS:1002016 spectral count protein level quantitation

Table 1907. Term [MS:1002016]
id	MS:1002016
name	spectral count protein level quantitation
def	"Spectral count protein level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001836 spectral counting quantitation analysis ! spectral counting quantitation analysis

2.1906. MS:1002017 spectral count proteingroup level quantitation

Table 1908. Term [MS:1002017]
id	MS:1002017
name	spectral count proteingroup level quantitation
def	"Spectral count proteingroup level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001836 spectral counting quantitation analysis ! spectral counting quantitation analysis

2.1907. MS:1002018 MS1 label-based analysis

Table 1909. Term [MS:1002018]
id	MS:1002018
name	MS1 label-based analysis
def	"MS1 label-based analysis." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1908. MS:1002019 label-free raw feature quantitation

Table 1910. Term [MS:1002019]
id	MS:1002019
name	label-free raw feature quantitation
def	"Label-free raw feature quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001834 LC-MS label-free quantitation analysis ! LC-MS label-free quantitation analysis

2.1909. MS:1002020 label-free peptide level quantitation

Table 1911. Term [MS:1002020]
id	MS:1002020
name	label-free peptide level quantitation
def	"Label-free peptide level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001834 LC-MS label-free quantitation analysis ! LC-MS label-free quantitation analysis

2.1910. MS:1002021 label-free protein level quantitation

Table 1912. Term [MS:1002021]
id	MS:1002021
name	label-free protein level quantitation
def	"Label-free protein level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001834 LC-MS label-free quantitation analysis ! LC-MS label-free quantitation analysis

2.1911. MS:1002022 label-free proteingroup level quantitation

Table 1913. Term [MS:1002022]
id	MS:1002022
name	label-free proteingroup level quantitation
def	"Label-free proteingroup level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001834 LC-MS label-free quantitation analysis ! LC-MS label-free quantitation analysis

2.1912. MS:1002023 MS2 tag-based analysis

Table 1914. Term [MS:1002023]
id	MS:1002023
name	MS2 tag-based analysis
def	"MS2 tag-based analysis." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.1913. MS:1002024 MS2 tag-based feature level quantitation

Table 1915. Term [MS:1002024]
id	MS:1002024
name	MS2 tag-based feature level quantitation
def	"MS2 tag-based feature level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002023 MS2 tag-based analysis ! MS2 tag-based analysis

2.1914. MS:1002025 MS2 tag-based peptide level quantitation

Table 1916. Term [MS:1002025]
id	MS:1002025
name	MS2 tag-based peptide level quantitation
def	"MS2 tag-based peptide level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002023 MS2 tag-based analysis ! MS2 tag-based analysis

2.1915. MS:1002026 MS2 tag-based protein level quantitation

Table 1917. Term [MS:1002026]
id	MS:1002026
name	MS2 tag-based protein level quantitation
def	"MS2 tag-based protein level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002023 MS2 tag-based analysis ! MS2 tag-based analysis

2.1916. MS:1002027 MS2 tag-based proteingroup level quantitation

Table 1918. Term [MS:1002027]
id	MS:1002027
name	MS2 tag-based proteingroup level quantitation
def	"MS2 tag-based proteingroup level quantitation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002023 MS2 tag-based analysis ! MS2 tag-based analysis

2.1917. MS:1002028 nucleic acid base modification

Table 1919. Term [MS:1002028]
id	MS:1002028
name	nucleic acid base modification
def	"Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details

2.1918. MS:1002029 original nucleic acid sequence

Table 1920. Term [MS:1002029]
id	MS:1002029
name	original nucleic acid sequence
def	"Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details

2.1919. MS:1002030 modified nucleic acid sequence

Table 1921. Term [MS:1002030]
id	MS:1002030
name	modified nucleic acid sequence
def	"Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001471 peptide modification details ! peptide modification details

2.1920. MS:1002031 PASSEL transition group browser URI

Table 1922. Term [MS:1002031]
id	MS:1002031
name	PASSEL transition group browser URI
def	"URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1921. MS:1002032 PeptideAtlas dataset URI

Table 1923. Term [MS:1002032]
id	MS:1002032
name	PeptideAtlas dataset URI
def	"URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.1922. MS:1002033 contact role

Table 1924. Term [MS:1002033]
id	MS:1002033
name	contact role
def	"Role of the contact person." [PSI:PI]
is_a	MS:1000585 contact attribute ! contact attribute

2.1923. MS:1002034 first author

Table 1925. Term [MS:1002034]
id	MS:1002034
name	first author
def	"The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution." [PSI:MS]
is_a	MS:1002033 contact role ! contact role

2.1924. MS:1002035 senior author

Table 1926. Term [MS:1002035]
id	MS:1002035
name	senior author
def	"The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution." [PSI:MS]
is_a	MS:1002033 contact role ! contact role

2.1925. MS:1002036 co-author

Table 1927. Term [MS:1002036]
id	MS:1002036
name	co-author
def	"One of a set of authors associated with a publication or release." [PSI:MS]
is_a	MS:1002033 contact role ! contact role

2.1926. MS:1002037 dataset submitter

Table 1928. Term [MS:1002037]
id	MS:1002037
name	dataset submitter
def	"A person who submits a dataset to a repository." [PSI:MS]
is_a	MS:1002033 contact role ! contact role

2.1927. MS:1002038 label free sample

Table 1929. Term [MS:1002038]
id	MS:1002038
name	label free sample
def	"A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym	"light sample" EXACT []
is_a	MS:1000548 sample attribute ! sample attribute

2.1928. MS:1002039 inlet attribute

Table 1930. Term [MS:1002039]
id	MS:1002039
name	inlet attribute
def	"Inlet properties that are associated with a value." [PSI:MS]
is_a	MS:1000547 object attribute ! object attribute
relationship	part_of MS:1000458 source ! source

2.1929. MS:1002040 inlet temperature

Table 1931. Term [MS:1002040]
id	MS:1002040
name	inlet temperature
def	"The temperature of the inlet of a mass spectrometer." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
is_a	MS:1002039 inlet attribute ! inlet attribute
relationship	has_units [UO:0000012] ! kelvin
relationship	has_units [UO:0000027] ! degree Celsius

2.1930. MS:1002041 source temperature

Table 1932. Term [MS:1002041]
id	MS:1002041
name	source temperature
def	"The temperature of the source of a mass spectrometer." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000482 source attribute ! source attribute
relationship	has_units [UO:0000012] ! kelvin
relationship	has_units [UO:0000027] ! degree Celsius

2.1931. MS:1002042 modulation time

Table 1933. Term [MS:1002042]
id	MS:1002042
name	modulation time
def	"The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000857 run attribute ! run attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.1932. MS:1002043 ProteinProspector

Table 1934. Term [MS:1002043]
id	MS:1002043
name	ProteinProspector
def	"ProteinProspector software for data acquisition and analysis." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1933. MS:1002044 ProteinProspector:score

Table 1935. Term [MS:1002044]
id	MS:1002044
name	ProteinProspector:score
def	"The ProteinProspector result 'Score'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1934. MS:1002045 ProteinProspector:expectation value

Table 1936. Term [MS:1002045]
id	MS:1002045
name	ProteinProspector:expectation value
def	"The ProteinProspector result 'Expectation value'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1935. MS:1002046 native source path

Table 1937. Term [MS:1002046]
id	MS:1002046
name	native source path
def	"The original source path used for directory-based sources." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001458 spectrum generation information ! spectrum generation information

2.1936. MS:1002047 MS-GF

Table 1938. Term [MS:1002047]
id	MS:1002047
name	MS-GF
def	"MS-GF software used to re-score the peptide-spectrum matches." [DOI:10.1074/mcp.M110.003731, PMID:20829449]
is_a	MS:1001456 analysis software ! analysis software

2.1937. MS:1002048 MS-GF+

Table 1939. Term [MS:1002048]
id	MS:1002048
name	MS-GF+
synonym	"MS-GFDB" EXACT []
def	"MS-GF+ software used to analyze the spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.1938. MS:1002049 MS-GF:RawScore

Table 1940. Term [MS:1002049]
id	MS:1002049
name	MS-GF:RawScore
def	"MS-GF raw score." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1939. MS:1002050 MS-GF:DeNovoScore

Table 1941. Term [MS:1002050]
id	MS:1002050
name	MS-GF:DeNovoScore
def	"MS-GF de novo score." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.1940. MS:1002051 MS-GF:Energy

Table 1942. Term [MS:1002051]
id	MS:1002051
name	MS-GF:Energy
def	"MS-GF energy score." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1941. MS:1002052 MS-GF:SpecEValue

Table 1943. Term [MS:1002052]
id	MS:1002052
name	MS-GF:SpecEValue
def	"MS-GF spectral E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.1942. MS:1002053 MS-GF:EValue

Table 1944. Term [MS:1002053]
id	MS:1002053
name	MS-GF:EValue
def	"MS-GF E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.1943. MS:1002054 MS-GF:QValue

Table 1945. Term [MS:1002054]
id	MS:1002054
name	MS-GF:QValue
def	"MS-GF Q-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002354 PSM-level q-value ! PSM-level q-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1944. MS:1002055 MS-GF:PepQValue

Table 1946. Term [MS:1002055]
id	MS:1002055
name	MS-GF:PepQValue
def	"MS-GF peptide-level Q-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1945. MS:1002056 MS-GF:PEP

Table 1947. Term [MS:1002056]
id	MS:1002056
name	MS-GF:PEP
def	"MS-GF posterior error probability." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.1946. MS:1002057 modification specificity protein N-term

Table 1948. Term [MS:1002057]
id	MS:1002057
name	modification specificity protein N-term
def	"As parameter for search engine: apply the modification only at the N-terminus of a protein." [PSI:PI]
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1947. MS:1002058 modification specificity protein C-term

Table 1949. Term [MS:1002058]
id	MS:1002058
name	modification specificity protein C-term
def	"As parameter for search engine: apply the modification only at the C-terminus of a protein." [PSI:PI]
is_a	MS:1001056 modification specificity rule ! modification specificity rule

2.1948. MS:1002059 Microsoft Excel

Table 1950. Term [MS:1002059]
id	MS:1002059
name	Microsoft Excel
def	"Microsoft Excel (can be used for spectral counting)." [PSI:PI]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.1949. MS:1002060 database UniProtKB/TrEMBL

Table 1951. Term [MS:1002060]
id	MS:1002060
name	database UniProtKB/TrEMBL
def	"The name of the UniProtKB/TrEMBL database." [PSI:PI]
is_a	MS:1002126 database UniProtKB ! database UniProtKB

2.1950. MS:1002061 decoy DB from UniProtKB/TrEMBL

Table 1952. Term [MS:1002061]
id	MS:1002061
name	decoy DB from UniProtKB/TrEMBL
def	"OBSOLETE Decoy database from a TrEMBL protein sequence database." [PSI:PI]
comment	This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices.
is_obsolete	true

2.1951. MS:1002062 metabolic labelling: natural N (mainly 14N)

Table 1953. Term [MS:1002062]
id	MS:1002062
name	metabolic labelling: natural N (mainly 14N)
def	"Metabolic labelling: natural N (mainly 14N)." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters

2.1952. MS:1002063 FindPairs

Table 1954. Term [MS:1002063]
id	MS:1002063
name	FindPairs
def	"Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite." [http://www.medizinisches-proteom-center.de/software]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.1953. MS:1002064 peptide consensus RT

Table 1955. Term [MS:1002064]
id	MS:1002064
name	peptide consensus RT
def	"Peptide consensus retention time." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1954. MS:1002065 peptide consensus m/z

Table 1956. Term [MS:1002065]
id	MS:1002065
name	peptide consensus m/z
def	"Peptide consensus mass/charge ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.1955. MS:1002066 ratio calculation method

Table 1957. Term [MS:1002066]
id	MS:1002066
name	ratio calculation method
def	"Method used to calculate the ratio." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.1956. MS:1002067 protein value: median of peptide ratios

Table 1958. Term [MS:1002067]
id	MS:1002067
name	protein value: median of peptide ratios
def	"Protein quantification value calculated as median of peptide ratios." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.1957. MS:1002068 metabolic labelling: heavy N (mainly 15N)

Table 1959. Term [MS:1002068]
id	MS:1002068
name	metabolic labelling: heavy N (mainly 15N)
def	"Metabolic labelling: heavy N (mainly 15N)." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters

2.1958. MS:1002069 metabolic labelling purity

Table 1960. Term [MS:1002069]
id	MS:1002069
name	metabolic labelling purity
def	"Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001055 modification parameters ! modification parameters

2.1959. MS:1002070 t-test

Table 1961. Term [MS:1002070]
id	MS:1002070
name	t-test
def	"Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1960. MS:1002071 ANOVA-test

Table 1962. Term [MS:1002071]
id	MS:1002071
name	ANOVA-test
def	"Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001861 quantification data processing ! quantification data processing

2.1961. MS:1002072 p-value

Table 1963. Term [MS:1002072]
id	MS:1002072
name	p-value
def	"P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.1962. MS:1002073 mzIdentML format

Table 1964. Term [MS:1002073]
id	MS:1002073
name	mzIdentML format
def	"The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'." [PSI:PI, http://www.psidev.info/mzidentml]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.1963. MS:1002074 quantification file format

Table 1965. Term [MS:1002074]
id	MS:1002074
name	quantification file format
def	"File format containing quantification results." [PSI:PI]
is_a	MS:1001459 file format ! file format

2.1964. MS:1002075 mzQuantML format

Table 1966. Term [MS:1002075]
id	MS:1002075
name	mzQuantML format
def	"The mzQuantML format for quantification data from the PSI. File extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml]
is_a	MS:1002074 quantification file format ! quantification file format

2.1965. MS:1002076 PAnalyzer

Table 1967. Term [MS:1002076]
id	MS:1002076
name	PAnalyzer
def	"PAnalyzer software for getting protein evidence categories." [http://code.google.com/p/ehu-bio/wiki/PAnalyzer]
is_a	MS:1001456 analysis software ! analysis software

2.1966. MS:1002077 impact

Table 1968. Term [MS:1002077]
id	MS:1002077
name	impact
def	"Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.1967. MS:1002078 ProteomeDiscoverer:1. Static Modification

Table 1969. Term [MS:1002078]
id	MS:1002078
name	ProteomeDiscoverer:1. Static Modification
def	"OBSOLETE ProteomeDiscoverer’s 1st static post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1968. MS:1002079 ProteomeDiscoverer:2. Static Modification

Table 1970. Term [MS:1002079]
id	MS:1002079
name	ProteomeDiscoverer:2. Static Modification
def	"OBSOLETE ProteomeDiscoverer’s 2nd static post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.1969. MS:1002080 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before

Table 1971. Term [MS:1002080]
id	MS:1002080
name	ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
def	"Precursor clipping range before." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
relationship	has_units [UO:0000221] ! dalton

2.1970. MS:1002081 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After

Table 1972. Term [MS:1002081]
id	MS:1002081
name	ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
def	"Precursor clipping range after." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
relationship	has_units [UO:0000221] ! dalton

2.1971. MS:1002082 first column elution time

Table 1973. Term [MS:1002082]
id	MS:1002082
name	first column elution time
def	"The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.1972. MS:1002083 second column elution time

Table 1974. Term [MS:1002083]
id	MS:1002083
name	second column elution time
def	"The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000503 scan attribute ! scan attribute
relationship	has_units [UO:0000010] ! second
relationship	has_units [UO:0000031] ! minute

2.1973. MS:1002084 multidimensional chromatography modulation description

Table 1975. Term [MS:1002084]
id	MS:1002084
name	multidimensional chromatography modulation description
def	"Multidimensional chromatography modulation description." [PSI:MS]
is_a	MS:1000857 run attribute ! run attribute

2.1974. MS:1002085 two-dimensional gas chromatography with fixed modulation time

Table 1976. Term [MS:1002085]
id	MS:1002085
name	two-dimensional gas chromatography with fixed modulation time
def	"Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition." [PSI:MS]
is_a	MS:1002084 multidimensional chromatography modulation description ! multidimensional chromatography modulation description

2.1975. MS:1002086 two-dimensional gas chromatography with discrete modulation time steps

Table 1977. Term [MS:1002086]
id	MS:1002086
name	two-dimensional gas chromatography with discrete modulation time steps
def	"Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS]
is_a	MS:1002084 multidimensional chromatography modulation description ! multidimensional chromatography modulation description

2.1976. MS:1002087 two-dimensional liquid chromatography with fixed modulation time

Table 1978. Term [MS:1002087]
id	MS:1002087
name	two-dimensional liquid chromatography with fixed modulation time
def	"Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition." [PSI:MS]
is_a	MS:1002084 multidimensional chromatography modulation description ! multidimensional chromatography modulation description

2.1977. MS:1002088 two-dimensional liquid chromatography with discrete modulation time steps

Table 1979. Term [MS:1002088]
id	MS:1002088
name	two-dimensional liquid chromatography with discrete modulation time steps
def	"Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS]
is_a	MS:1002084 multidimensional chromatography modulation description ! multidimensional chromatography modulation description

2.1978. MS:1002089 ProteomeDiscoverer:Peptide Without Protein XCorr Threshold

Table 1980. Term [MS:1002089]
id	MS:1002089
name	ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
def	"XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1979. MS:1002090 Calculate Probability Scores

Table 1981. Term [MS:1002090]
id	MS:1002090
name	Calculate Probability Scores
def	"Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002094 common search engine input parameter ! common search engine input parameter

2.1980. MS:1002091 ProteomeDiscoverer:Maximum Delta Cn

Table 1982. Term [MS:1002091]
id	MS:1002091
name	ProteomeDiscoverer:Maximum Delta Cn
def	"Delta Cn threshold for filtering out PSM’s." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.1981. MS:1002092 Percolator:Validation based on

Table 1983. Term [MS:1002092]
id	MS:1002092
name	Percolator:Validation based on
def	"Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002107 Percolator input parameter ! Percolator input parameter

2.1982. MS:1002093 search engine input parameter

Table 1984. Term [MS:1002093]
id	MS:1002093
name	search engine input parameter
def	"Search engine input parameter." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1983. MS:1002094 common search engine input parameter

Table 1985. Term [MS:1002094]
id	MS:1002094
name	common search engine input parameter
def	"Search engine input parameter that is shared by more than one search engine." [PSI:PI]
is_a	MS:1002093 search engine input parameter ! search engine input parameter

2.1984. MS:1002095 Mascot input parameter

Table 1986. Term [MS:1002095]
id	MS:1002095
name	Mascot input parameter
def	"Search engine input parameters specific to Mascot." [PSI:PI, source:http://www.matrixscience.com/help/search_field_help.html]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1985. MS:1002096 SEQUEST input parameter

Table 1987. Term [MS:1002096]
id	MS:1002096
name	SEQUEST input parameter
def	"Search engine input parameters specific to SEQUEST." [PSI:PI, source:http://fields.scripps.edu/sequest/parameters.html]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1986. MS:1002097 Phenyx input parameter

Table 1988. Term [MS:1002097]
id	MS:1002097
name	Phenyx input parameter
def	"Search engine input parameters specific to Phenyx." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1987. MS:1002098 ProteinExtractor input parameter

Table 1989. Term [MS:1002098]
id	MS:1002098
name	ProteinExtractor input parameter
def	"Search engine input parameters specific to ProteinExtractor." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1988. MS:1002099 OMSSA input parameter

Table 1990. Term [MS:1002099]
id	MS:1002099
name	OMSSA input parameter
def	"Search engine input parameters specific to OMSSA." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1989. MS:1002100 ProteinScape input parameter

Table 1991. Term [MS:1002100]
id	MS:1002100
name	ProteinScape input parameter
def	"Search engine input parameters specific to ProteinScape." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1990. MS:1002101 ProteomeDiscoverer input parameter

Table 1992. Term [MS:1002101]
id	MS:1002101
name	ProteomeDiscoverer input parameter
def	"Search engine input parameters specific to ProteomeDiscoverer." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.1991. MS:1002103 software input parameter

Table 1993. Term [MS:1002103]
id	MS:1002103
name	software input parameter
def	"Software input parameters." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.1992. MS:1002104 common software input parameter

Table 1994. Term [MS:1002104]
id	MS:1002104
name	common software input parameter
def	"Software input parameter that is shared by more than one software." [PSI:PI]
is_a	MS:1002103 software input parameter ! software input parameter

2.1993. MS:1002105 software specific input parameter

Table 1995. Term [MS:1002105]
id	MS:1002105
name	software specific input parameter
def	"Software specific input parameter." [PSI:PI]
is_a	MS:1002103 software input parameter ! software input parameter

2.1994. MS:1002106 Scaffold input parameter

Table 1996. Term [MS:1002106]
id	MS:1002106
name	Scaffold input parameter
def	"Search engine input parameters specific to Scaffold." [PSI:PI]
is_a	MS:1002105 software specific input parameter ! software specific input parameter

2.1995. MS:1002107 Percolator input parameter

Table 1997. Term [MS:1002107]
id	MS:1002107
name	Percolator input parameter
def	"Search engine input parameters specific to Percolator." [PSI:PI]
is_a	MS:1002105 software specific input parameter ! software specific input parameter

2.1996. MS:1002108 higher score better

Table 1998. Term [MS:1002108]
id	MS:1002108
name	higher score better
def	"Indicates that a higher score is better." [PSI:PI]
relationship	part_of MS:1001153 search engine specific score ! search engine specific score

2.1997. MS:1002109 lower score better

Table 1999. Term [MS:1002109]
id	MS:1002109
name	lower score better
def	"Indicates that a lower score is better." [PSI:PI]
relationship	part_of MS:1001153 search engine specific score ! search engine specific score

2.1998. MS:1002110 assay attribute

Table 2000. Term [MS:1002110]
id	MS:1002110
name	assay attribute
def	"Attribute describing an assay." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.1999. MS:1002111 assay label attribute

Table 2001. Term [MS:1002111]
id	MS:1002111
name	assay label attribute
def	"Attribute describing an assay label." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2000. MS:1002112 protein group list attribute

Table 2002. Term [MS:1002112]
id	MS:1002112
name	protein group list attribute
def	"Attribute describing a protein group list." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2001. MS:1002113 protein group attribute

Table 2003. Term [MS:1002113]
id	MS:1002113
name	protein group attribute
def	"Attribute describing a protein group." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2002. MS:1002114 protein list attribute

Table 2004. Term [MS:1002114]
id	MS:1002114
name	protein list attribute
def	"Attribute describing a protein list." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2003. MS:1002115 peptide consensus list attribute

Table 2005. Term [MS:1002115]
id	MS:1002115
name	peptide consensus list attribute
def	"Attribute describing a peptide consensus list." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2004. MS:1002116 peptide consensus attribute

Table 2006. Term [MS:1002116]
id	MS:1002116
name	peptide consensus attribute
def	"Attribute describing a peptide consensus." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2005. MS:1002117 small molecule list attribute

Table 2007. Term [MS:1002117]
id	MS:1002117
name	small molecule list attribute
def	"Attribute describing a small molecule list." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2006. MS:1002118 small molecule attribute

Table 2008. Term [MS:1002118]
id	MS:1002118
name	small molecule attribute
def	"Attribute describing a small molecule." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2007. MS:1002119 small molecule modification attribute

Table 2009. Term [MS:1002119]
id	MS:1002119
name	small molecule modification attribute
def	"Attribute describing a small molecule modification." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2008. MS:1002120 experiment name

Table 2010. Term [MS:1002120]
id	MS:1002120
name	experiment name
def	"The name for identifying an experiment." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2009. MS:1002121 spectral count feature

Table 2011. Term [MS:1002121]
id	MS:1002121
name	spectral count feature
def	"Dummy decribing a spectral count feature." [PSI:PI]
is_a	MS:1001828 feature attribute ! feature attribute

2.2010. MS:1002122 counts reporting

Table 2012. Term [MS:1002122]
id	MS:1002122
name	counts reporting
def	"FeatureList of spectral counts." [PSI:PI]
is_a	MS:1001825 feature list attribute ! feature list attribute

2.2011. MS:1002123 x-Tracker

Table 2013. Term [MS:1002123]
id	MS:1002123
name	x-Tracker
def	"X-Tracker generic tool for quantitative proteomics." [https://bessantlab.org/software/x-tracker/]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.2012. MS:1002124 ProteoSuite

Table 2014. Term [MS:1002124]
id	MS:1002124
name	ProteoSuite
def	"ProteoSuite software for the analysis of quantitative proteomics data." [DOI:10.1089/omi.2012.0022, PMID:22804616, http://www.proteosuite.org/]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.2013. MS:1002125 combined FDRScore

Table 2015. Term [MS:1002125]
id	MS:1002125
name	combined FDRScore
def	"OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293]
comment	This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375).
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
is_obsolete	true

2.2014. MS:1002126 database UniProtKB

Table 2016. Term [MS:1002126]
id	MS:1002126
name	database UniProtKB
def	"The name of the UniProtKB knowledgebase." [PSI:PI]
is_a	MS:1001013 database name ! database name

2.2015. MS:1002127 identification file attribute

Table 2017. Term [MS:1002127]
id	MS:1002127
name	identification file attribute
def	"Attribute describing an identification file." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2016. MS:1002128 method file format

Table 2018. Term [MS:1002128]
id	MS:1002128
name	method file format
def	"Attribute describing a method file format." [PSI:PI]
is_a	MS:1001459 file format ! file format

2.2017. MS:1002129 ITRAQAnalyzer

Table 2019. Term [MS:1002129]
id	MS:1002129
name	ITRAQAnalyzer
def	"Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1000752 TOPP software ! TOPP software

2.2018. MS:1002130 identification file format

Table 2020. Term [MS:1002130]
id	MS:1002130
name	identification file format
def	"Attribute describing an identification file format." [PSI:PI]
is_a	MS:1001459 file format ! file format

2.2019. MS:1002131 TOPP noise filter

Table 2021. Term [MS:1002131]
id	MS:1002131
name	TOPP noise filter
def	"Noise filter component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2020. MS:1002132 TOPP NoiseFilterGaussian

Table 2022. Term [MS:1002132]
id	MS:1002132
name	TOPP NoiseFilterGaussian
def	"Removes noise from profile spectra by using a gaussian smoothing." [PSI:PI]
is_a	MS:1002131 TOPP noise filter ! TOPP noise filter

2.2021. MS:1002133 TOPP NoiseFilterSGolay

Table 2023. Term [MS:1002133]
id	MS:1002133
name	TOPP NoiseFilterSGolay
def	"Removes noise from profile spectra by using a Savitzky-Golay smoothing." [PSI:PI]
is_a	MS:1002131 TOPP noise filter ! TOPP noise filter

2.2022. MS:1002134 TOPP peak picker

Table 2024. Term [MS:1002134]
id	MS:1002134
name	TOPP peak picker
def	"Peak picker component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2023. MS:1002135 TOPP PeakPickerHiRes

Table 2025. Term [MS:1002135]
id	MS:1002135
name	TOPP PeakPickerHiRes
def	"Finds mass spectrometric peaks in high-resoluted profile mass spectra." [PSI:PI]
is_a	MS:1002134 TOPP peak picker ! TOPP peak picker

2.2024. MS:1002136 TOPP PeakPickerWavelet

Table 2026. Term [MS:1002136]
id	MS:1002136
name	TOPP PeakPickerWavelet
def	"Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra." [PSI:PI]
is_a	MS:1002134 TOPP peak picker ! TOPP peak picker

2.2025. MS:1002137 TOPP spectra filter

Table 2027. Term [MS:1002137]
id	MS:1002137
name	TOPP spectra filter
def	"Spectra filter component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2026. MS:1002138 TOPP SpectraFilterBernNorm

Table 2028. Term [MS:1002138]
id	MS:1002138
name	TOPP SpectraFilterBernNorm
def	"Applies a Bern et al normalization to peak spectra." [PMID:15262780, DOI:10.1093/bioinformatics/bth947]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2027. MS:1002139 TOPP SpectraFilterMarkerMower

Table 2029. Term [MS:1002139]
id	MS:1002139
name	TOPP SpectraFilterMarkerMower
def	"Applies a filter to peak spectra for marked peaks." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2028. MS:1002140 TOPP SpectraFilterNLargest

Table 2030. Term [MS:1002140]
id	MS:1002140
name	TOPP SpectraFilterNLargest
def	"Retains the n largest peaks of a peak spectra." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2029. MS:1002141 TOPP SpectraFilterNormalizer

Table 2031. Term [MS:1002141]
id	MS:1002141
name	TOPP SpectraFilterNormalizer
def	"Applies a TIC/maximal intensity normalization to peak spectra." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2030. MS:1002142 TOPP SpectraFilterParentPeakMower

Table 2032. Term [MS:1002142]
id	MS:1002142
name	TOPP SpectraFilterParentPeakMower
def	"Filters putative unfragmented precursor ions from tandem spectra." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2031. MS:1002143 TOPP SpectraFilterScaler

Table 2033. Term [MS:1002143]
id	MS:1002143
name	TOPP SpectraFilterScaler
def	"Applies a filter to peak spectra after intensity scaling according to rank." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2032. MS:1002144 TOPP SpectraFilterSqrtMower

Table 2034. Term [MS:1002144]
id	MS:1002144
name	TOPP SpectraFilterSqrtMower
def	"Applies a filter to peak spectra after intensity scaling to the square root." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2033. MS:1002145 TOPP SpectraFilterThresholdMower

Table 2035. Term [MS:1002145]
id	MS:1002145
name	TOPP SpectraFilterThresholdMower
def	"Applies a filter of peaks below a given threshold to peak spectra." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2034. MS:1002146 TOPP SpectraFilterWindowMower

Table 2036. Term [MS:1002146]
id	MS:1002146
name	TOPP SpectraFilterWindowMower
def	"Applies a filter of the largest peaks in a sliding window over a peak spectrum." [PSI:PI]
is_a	MS:1002137 TOPP spectra filter ! TOPP spectra filter

2.2035. MS:1002147 TOPP map aligner

Table 2037. Term [MS:1002147]
id	MS:1002147
name	TOPP map aligner
def	"Map aligner component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2036. MS:1002148 TOPP MapAlignerIdentification

Table 2038. Term [MS:1002148]
id	MS:1002148
name	TOPP MapAlignerIdentification
def	"Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI]
is_a	MS:1002147 TOPP map aligner ! TOPP map aligner

2.2037. MS:1002149 TOPP MapAlignerPoseClustering

Table 2039. Term [MS:1002149]
id	MS:1002149
name	TOPP MapAlignerPoseClustering
def	"Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI]
is_a	MS:1002147 TOPP map aligner ! TOPP map aligner

2.2038. MS:1002150 TOPP MapAlignerSpectrum

Table 2040. Term [MS:1002150]
id	MS:1002150
name	TOPP MapAlignerSpectrum
def	"Corrects retention time distortions between maps by spectrum alignment." [PSI:PI]
is_a	MS:1002147 TOPP map aligner ! TOPP map aligner

2.2039. MS:1002151 numerator data type attribute

Table 2041. Term [MS:1002151]
id	MS:1002151
name	numerator data type attribute
def	"Attribute describing the data type of the numerator of a ratio." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2040. MS:1002152 denominator data type attribute

Table 2042. Term [MS:1002152]
id	MS:1002152
name	denominator data type attribute
def	"Attribute describing the data type of the denominator of a ratio." [PSI:PI]
is_a	MS:1001806 quantification object attribute ! quantification object attribute

2.2041. MS:1002153 protein level PSM counts

Table 2043. Term [MS:1002153]
id	MS:1002153
name	protein level PSM counts
def	"The number of spectra identified for this protein in spectral counting." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002738 protein-level quantification datatype ! protein-level quantification datatype

2.2042. MS:1002154 TOPP DTAExtractor

Table 2044. Term [MS:1002154]
id	MS:1002154
name	TOPP DTAExtractor
def	"Extracts spectra of an MS run file to several files in DTA format." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2043. MS:1002155 TOPP IDMerger

Table 2045. Term [MS:1002155]
id	MS:1002155
name	TOPP IDMerger
def	"Merges several protein/peptide identification files into one file." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2044. MS:1002156 TOPP IDFileConverter

Table 2046. Term [MS:1002156]
id	MS:1002156
name	TOPP IDFileConverter
def	"Converts identification engine file formats." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2045. MS:1002157 TOPP SpectraMerger

Table 2047. Term [MS:1002157]
id	MS:1002157
name	TOPP SpectraMerger
def	"Merges spectra from an LC/MS map, either by precursor or by RT blocks." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2046. MS:1002158 TOPP MzTabExporter

Table 2048. Term [MS:1002158]
id	MS:1002158
name	TOPP MzTabExporter
def	"Exports various XML formats to an mzTab file." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2047. MS:1002159 TOPP MassTraceExtractor

Table 2049. Term [MS:1002159]
id	MS:1002159
name	TOPP MassTraceExtractor
def	"Annotates mass traces in centroided LC/MS maps." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2048. MS:1002160 TOPP PrecursorMassCorrector

Table 2050. Term [MS:1002160]
id	MS:1002160
name	TOPP PrecursorMassCorrector
def	"Correct the precursor entries of tandem MS scans." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2049. MS:1002161 TOPP HighResPrecursorMassCorrector

Table 2051. Term [MS:1002161]
id	MS:1002161
name	TOPP HighResPrecursorMassCorrector
def	"Performs precursor mz correction on centroided high resolution data." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2050. MS:1002162 TOPP AdditiveSeries

Table 2052. Term [MS:1002162]
id	MS:1002162
name	TOPP AdditiveSeries
def	"Computes an additive series to quantify a peptide in a set of samples." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2051. MS:1002163 TOPP Decharger

Table 2053. Term [MS:1002163]
id	MS:1002163
name	TOPP Decharger
def	"Decharges and merges different feature charge variants of the same chemical entity." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2052. MS:1002164 TOPP EICExtractor

Table 2054. Term [MS:1002164]
id	MS:1002164
name	TOPP EICExtractor
def	"Quantifies signals at given positions in (raw or picked) LC/MS maps." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2053. MS:1002165 TOPP feature finder

Table 2055. Term [MS:1002165]
id	MS:1002165
name	TOPP feature finder
def	"Feature finder component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2054. MS:1002166 TOPP FeatureFinderCentroided

Table 2056. Term [MS:1002166]
id	MS:1002166
name	TOPP FeatureFinderCentroided
def	"Detects two-dimensional features in centroided LC-MS data." [PSI:PI]
is_a	MS:1002165 TOPP feature finder ! TOPP feature finder

2.2055. MS:1002167 TOPP FeatureFinderRaw

Table 2057. Term [MS:1002167]
id	MS:1002167
name	TOPP FeatureFinderRaw
def	"Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI]
is_a	MS:1002165 TOPP feature finder ! TOPP feature finder

2.2056. MS:1002168 TOPP FeatureFinderIsotopeWavelet

Table 2058. Term [MS:1002168]
id	MS:1002168
name	TOPP FeatureFinderIsotopeWavelet
def	"Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm." [PSI:PI]
is_a	MS:1002165 TOPP feature finder ! TOPP feature finder

2.2057. MS:1002169 TOPP FeatureFinderMetabo

Table 2059. Term [MS:1002169]
id	MS:1002169
name	TOPP FeatureFinderMetabo
def	"Detects two-dimensional features in centroided LC-MS data of metabolites." [PSI:PI]
is_a	MS:1002165 TOPP feature finder ! TOPP feature finder

2.2058. MS:1002170 TOPP FeatureFinderMRM

Table 2060. Term [MS:1002170]
id	MS:1002170
name	TOPP FeatureFinderMRM
def	"Quantifies features LC-MS/MS MRM data." [PSI:PI]
is_a	MS:1002165 TOPP feature finder ! TOPP feature finder

2.2059. MS:1002171 TOPP ProteinQuantifier

Table 2061. Term [MS:1002171]
id	MS:1002171
name	TOPP ProteinQuantifier
def	"Computes protein abundances from annotated feature/consensus maps." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2060. MS:1002172 TOPP ConsensusMapNormalizer

Table 2062. Term [MS:1002172]
id	MS:1002172
name	TOPP ConsensusMapNormalizer
def	"Normalizes maps of one consensus XML file (after linking)." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2061. MS:1002173 TOPP MapRTTransformer

Table 2063. Term [MS:1002173]
id	MS:1002173
name	TOPP MapRTTransformer
def	"Applies retention time transformations to maps." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2062. MS:1002174 TOPP feature linker

Table 2064. Term [MS:1002174]
id	MS:1002174
name	TOPP feature linker
def	"Feature linker component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2063. MS:1002175 TOPP FeatureLinkerLabeled

Table 2065. Term [MS:1002175]
id	MS:1002175
name	TOPP FeatureLinkerLabeled
def	"Groups corresponding isotope-labeled features in a feature map." [PSI:PI]
is_a	MS:1002174 TOPP feature linker ! TOPP feature linker

2.2064. MS:1002176 TOPP FeatureLinkerUnlabeled

Table 2066. Term [MS:1002176]
id	MS:1002176
name	TOPP FeatureLinkerUnlabeled
def	"Groups corresponding features from multiple maps." [PSI:PI]
is_a	MS:1002174 TOPP feature linker ! TOPP feature linker

2.2065. MS:1002177 TOPP FeatureLinkerUnlabeledQT

Table 2067. Term [MS:1002177]
id	MS:1002177
name	TOPP FeatureLinkerUnlabeledQT
def	"Groups corresponding features from multiple maps using a quality threshold clustering approach." [PSI:PI]
is_a	MS:1002174 TOPP feature linker ! TOPP feature linker

2.2066. MS:1002178 TOPP CompNovo

Table 2068. Term [MS:1002178]
id	MS:1002178
name	TOPP CompNovo
def	"Performs a peptide/protein identification with the CompNovo engine." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2067. MS:1002179 TOPP CompNovoCID

Table 2069. Term [MS:1002179]
id	MS:1002179
name	TOPP CompNovoCID
def	"Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2068. MS:1002180 TOPP software adaptor

Table 2070. Term [MS:1002180]
id	MS:1002180
name	TOPP software adaptor
def	"Software adaptor to an external program in the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2069. MS:1002181 TOPP InspectAdapter

Table 2071. Term [MS:1002181]
id	MS:1002181
name	TOPP InspectAdapter
def	"Identifies MS2 spectra using the external program Inspect." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2070. MS:1002182 TOPP MascotAdapter

Table 2072. Term [MS:1002182]
id	MS:1002182
name	TOPP MascotAdapter
def	"Identifies MS2 spectra using the external program Mascot." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2071. MS:1002183 TOPP MascotAdapterOnline

Table 2073. Term [MS:1002183]
id	MS:1002183
name	TOPP MascotAdapterOnline
def	"Identifies MS2 spectra using the online version of the external program Mascot." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2072. MS:1002184 TOPP OMSSAAdapter

Table 2074. Term [MS:1002184]
id	MS:1002184
name	TOPP OMSSAAdapter
def	"Identifies MS2 spectra using the external program OMSSA." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2073. MS:1002185 TOPP PepNovoAdapter

Table 2075. Term [MS:1002185]
id	MS:1002185
name	TOPP PepNovoAdapter
def	"Identifies MS2 spectra using the external program PepNovo." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2074. MS:1002186 TOPP XTandemAdapter

Table 2076. Term [MS:1002186]
id	MS:1002186
name	TOPP XTandemAdapter
def	"Identifies MS2 spectra using the external program XTandem." [PSI:PI]
is_a	MS:1002180 TOPP software adaptor ! TOPP software adaptor

2.2075. MS:1002187 TOPP SpecLibSearcher

Table 2077. Term [MS:1002187]
id	MS:1002187
name	TOPP SpecLibSearcher
def	"Identifies peptide MS2 spectra by spectral matching with a searchable spectral library." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2076. MS:1002188 TOPP ConsensusID

Table 2078. Term [MS:1002188]
id	MS:1002188
name	TOPP ConsensusID
def	"Computes a consensus identification from peptide identifications of several identification engines." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2077. MS:1002189 TOPP IDConflictResolver

Table 2079. Term [MS:1002189]
id	MS:1002189
name	TOPP IDConflictResolver
def	"Resolves ambiguous annotations of features with peptide identifications." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2078. MS:1002190 TOPP IDFilter

Table 2080. Term [MS:1002190]
id	MS:1002190
name	TOPP IDFilter
def	"Filters results from protein or peptide identification engines based on different criteria." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2079. MS:1002191 TOPP IDMapper

Table 2081. Term [MS:1002191]
id	MS:1002191
name	TOPP IDMapper
def	"Assigns protein/peptide identifications to feature or consensus features." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2080. MS:1002192 TOPP IDPosteriorErrorProbability

Table 2082. Term [MS:1002192]
id	MS:1002192
name	TOPP IDPosteriorErrorProbability
def	"Estimates posterior error probabilities using a mixture model." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2081. MS:1002193 TOPP IDRTCalibration

Table 2083. Term [MS:1002193]
id	MS:1002193
name	TOPP IDRTCalibration
def	"Calibrate Retention times of peptide hits to standards." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2082. MS:1002194 TOPP PeptideIndexer

Table 2084. Term [MS:1002194]
id	MS:1002194
name	TOPP PeptideIndexer
def	"Refreshes the protein references for all peptide hits." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2083. MS:1002195 TOPP PrecursorIonSelector

Table 2085. Term [MS:1002195]
id	MS:1002195
name	TOPP PrecursorIonSelector
def	"A tool for precursor ion selection based on identification results." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2084. MS:1002196 TOPP MRMMapper

Table 2086. Term [MS:1002196]
id	MS:1002196
name	TOPP MRMMapper
def	"MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2085. MS:1002197 TOPP OpenSwath component

Table 2087. Term [MS:1002197]
id	MS:1002197
name	TOPP OpenSwath component
def	"OpenSwath component of the TOPP software." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2086. MS:1002198 TOPP OpenSwathAnalyzer

Table 2088. Term [MS:1002198]
id	MS:1002198
name	TOPP OpenSwathAnalyzer
def	"Picks peaks and finds features in an SRM experiment." [PSI:PI]
is_a	MS:1002197 TOPP OpenSwath component ! TOPP OpenSwath component

2.2087. MS:1002199 TOPP OpenSwathChromatogramExtractor

Table 2089. Term [MS:1002199]
id	MS:1002199
name	TOPP OpenSwathChromatogramExtractor
def	"Extract chromatograms (XIC) from a MS2 map file." [PSI:PI]
is_a	MS:1002197 TOPP OpenSwath component ! TOPP OpenSwath component

2.2088. MS:1002200 TOPP OpenSwathDecoyGenerator

Table 2090. Term [MS:1002200]
id	MS:1002200
name	TOPP OpenSwathDecoyGenerator
def	"Generates decoys according to different models for a specific TraML." [PSI:PI]
is_a	MS:1002197 TOPP OpenSwath component ! TOPP OpenSwath component

2.2089. MS:1002201 TOPP OpenSwathFeatureXMLToTSV

Table 2091. Term [MS:1002201]
id	MS:1002201
name	TOPP OpenSwathFeatureXMLToTSV
def	"Converts a featureXML to a mProphet tsv (tab separated values)." [PSI:PI]
is_a	MS:1002197 TOPP OpenSwath component ! TOPP OpenSwath component

2.2090. MS:1002202 TOPP OpenSwathRTNormalizer

Table 2092. Term [MS:1002202]
id	MS:1002202
name	TOPP OpenSwathRTNormalizer
def	"Generates a transformation file for retention time space into normalized space." [PSI:PI]
is_a	MS:1002197 TOPP OpenSwath component ! TOPP OpenSwath component

2.2091. MS:1002203 TOPP ProteinInference

Table 2093. Term [MS:1002203]
id	MS:1002203
name	TOPP ProteinInference
def	"Infer proteins from a list of (high-confidence) peptides." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2092. MS:1002204 TOPP FalseDiscoveryRate

Table 2094. Term [MS:1002204]
id	MS:1002204
name	TOPP FalseDiscoveryRate
def	"Estimates the false discovery rate on peptide and protein level using decoy searches." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2093. MS:1002205 ProteoWizard msconvert

Table 2095. Term [MS:1002205]
id	MS:1002205
name	ProteoWizard msconvert
def	"Converts, filters, and processes mass spectrometry data in variety of formats." [PSI:MS]
is_a	MS:1000615 ProteoWizard software ! ProteoWizard software

2.2094. MS:1002206 ProteoWizard idconvert

Table 2096. Term [MS:1002206]
id	MS:1002206
name	ProteoWizard idconvert
def	"Converts, filters, and processes identifications from shotgun proteomics experiments." [PSI:MS]
is_a	MS:1000615 ProteoWizard software ! ProteoWizard software

2.2095. MS:1002207 ProteoWizard chainsaw

Table 2097. Term [MS:1002207]
id	MS:1002207
name	ProteoWizard chainsaw
def	"Filters and processes protein sequence databases." [PSI:MS]
is_a	MS:1000615 ProteoWizard software ! ProteoWizard software

2.2096. MS:1002208 ProteoWizard msaccess

Table 2098. Term [MS:1002208]
id	MS:1002208
name	ProteoWizard msaccess
def	"Filters, processes, and displays mass spectrometry data in a variety of ways." [PSI:MS]
is_a	MS:1000615 ProteoWizard software ! ProteoWizard software

2.2097. MS:1002209 ProteoWizard SeeMS

Table 2099. Term [MS:1002209]
id	MS:1002209
name	ProteoWizard SeeMS
def	"An interactive GUI application to view and filter mass spectrometry data in a variety of formats." [PSI:MS]
is_a	MS:1000615 ProteoWizard software ! ProteoWizard software

2.2098. MS:1002210 IsobariQ

Table 2100. Term [MS:1002210]
id	MS:1002210
name	IsobariQ
def	"A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data." [PMID:21067241, DOI:10.1021/pr1009977, http://folk.uio.no/magnusar/isobariq]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software

2.2099. MS:1002211 Variance stabilizing normalization

Table 2101. Term [MS:1002211]
id	MS:1002211
name	Variance stabilizing normalization
def	"The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation." [PMID:16646781]
is_a	MS:1001861 quantification data processing ! quantification data processing

2.2100. MS:1002212 IPTL quantitation analysis

Table 2102. Term [MS:1002212]
id	MS:1002212
name	IPTL quantitation analysis
def	"Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2101. MS:1002213 PAnalyzer:conclusive protein

Table 2103. Term [MS:1002213]
id	MS:1002213
name	PAnalyzer:conclusive protein
def	"A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001600 protein inference confidence category ! protein inference confidence category

2.2102. MS:1002214 PAnalyzer:indistinguishable protein

Table 2104. Term [MS:1002214]
id	MS:1002214
name	PAnalyzer:indistinguishable protein
def	"A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001600 protein inference confidence category ! protein inference confidence category

2.2103. MS:1002215 PAnalyzer:non-conclusive protein

Table 2105. Term [MS:1002215]
id	MS:1002215
name	PAnalyzer:non-conclusive protein
def	"A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001600 protein inference confidence category ! protein inference confidence category

2.2104. MS:1002216 PAnalyzer:ambiguous group member

Table 2106. Term [MS:1002216]
id	MS:1002216
name	PAnalyzer:ambiguous group member
def	"A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001600 protein inference confidence category ! protein inference confidence category

2.2105. MS:1002217 decoy peptide

Table 2107. Term [MS:1002217]
id	MS:1002217
name	decoy peptide
def	"A putative identified peptide issued from a decoy sequence database." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2106. MS:1002218 percent collision energy ramp start

Table 2108. Term [MS:1002218]
id	MS:1002218
name	percent collision energy ramp start
def	"Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000138 normalized collision energy ! normalized collision energy
relationship	has_units [UO:0000187] ! percent

2.2107. MS:1002219 percent collision energy ramp end

Table 2109. Term [MS:1002219]
id	MS:1002219
name	percent collision energy ramp end
def	"Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000138 normalized collision energy ! normalized collision energy
relationship	has_units [UO:0000187] ! percent

2.2108. MS:1002220 MRMaid

Table 2110. Term [MS:1002220]
id	MS:1002220
name	MRMaid
def	"A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI’s PRIDE database." [PSI:PI]
is_a	MS:1000871 SRM software ! SRM software

2.2109. MS:1002221 MRMaid:peptide score

Table 2111. Term [MS:1002221]
id	MS:1002221
name	MRMaid:peptide score
def	"Score in MRMaid to indicate the expected performance of the peptide in SRM." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2110. MS:1002222 SRM transition attribute

Table 2112. Term [MS:1002222]
id	MS:1002222
name	SRM transition attribute
def	"Attribute associated with a SRM transition." [PSI:MS]
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	part_of MS:1000908 transition ! transition

2.2111. MS:1002223 precursor ion detection probability

Table 2113. Term [MS:1002223]
id	MS:1002223
name	precursor ion detection probability
def	"Probability of detecting precursor when parent protein is present." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002222 SRM transition attribute ! SRM transition attribute

2.2112. MS:1002224 product ion detection probability

Table 2114. Term [MS:1002224]
id	MS:1002224
name	product ion detection probability
def	"Probability of detecting product ion when precursor ion is present." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002222 SRM transition attribute ! SRM transition attribute

2.2113. MS:1002225 average product ion intensity

Table 2115. Term [MS:1002225]
id	MS:1002225
name	average product ion intensity
def	"Average value of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a	MS:1001226 product ion intensity ! product ion intensity
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100

2.2114. MS:1002226 product ion intensity standard deviation

Table 2116. Term [MS:1002226]
id	MS:1002226
name	product ion intensity standard deviation
def	"Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a	MS:1001226 product ion intensity ! product ion intensity
relationship	has_units MS:1000131 number of detector counts ! number of detector counts
relationship	has_units MS:1000132 percent of base peak ! percent of base peak
relationship	has_units MS:1000814 counts per second ! counts per second
relationship	has_units MS:1000905 percent of base peak times 100 ! percent of base peak times 100

2.2115. MS:1002227 number of product ion observations

Table 2117. Term [MS:1002227]
id	MS:1002227
name	number of product ion observations
def	"The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002222 SRM transition attribute ! SRM transition attribute

2.2116. MS:1002228 number of precursor ion observations

Table 2118. Term [MS:1002228]
id	MS:1002228
name	number of precursor ion observations
def	"The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002222 SRM transition attribute ! SRM transition attribute

2.2117. MS:1002229 ProteomeDiscoverer:Mascot:Significance Middle

Table 2119. Term [MS:1002229]
id	MS:1002229
name	ProteomeDiscoverer:Mascot:Significance Middle
def	"Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2118. MS:1002230 ProteomeDiscoverer:Mascot:Significance High

Table 2120. Term [MS:1002230]
id	MS:1002230
name	ProteomeDiscoverer:Mascot:Significance High
def	"Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2119. MS:1002231 regular expressions for a GUID

Table 2121. Term [MS:1002231]
id	MS:1002231
name	regular expressions for a GUID
def	"([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})." [PSI:PI]
is_a	MS:1002479 regular expression ! regular expression

2.2120. MS:1002232 ProteomeDiscoverer:Default FDR calculator

Table 2122. Term [MS:1002232]
id	MS:1002232
name	ProteomeDiscoverer:Default FDR calculator
def	"The default FDR calculator as globally unique identifier (GUID)." [PSI:PI]
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
relationship	has_regexp MS:1002231 regular expressions for a GUID ! regular expressions for a GUID

2.2121. MS:1002233 ProteomeDiscoverer:SEQUEST:Low resolution spectra contained

Table 2123. Term [MS:1002233]
id	MS:1002233
name	ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
def	"Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2122. MS:1002234 selected precursor m/z

Table 2124. Term [MS:1002234]
id	MS:1002234
name	selected precursor m/z
def	"Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI]
synonym	"selected ion m/z" RELATED []
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
relationship	has_units MS:1000040 m/z ! m/z

2.2123. MS:1002235 ProteoGrouper:PDH score

Table 2125. Term [MS:1002235]
id	MS:1002235
name	ProteoGrouper:PDH score
def	"A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2124. MS:1002236 ProteoGrouper:PAG score

Table 2126. Term [MS:1002236]
id	MS:1002236
name	ProteoGrouper:PAG score
def	"A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups

2.2125. MS:1002237 mzidLib

Table 2127. Term [MS:1002237]
id	MS:1002237
name	mzidLib
def	"A library of Java routines for manipulating mzIdentML files." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2126. MS:1002238 mzidLib:Omssa2Mzid

Table 2128. Term [MS:1002238]
id	MS:1002238
name	mzidLib:Omssa2Mzid
def	"A converter for OMSSA OMX to mzIdentML." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2127. MS:1002239 mzidLib:Tandem2Mzid

Table 2129. Term [MS:1002239]
id	MS:1002239
name	mzidLib:Tandem2Mzid
def	"A converter for Tandem XML to mzIdentML." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2128. MS:1002240 mzidLib:Csv2Mzid

Table 2130. Term [MS:1002240]
id	MS:1002240
name	mzidLib:Csv2Mzid
def	"A converter for CSV files (following OMSSA CSV style) to mzIdentML." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2129. MS:1002241 mzidLib:ProteoGrouper

Table 2131. Term [MS:1002241]
id	MS:1002241
name	mzidLib:ProteoGrouper
def	"A generic and parameterizable protein inference algorithm for mzIdentML files." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2130. MS:1002242 mzidLib:Thresholder

Table 2132. Term [MS:1002242]
id	MS:1002242
name	mzidLib:Thresholder
def	"A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2131. MS:1002243 mzidLib:Perform emPAI on mzid

Table 2133. Term [MS:1002243]
id	MS:1002243
name	mzidLib:Perform emPAI on mzid
def	"A routine for adding emPAI quantitative values to an mzIdentML file." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2132. MS:1002244 mzidLib:FalseDiscoveryRate

Table 2134. Term [MS:1002244]
id	MS:1002244
name	mzidLib:FalseDiscoveryRate
def	"A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2133. MS:1002245 mzidLib:Mzidentml2Csv

Table 2135. Term [MS:1002245]
id	MS:1002245
name	mzidLib:Mzidentml2Csv
def	"A tool for converting mzIdentML files to CSV format." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2134. MS:1002246 mzidLib:CombineSearchEngines

Table 2136. Term [MS:1002246]
id	MS:1002246
name	mzidLib:CombineSearchEngines
def	"A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file." [PMID:19253293]
is_a	MS:1002237 mzidLib ! mzidLib

2.2135. MS:1002247 mzidLib:InsertMetaDataFromFasta

Table 2137. Term [MS:1002247]
id	MS:1002247
name	mzidLib:InsertMetaDataFromFasta
def	"A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files." [PSI:PI]
is_a	MS:1002237 mzidLib ! mzidLib

2.2136. MS:1002248 SEQUEST:spscore

Table 2138. Term [MS:1002248]
id	MS:1002248
name	SEQUEST:spscore
def	"The SEQUEST result 'SpScore'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2137. MS:1002249 SEQUEST:sprank

Table 2139. Term [MS:1002249]
id	MS:1002249
name	SEQUEST:sprank
def	"The SEQUEST result 'SpRank'." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2138. MS:1002250 SEQUEST:deltacnstar

Table 2140. Term [MS:1002250]
id	MS:1002250
name	SEQUEST:deltacnstar
def	"The SEQUEST result 'DeltaCnStar'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2139. MS:1002251 Comet

Table 2141. Term [MS:1002251]
id	MS:1002251
name	Comet
def	"Comet open-source sequence search engine developed at the University of Washington." [PMID:23148064]
is_a	MS:1001456 analysis software ! analysis software

2.2140. MS:1002252 Comet:xcorr

Table 2142. Term [MS:1002252]
id	MS:1002252
name	Comet:xcorr
def	"The Comet result 'XCorr'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2141. MS:1002253 Comet:deltacn

Table 2143. Term [MS:1002253]
id	MS:1002253
name	Comet:deltacn
def	"The Comet result 'DeltaCn'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2142. MS:1002254 Comet:deltacnstar

Table 2144. Term [MS:1002254]
id	MS:1002254
name	Comet:deltacnstar
def	"The Comet result 'DeltaCnStar'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2143. MS:1002255 Comet:spscore

Table 2145. Term [MS:1002255]
id	MS:1002255
name	Comet:spscore
def	"The Comet result 'SpScore'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2144. MS:1002256 Comet:sprank

Table 2146. Term [MS:1002256]
id	MS:1002256
name	Comet:sprank
def	"The Comet result 'SpRank'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2145. MS:1002257 Comet:expectation value

Table 2147. Term [MS:1002257]
id	MS:1002257
name	Comet:expectation value
def	"The Comet result 'Expectation value'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001153 search engine specific score ! search engine specific score

2.2146. MS:1002258 Comet:matched ions

Table 2148. Term [MS:1002258]
id	MS:1002258
name	Comet:matched ions
def	"The Comet result 'Matched Ions'." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2147. MS:1002259 Comet:total ions

Table 2149. Term [MS:1002259]
id	MS:1002259
name	Comet:total ions
def	"The Comet result 'Total Ions'." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2148. MS:1002260 PSM:FDR threshold

Table 2150. Term [MS:1002260]
id	MS:1002260
name	PSM:FDR threshold
def	"False-discovery rate threshold for peptide-spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002483 PSM-level statistical threshold ! PSM-level statistical threshold

2.2149. MS:1002261 Byonic

Table 2151. Term [MS:1002261]
id	MS:1002261
name	Byonic
def	"Byonic search engine from Protein Metrics." [PMID:23255153]
is_a	MS:1001456 analysis software ! analysis software

2.2150. MS:1002262 Byonic:Score

Table 2152. Term [MS:1002262]
id	MS:1002262
name	Byonic:Score
def	"The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2151. MS:1002263 Byonic:Delta Score

Table 2153. Term [MS:1002263]
id	MS:1002263
name	Byonic:Delta Score
def	"The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2152. MS:1002264 Byonic:DeltaMod Score

Table 2154. Term [MS:1002264]
id	MS:1002264
name	Byonic:DeltaMod Score
def	"The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2153. MS:1002265 Byonic:PEP

Table 2155. Term [MS:1002265]
id	MS:1002265
name	Byonic:PEP
def	"Byonic posterior error probability." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2154. MS:1002266 Byonic:Peptide LogProb

Table 2156. Term [MS:1002266]
id	MS:1002266
name	Byonic:Peptide LogProb
def	"The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2155. MS:1002267 Byonic:Protein LogProb

Table 2157. Term [MS:1002267]
id	MS:1002267
name	Byonic:Protein LogProb
def	"The log p-value of the protein." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002109 lower score better ! lower score better

2.2156. MS:1002268 Byonic:Best LogProb

Table 2158. Term [MS:1002268]
id	MS:1002268
name	Byonic:Best LogProb
def	"Best (most negative) log p-value of an individual PSM." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002109 lower score better ! lower score better

2.2157. MS:1002269 Byonic:Best Score

Table 2159. Term [MS:1002269]
id	MS:1002269
name	Byonic:Best Score
def	"Best (largest) Byonic score of a PSM." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2158. MS:1002270 chromatography separation

Table 2160. Term [MS:1002270]
id	MS:1002270
name	chromatography separation
def	"A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure." [PSI:MS]
is_a	MS:1000857 run attribute ! run attribute

2.2159. MS:1002271 liquid chromatography separation

Table 2161. Term [MS:1002271]
id	MS:1002271
name	liquid chromatography separation
def	"Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid." [PSI:MS]
is_a	MS:1002270 chromatography separation ! chromatography separation

2.2160. MS:1002272 gas chromatography separation

Table 2162. Term [MS:1002272]
id	MS:1002272
name	gas chromatography separation
def	"Gas chromatography (GC) is a separation technique in which the mobile phase is a gas." [PSI:MS]
is_a	MS:1002270 chromatography separation ! chromatography separation

2.2161. MS:1002273 detector potential

Table 2163. Term [MS:1002273]
id	MS:1002273
name	detector potential
def	"Detector potential difference in volts." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000481 detector attribute ! detector attribute
relationship	has_units [UO:0000218] ! volt

2.2162. MS:1002274 SQ Detector 2

Table 2164. Term [MS:1002274]
id	MS:1002274
name	SQ Detector 2
def	"Waters quadrupole based SQ Detector 2." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2163. MS:1002275 Xevo G2-S Tof

Table 2165. Term [MS:1002275]
id	MS:1002275
name	Xevo G2-S Tof
def	"Waters oa-ToF based Xevo G2-S Tof." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2164. MS:1002276 Xevo G2-S QTof

Table 2166. Term [MS:1002276]
id	MS:1002276
name	Xevo G2-S QTof
def	"Waters oa-ToF based Xevo G2-S QTof." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2165. MS:1002277 AutoSpec Premier

Table 2167. Term [MS:1002277]
id	MS:1002277
name	AutoSpec Premier
def	"Waters AutoSpec Premier magnetic sector instrument." [PSI:MS]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2166. MS:1002278 Pegasus III

Table 2168. Term [MS:1002278]
id	MS:1002278
name	Pegasus III
def	"LECO nominal mass resolution time-of-flight GC mass spectrometer." [PSI:MS]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.2167. MS:1002279 maXis 4G

Table 2169. Term [MS:1002279]
id	MS:1002279
name	maXis 4G
def	"Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001547 Bruker Daltonics maXis series ! Bruker Daltonics maXis series

2.2168. MS:1002280 compact

Table 2170. Term [MS:1002280]
id	MS:1002280
name	compact
def	"Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.2169. MS:1002281 SRM feature level quantitation

Table 2171. Term [MS:1002281]
id	MS:1002281
name	SRM feature level quantitation
def	"Selected Reaction Monitoring feature level quantitation." [PSI:PI]
is_a	MS:1001838 SRM quantitation analysis ! SRM quantitation analysis

2.2170. MS:1002282 SRM peptide level quantitation

Table 2172. Term [MS:1002282]
id	MS:1002282
name	SRM peptide level quantitation
def	"Selected Reaction Monitoring peptide level quantitation." [PSI:PI]
is_a	MS:1001838 SRM quantitation analysis ! SRM quantitation analysis

2.2171. MS:1002283 SRM protein level quantitation

Table 2173. Term [MS:1002283]
id	MS:1002283
name	SRM protein level quantitation
def	"Selected Reaction Monitoring protein level quantitation." [PSI:PI]
is_a	MS:1001838 SRM quantitation analysis ! SRM quantitation analysis

2.2172. MS:1002284 SRM proteingroup level quantitation

Table 2174. Term [MS:1002284]
id	MS:1002284
name	SRM proteingroup level quantitation
def	"Selected Reaction Monitoring proteingroup level quantitation." [PSI:PI]
is_a	MS:1001838 SRM quantitation analysis ! SRM quantitation analysis

2.2173. MS:1002285 Trans-Proteomic Pipeline

Table 2175. Term [MS:1002285]
id	MS:1002285
name	Trans-Proteomic Pipeline
def	"A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology." [PSI:PI]
synonym	"TPP" EXACT []
is_a	MS:1001456 analysis software ! analysis software

2.2174. MS:1002286 Trans-Proteomic Pipeline software

Table 2176. Term [MS:1002286]
id	MS:1002286
name	Trans-Proteomic Pipeline software
def	"A software program that is a component of the Trans-Proteomic Pipeline." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software
relationship	part_of MS:1002285 Trans-Proteomic Pipeline ! Trans-Proteomic Pipeline

2.2175. MS:1002287 PeptideProphet

Table 2177. Term [MS:1002287]
id	MS:1002287
name	PeptideProphet
def	"A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format." [PMID:12403597, PMID:23176103]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2176. MS:1002288 iProphet

Table 2178. Term [MS:1002288]
id	MS:1002288
name	iProphet
def	"A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204]
synonym	"InterProphet" EXACT []
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2177. MS:1002289 ProteinProphet

Table 2179. Term [MS:1002289]
id	MS:1002289
name	ProteinProphet
def	"A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format." [PMID:14632076]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2178. MS:1002290 XPRESS

Table 2180. Term [MS:1002290]
id	MS:1002290
name	XPRESS
def	"A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2179. MS:1002291 Libra

Table 2181. Term [MS:1002291]
id	MS:1002291
name	Libra
def	"A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc." [PSI:PI]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2180. MS:1002292 PTMProphet

Table 2182. Term [MS:1002292]
id	MS:1002292
name	PTMProphet
def	"A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites." [PSI:PI]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2181. MS:1002293 Bruker Daltonics SCION series

Table 2183. Term [MS:1002293]
id	MS:1002293
name	Bruker Daltonics SCION series
def	"Bruker Daltonics' SCION series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.2182. MS:1002294 Bruker Daltonics EVOQ series

Table 2184. Term [MS:1002294]
id	MS:1002294
name	Bruker Daltonics EVOQ series
def	"Bruker Daltonics' EVOQ series." [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.2183. MS:1002295 SCION SQ

Table 2185. Term [MS:1002295]
id	MS:1002295
name	SCION SQ
def	"Bruker Daltonics' SCION SQ: GC-single quadrupole." [PSI:MS]
is_a	MS:1002293 Bruker Daltonics SCION series ! Bruker Daltonics SCION series

2.2184. MS:1002296 SCION TQ

Table 2186. Term [MS:1002296]
id	MS:1002296
name	SCION TQ
def	"Bruker Daltonics' SCION TQ: GC-triple quadrupole." [PSI:MS]
is_a	MS:1002293 Bruker Daltonics SCION series ! Bruker Daltonics SCION series

2.2185. MS:1002297 EVOQ Elite

Table 2187. Term [MS:1002297]
id	MS:1002297
name	EVOQ Elite
def	"Bruker Daltonics' EVOQ Elite: LC-triple quadrupole." [PSI:MS]
is_a	MS:1002294 Bruker Daltonics EVOQ series ! Bruker Daltonics EVOQ series

2.2186. MS:1002298 EVOQ Qube

Table 2188. Term [MS:1002298]
id	MS:1002298
name	EVOQ Qube
def	"Bruker Daltonics' EVOQ Qube: LC-triple quadrupole." [PSI:MS]
is_a	MS:1002294 Bruker Daltonics EVOQ series ! Bruker Daltonics EVOQ series

2.2187. MS:1002299 micrOTOF-Q III

Table 2189. Term [MS:1002299]
id	MS:1002299
name	micrOTOF-Q III
def	"Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.2188. MS:1002300 amaZon Speed ETD

Table 2190. Term [MS:1002300]
id	MS:1002300
name	amaZon Speed ETD
def	"Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001545 Bruker Daltonics amaZon series ! Bruker Daltonics amaZon series

2.2189. MS:1002301 amaZon Speed

Table 2191. Term [MS:1002301]
id	MS:1002301
name	amaZon Speed
def	"Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a	MS:1001545 Bruker Daltonics amaZon series ! Bruker Daltonics amaZon series

2.2190. MS:1002302 Bruker Container format

Table 2192. Term [MS:1002302]
id	MS:1002302
name	Bruker Container format
def	"Bruker Container raw file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2191. MS:1002303 Bruker Container nativeID format

Table 2193. Term [MS:1002303]
id	MS:1002303
name	Bruker Container nativeID format
def	"Native identifier (UUID)." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.2192. MS:1002304 domain range

Table 2194. Term [MS:1002304]
id	MS:1002304
name	domain range
def	"Domain range of a numerical value." [PSI:PI]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.2193. MS:1002305 value between 0 and 1 inclusive

Table 2195. Term [MS:1002305]
id	MS:1002305
name	value between 0 and 1 inclusive
def	"Value range for probabilities." [PSI:PI]
is_a	MS:1002304 domain range ! domain range

2.2194. MS:1002306 value greater than zero

Table 2196. Term [MS:1002306]
id	MS:1002306
name	value greater than zero
def	"Positive value range." [PSI:PI]
is_a	MS:1002304 domain range ! domain range

2.2195. MS:1002307 fragmentation ion type

Table 2197. Term [MS:1002307]
id	MS:1002307
name	fragmentation ion type
def	"Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion." [PSI:PI]
is_a	MS:1001221 product ion attribute ! product ion attribute

2.2196. MS:1002308 fluorescence detector

Table 2198. Term [MS:1002308]
id	MS:1002308
name	fluorescence detector
def	"A detector using a fluorescent signal after excitation with light." [PSI:MS]
is_a	MS:1000026 detector type ! detector type

2.2197. MS:1002309 Byonic: Peptide AbsLogProb

Table 2199. Term [MS:1002309]
id	MS:1002309
name	Byonic: Peptide AbsLogProb
def	"The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2198. MS:1002310 Byonic: Protein AbsLogProb

Table 2200. Term [MS:1002310]
id	MS:1002310
name	Byonic: Protein AbsLogProb
def	"The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2199. MS:1002311 Byonic: Peptide AbsLogProb2D

Table 2201. Term [MS:1002311]
id	MS:1002311
name	Byonic: Peptide AbsLogProb2D
def	"The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2200. MS:1002312 MS-Numpress linear prediction compression

Table 2202. Term [MS:1002312]
id	MS:1002312
name	MS-Numpress linear prediction compression
def	"Compression using MS-Numpress linear prediction compression." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2201. MS:1002313 MS-Numpress positive integer compression

Table 2203. Term [MS:1002313]
id	MS:1002313
name	MS-Numpress positive integer compression
def	"Compression using MS-Numpress positive integer compression." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2202. MS:1002314 MS-Numpress short logged float compression

Table 2204. Term [MS:1002314]
id	MS:1002314
name	MS-Numpress short logged float compression
def	"Compression using MS-Numpress short logged float compression." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2203. MS:1002315 consensus result

Table 2205. Term [MS:1002315]
id	MS:1002315
name	consensus result
def	"Indicates a consensus result from several search engine runs." [PSI:PI]
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2204. MS:1002316 ProteomeDiscoverer:Amanda:high confidence threshold

Table 2206. Term [MS:1002316]
id	MS:1002316
name	ProteomeDiscoverer:Amanda:high confidence threshold
def	"Strict confidence probability score." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2205. MS:1002317 ProteomeDiscoverer:Amanda:middle confidence threshold

Table 2207. Term [MS:1002317]
id	MS:1002317
name	ProteomeDiscoverer:Amanda:middle confidence threshold
def	"Relaxed confidence probability score." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2206. MS:1002318 ProteomeDiscoverer:automatic workload

Table 2208. Term [MS:1002318]
id	MS:1002318
name	ProteomeDiscoverer:automatic workload
def	"Flag indicating automatic estimation of the workload level." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2207. MS:1002319 Amanda:AmandaScore

Table 2209. Term [MS:1002319]
id	MS:1002319
name	Amanda:AmandaScore
def	"The Amanda score of the scoring function for a PSM." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2208. MS:1002320 ProteomeDiscoverer:max differential modifications

Table 2210. Term [MS:1002320]
id	MS:1002320
name	ProteomeDiscoverer:max differential modifications
def	"Maximum dynamic modifications per PSM." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2209. MS:1002321 ProteomeDiscoverer:max equal modifications

Table 2211. Term [MS:1002321]
id	MS:1002321
name	ProteomeDiscoverer:max equal modifications
def	"Maximum equal modifications per PSM." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2210. MS:1002322 ProteomeDiscoverer:min peptide length

Table 2212. Term [MS:1002322]
id	MS:1002322
name	ProteomeDiscoverer:min peptide length
def	"Minimum peptide length." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2211. MS:1002323 ProteomeDiscoverer:max peptide length

Table 2213. Term [MS:1002323]
id	MS:1002323
name	ProteomeDiscoverer:max peptide length
def	"Maximum peptide length." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2212. MS:1002324 ProteomeDiscoverer:max number neutral loss

Table 2214. Term [MS:1002324]
id	MS:1002324
name	ProteomeDiscoverer:max number neutral loss
def	"Maximum number of same neutral losses." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2213. MS:1002325 ProteomeDiscoverer:max number neutral loss modifications

Table 2215. Term [MS:1002325]
id	MS:1002325
name	ProteomeDiscoverer:max number neutral loss modifications
def	"Max number of same neutral losses of modifications." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2214. MS:1002326 ProteomeDiscoverer:use flanking ions

Table 2216. Term [MS:1002326]
id	MS:1002326
name	ProteomeDiscoverer:use flanking ions
def	"Flag for usage of flanking ions." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2215. MS:1002327 ProteomeDiscoverer:max number of same modifs

Table 2217. Term [MS:1002327]
id	MS:1002327
name	ProteomeDiscoverer:max number of same modifs
def	"The maximum number of possible equal modifications per PSM." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2216. MS:1002328 ProteomeDiscoverer:perform deisotoping

Table 2218. Term [MS:1002328]
id	MS:1002328
name	ProteomeDiscoverer:perform deisotoping
def	"Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2217. MS:1002329 ProteomeDiscoverer:ion settings

Table 2219. Term [MS:1002329]
id	MS:1002329
name	ProteomeDiscoverer:ion settings
def	"Specifies the fragment ions and neutral losses that are calculated." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2218. MS:1002330 ProteomeDiscoverer:3. Static Modification

Table 2220. Term [MS:1002330]
id	MS:1002330
name	ProteomeDiscoverer:3. Static Modification
def	"OBSOLETE ProteomeDiscoverer’s 3rd static post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.2219. MS:1002331 ProteomeDiscoverer:5. Dynamic Modification

Table 2221. Term [MS:1002331]
id	MS:1002331
name	ProteomeDiscoverer:5. Dynamic Modification
def	"OBSOLETE ProteomeDiscoverer’s 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment	This term was made obsolete because it’s recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter
is_obsolete	true

2.2220. MS:1002332 lab head

Table 2222. Term [MS:1002332]
id	MS:1002332
name	lab head
def	"The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group." [PSI:PI]
is_a	MS:1002033 contact role ! contact role

2.2221. MS:1002333 conversion software

Table 2223. Term [MS:1002333]
id	MS:1002333
name	conversion software
def	"Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process." [PSI:PI]
is_a	MS:1001457 data processing software ! data processing software

2.2222. MS:1002334 ProCon

Table 2224. Term [MS:1002334]
id	MS:1002334
name	ProCon
def	"Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon]
is_a	MS:1002333 conversion software ! conversion software

2.2223. MS:1002335 PRIDE Converter2

Table 2225. Term [MS:1002335]
id	MS:1002335
name	PRIDE Converter2
def	"Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509]
is_a	MS:1002333 conversion software ! conversion software

2.2224. MS:1002336 Amanda

Table 2226. Term [MS:1002336]
id	MS:1002336
name	Amanda
def	"Amanda scoring system for PSM identification." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2225. MS:1002337 Andromeda

Table 2227. Term [MS:1002337]
id	MS:1002337
name	Andromeda
def	"Andromeda is a peptide search engine." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2226. MS:1002338 Andromeda:score

Table 2228. Term [MS:1002338]
id	MS:1002338
name	Andromeda:score
def	"The probability based score of the Andromeda search engine." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2227. MS:1002339 site:global FDR

Table 2229. Term [MS:1002339]
id	MS:1002339
name	site:global FDR
def	"Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2228. MS:1002340 ProteomeXchange project tag

Table 2230. Term [MS:1002340]
id	MS:1002340
name	ProteomeXchange project tag
def	"Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2229. MS:1002341 second-pass peptide identification

Table 2231. Term [MS:1002341]
id	MS:1002341
name	second-pass peptide identification
def	"A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2230. MS:1002342 MZmine

Table 2232. Term [MS:1002342]
id	MS:1002342
name	MZmine
def	"A framework for differential analysis of mass spectrometry data." [PMID:16403790, PMID:20650010]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2231. MS:1002343 ion stability type

Table 2233. Term [MS:1002343]
id	MS:1002343
name	ion stability type
def	"OBSOLETE Stability type of the ion." [PSI:PI]
comment	This child of the former purgatory term ion was made obsolete.
is_obsolete	true

2.2232. MS:1002344 Maltcms

Table 2234. Term [MS:1002344]
id	MS:1002344
name	Maltcms
def	"Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers." [PSI:PI, http://maltcms.sf.net]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2233. MS:1002345 PSM-level attribute

Table 2235. Term [MS:1002345]
id	MS:1002345
name	PSM-level attribute
def	"Attribute of a single peptide-spectrum match." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2234. MS:1002346 protein group-level identification attribute

Table 2236. Term [MS:1002346]
id	MS:1002346
name	protein group-level identification attribute
def	"Protein group level information." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2235. MS:1002347 PSM-level identification statistic

Table 2237. Term [MS:1002347]
id	MS:1002347
name	PSM-level identification statistic
def	"Identification confidence metric for a peptide spectrum match." [PSI:PI]
is_a	MS:1002345 PSM-level attribute ! PSM-level attribute

2.2236. MS:1002348 protein group-level identification statistic

Table 2238. Term [MS:1002348]
id	MS:1002348
name	protein group-level identification statistic
def	"Identification confidence metric for a protein group." [PSI:PI]
is_a	MS:1002346 protein group-level identification attribute ! protein group-level identification attribute

2.2237. MS:1002349 value greater than zero but less than or equal to one

Table 2239. Term [MS:1002349]
id	MS:1002349
name	value greater than zero but less than or equal to one
def	"Positive value range less than or equal to 1." [PSI:PI]
is_a	MS:1002304 domain range ! domain range

2.2238. MS:1002350 PSM-level global FDR

Table 2240. Term [MS:1002350]
id	MS:1002350
name	PSM-level global FDR
def	"Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002701 PSM-level result list statistic ! PSM-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2239. MS:1002351 PSM-level local FDR

Table 2241. Term [MS:1002351]
id	MS:1002351
name	PSM-level local FDR
def	"Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2240. MS:1002352 PSM-level p-value

Table 2242. Term [MS:1002352]
id	MS:1002352
name	PSM-level p-value
def	"Estimation of the p-value for peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2241. MS:1002353 PSM-level e-value

Table 2243. Term [MS:1002353]
id	MS:1002353
name	PSM-level e-value
def	"Estimation of the e-value for peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.2242. MS:1002354 PSM-level q-value

Table 2244. Term [MS:1002354]
id	MS:1002354
name	PSM-level q-value
def	"Estimation of the q-value for peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2243. MS:1002355 PSM-level FDRScore

Table 2245. Term [MS:1002355]
id	MS:1002355
name	PSM-level FDRScore
def	"mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to 1

2.2244. MS:1002356 PSM-level combined FDRScore

Table 2246. Term [MS:1002356]
id	MS:1002356
name	PSM-level combined FDRScore
def	"mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to 1

2.2245. MS:1002357 PSM-level probability

Table 2247. Term [MS:1002357]
id	MS:1002357
name	PSM-level probability
def	"Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2246. MS:1002358 search engine specific peptide sequence-level identification statistic

Table 2248. Term [MS:1002358]
id	MS:1002358
name	search engine specific peptide sequence-level identification statistic
def	"Search engine specific distinct peptide score." [PSI:PI]
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic

2.2247. MS:1002359 peptide sequence-level local FDR

Table 2249. Term [MS:1002359]
id	MS:1002359
name	peptide sequence-level local FDR
def	"Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2248. MS:1002360 distinct peptide-level FDRScore

Table 2250. Term [MS:1002360]
id	MS:1002360
name	distinct peptide-level FDRScore
def	"MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2249. MS:1002361 distinct peptide-level combined FDRScore

Table 2251. Term [MS:1002361]
id	MS:1002361
name	distinct peptide-level combined FDRScore
def	"Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2250. MS:1002362 peptide sequence-level probability

Table 2252. Term [MS:1002362]
id	MS:1002362
name	peptide sequence-level probability
def	"Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001092 peptide sequence-level identification statistic ! peptide sequence-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2251. MS:1002363 search engine specific score for proteins

Table 2253. Term [MS:1002363]
id	MS:1002363
name	search engine specific score for proteins
def	"Search engine specific protein scores." [PSI:PI]
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.2252. MS:1002364 protein-level local FDR

Table 2254. Term [MS:1002364]
id	MS:1002364
name	protein-level local FDR
def	"Estimation of the local false discovery rate of proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.2253. MS:1002365 FDRScore for proteins

Table 2255. Term [MS:1002365]
id	MS:1002365
name	FDRScore for proteins
def	"MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2254. MS:1002366 combined FDRScore for proteins

Table 2256. Term [MS:1002366]
id	MS:1002366
name	combined FDRScore for proteins
def	"MzidLibrary Combined FDRScore for proteins." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2255. MS:1002367 probability for proteins

Table 2257. Term [MS:1002367]
id	MS:1002367
name	probability for proteins
def	"Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2256. MS:1002368 search engine specific score for protein groups

Table 2258. Term [MS:1002368]
id	MS:1002368
name	search engine specific score for protein groups
def	"Search engine specific protein group scores." [PSI:PI]
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic

2.2257. MS:1002369 protein group-level global FDR

Table 2259. Term [MS:1002369]
id	MS:1002369
name	protein group-level global FDR
def	"Estimation of the global false discovery rate of protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002706 protein group-level result list statistic ! protein group-level result list statistic

2.2258. MS:1002370 protein group-level local FDR

Table 2260. Term [MS:1002370]
id	MS:1002370
name	protein group-level local FDR
def	"Estimation of the local false discovery rate of protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic

2.2259. MS:1002371 protein group-level p-value

Table 2261. Term [MS:1002371]
id	MS:1002371
name	protein group-level p-value
def	"Estimation of the p-value for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2260. MS:1002372 protein group-level e-value

Table 2262. Term [MS:1002372]
id	MS:1002372
name	protein group-level e-value
def	"Estimation of the e-value for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.2261. MS:1002373 protein group-level q-value

Table 2263. Term [MS:1002373]
id	MS:1002373
name	protein group-level q-value
def	"Estimation of the q-value for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2262. MS:1002374 protein group-level FDRScore

Table 2264. Term [MS:1002374]
id	MS:1002374
name	protein group-level FDRScore
def	"mzidLibrary FDRScore for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2263. MS:1002375 protein group-level combined FDRScore

Table 2265. Term [MS:1002375]
id	MS:1002375
name	protein group-level combined FDRScore
def	"mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_domain MS:1002349 value greater than zero but less than or equal to one ! value greater than zero but less than or equal to one

2.2264. MS:1002376 protein group-level probability

Table 2266. Term [MS:1002376]
id	MS:1002376
name	protein group-level probability
def	"Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2265. MS:1002377 ProteomeDiscoverer:Relaxed Score Threshold

Table 2267. Term [MS:1002377]
id	MS:1002377
name	ProteomeDiscoverer:Relaxed Score Threshold
def	"Specifies the threshold value for relaxed scoring." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2266. MS:1002378 ProteomeDiscoverer:Strict Score Threshold

Table 2268. Term [MS:1002378]
id	MS:1002378
name	ProteomeDiscoverer:Strict Score Threshold
def	"Specifies the threshold value for strict scoring." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2267. MS:1002379 ProteomeDiscoverer:Peptide Without Protein Cut Off Score

Table 2269. Term [MS:1002379]
id	MS:1002379
name	ProteomeDiscoverer:Peptide Without Protein Cut Off Score
def	"Cut off score for storing peptides that do not belong to a protein." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2268. MS:1002380 false localization rate

Table 2270. Term [MS:1002380]
id	MS:1002380
name	false localization rate
def	"Estimation of the false localization rate for modification site assignment." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2269. MS:1002381 MALDI Solutions LC-MALDI

Table 2271. Term [MS:1002381]
id	MS:1002381
name	MALDI Solutions LC-MALDI
def	"Software for automated LC-MALDI analysis and reporting." [PSI:PI]
is_a	MS:1001455 acquisition software ! acquisition software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software
is_a	MS:1001557 Shimadzu Corporation software ! Shimadzu Corporation software

2.2270. MS:1002382 Shimadzu MALDI-7090

Table 2272. Term [MS:1002382]
id	MS:1002382
name	Shimadzu MALDI-7090
def	"Shimadzu MALDI-7090: MALDI-TOF-TOF." [PSI:PI]
is_a	MS:1000602 Shimadzu MALDI-TOF instrument model ! Shimadzu MALDI-TOF instrument model

2.2271. MS:1002383 SCiLS software

Table 2273. Term [MS:1002383]
id	MS:1002383
name	SCiLS software
def	"SCiLS software for data acquisition and analysis." [PSI:MS]
is_a	MS:1000531 software ! software

2.2272. MS:1002384 SCiLS Lab

Table 2274. Term [MS:1002384]
id	MS:1002384
name	SCiLS Lab
def	"SCiLS Lab software." [PSI:MS]
is_a	MS:1002383 SCiLS software ! SCiLS software
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2273. MS:1002385 SCiLS Lab format

Table 2275. Term [MS:1002385]
id	MS:1002385
name	SCiLS Lab format
def	"SCiLS Lab file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2274. MS:1002386 preprocessing software

Table 2276. Term [MS:1002386]
id	MS:1002386
name	preprocessing software
def	"Preprocessing software." [PSI:PI]
is_a	MS:1001457 data processing software ! data processing software

2.2275. MS:1002387 PIA

Table 2277. Term [MS:1002387]
id	MS:1002387
name	PIA
def	"PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia]
is_a	MS:1002414 postprocessing software ! postprocessing software
is_a	MS:1001456 analysis software ! analysis software

2.2276. MS:1002388 PIA XML format

Table 2278. Term [MS:1002388]
id	MS:1002388
name	PIA XML format
def	"A compilation of search engine results in the PIA XML format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.2277. MS:1002389 PIA workflow parameter

Table 2279. Term [MS:1002389]
id	MS:1002389
name	PIA workflow parameter
def	"A parameter set for a single PIA analysis." [PSI:PI]
is_a	MS:1002105 software specific input parameter ! software specific input parameter
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.2278. MS:1002390 PIA:FDRScore calculated

Table 2280. Term [MS:1002390]
id	MS:1002390
name	PIA:FDRScore calculated
def	"Indicates whether the FDR score was calculated for the input file." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2279. MS:1002391 PIA:Combined FDRScore calculated

Table 2281. Term [MS:1002391]
id	MS:1002391
name	PIA:Combined FDRScore calculated
def	"Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2280. MS:1002392 PIA:PSM sets created

Table 2282. Term [MS:1002392]
id	MS:1002392
name	PIA:PSM sets created
def	"Indicates whether PSM sets were created." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2281. MS:1002393 PIA:used top identifications for FDR

Table 2283. Term [MS:1002393]
id	MS:1002393
name	PIA:used top identifications for FDR
def	"The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2282. MS:1002394 PIA:protein score

Table 2284. Term [MS:1002394]
id	MS:1002394
name	PIA:protein score
def	"The score given to a protein by any protein inference." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2283. MS:1002395 PIA:protein inference

Table 2285. Term [MS:1002395]
id	MS:1002395
name	PIA:protein inference
def	"The used algorithm for the protein inference using PIA." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2284. MS:1002396 PIA:protein inference filter

Table 2286. Term [MS:1002396]
id	MS:1002396
name	PIA:protein inference filter
def	"A filter used by PIA for the protein inference." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2285. MS:1002397 PIA:protein inference scoring

Table 2287. Term [MS:1002397]
id	MS:1002397
name	PIA:protein inference scoring
def	"The used scoring method for the protein inference using PIA." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2286. MS:1002398 PIA:protein inference used score

Table 2288. Term [MS:1002398]
id	MS:1002398
name	PIA:protein inference used score
def	"The used base score for the protein inference using PIA." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2287. MS:1002399 PIA:protein inference used PSMs

Table 2289. Term [MS:1002399]
id	MS:1002399
name	PIA:protein inference used PSMs
def	"The method to determine the PSMs used for scoring by the protein inference." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2288. MS:1002400 PIA:filter

Table 2290. Term [MS:1002400]
id	MS:1002400
name	PIA:filter
def	"A filter used for the report generation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002389 PIA workflow parameter ! PIA workflow parameter

2.2289. MS:1002401 leading protein

Table 2291. Term [MS:1002401]
id	MS:1002401
name	leading protein
def	"At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members." [PSI:PI]
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2290. MS:1002402 non-leading protein

Table 2292. Term [MS:1002402]
id	MS:1002402
name	non-leading protein
def	"Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence." [PSI:PI]
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2291. MS:1002403 group representative

Table 2293. Term [MS:1002403]
id	MS:1002403
name	group representative
def	"An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative." [PSI:PI]
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2292. MS:1002404 count of identified proteins

Table 2294. Term [MS:1002404]
id	MS:1002404
name	count of identified proteins
def	"The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002704 protein-level result list attribute ! protein-level result list attribute

2.2293. MS:1002405 protein group-level result list attribute

Table 2295. Term [MS:1002405]
id	MS:1002405
name	protein group-level result list attribute
def	"Details describing a protein cluster." [PSI:PI]
is_a	MS:1002699 result list attribute ! result list attribute

2.2294. MS:1002406 count of identified clusters

Table 2296. Term [MS:1002406]
id	MS:1002406
name	count of identified clusters
def	"The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002405 protein group-level result list attribute ! protein group-level result list attribute

2.2295. MS:1002407 cluster identifier

Table 2297. Term [MS:1002407]
id	MS:1002407
name	cluster identifier
def	"An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002698 protein cluster identification attribute ! protein cluster identification attribute

2.2296. MS:1002408 number of distinct protein sequences

Table 2298. Term [MS:1002408]
id	MS:1002408
name	number of distinct protein sequences
def	"The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002405 protein group-level result list attribute ! protein group-level result list attribute

2.2297. MS:1002409 marginally distinguished protein

Table 2299. Term [MS:1002409]
id	MS:1002409
name	marginally distinguished protein
def	"Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group." [PSI:PI]
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2298. MS:1002410 Anubis

Table 2300. Term [MS:1002410]
id	MS:1002410
name	Anubis
def	"Anubis software for selected reaction monitoring data." [PSI:PI, http://quantitativeproteomics.org/anubis]
is_a	MS:1000871 SRM software ! SRM software
is_a	MS:1001139 quantitation software name ! quantitation software name

2.2299. MS:1002411 TraML format

Table 2301. Term [MS:1002411]
id	MS:1002411
name	TraML format
def	"The TraML format for transitions in SRM from the PSI. File extension '.TraML'." [PSI:PI, http://www.psidev.info/traml]
is_a	MS:1002128 method file format ! method file format

2.2300. MS:1002412 total XIC area

Table 2302. Term [MS:1002412]
id	MS:1002412
name	total XIC area
def	"Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.2301. MS:1002413 product background

Table 2303. Term [MS:1002413]
id	MS:1002413
name	product background
def	"The background area for the quantified transition." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2302. MS:1002414 postprocessing software

Table 2304. Term [MS:1002414]
id	MS:1002414
name	postprocessing software
def	"Postprocessing software." [PSI:PI]
is_a	MS:1001457 data processing software ! data processing software

2.2303. MS:1002415 protein group passes threshold

Table 2305. Term [MS:1002415]
id	MS:1002415
name	protein group passes threshold
def	"A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002346 protein group-level identification attribute ! protein group-level identification attribute

2.2304. MS:1002416 Orbitrap Fusion

Table 2306. Term [MS:1002416]
id	MS:1002416
name	Orbitrap Fusion
def	"Thermo Scientific Orbitrap Fusion." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2305. MS:1002417 Orbitrap Fusion ETD

Table 2307. Term [MS:1002417]
id	MS:1002417
name	Orbitrap Fusion ETD
def	"Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2306. MS:1002418 TSQ Quantiva

Table 2308. Term [MS:1002418]
id	MS:1002418
name	TSQ Quantiva
def	"Thermo Scientific TSQ Quantiva MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2307. MS:1002419 TSQ Endura

Table 2309. Term [MS:1002419]
id	MS:1002419
name	TSQ Endura
def	"Thermo Scientific TSQ Endura MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2308. MS:1002420 PASSEL experiment URI

Table 2310. Term [MS:1002420]
id	MS:1002420
name	PASSEL experiment URI
def	"URI that allows access to a PASSEL experiment." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2309. MS:1002421 Paragon input parameter

Table 2311. Term [MS:1002421]
id	MS:1002421
name	Paragon input parameter
def	"Search engine input parameters specific to Paragon." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.2310. MS:1002422 Paragon: sample type

Table 2312. Term [MS:1002422]
id	MS:1002422
name	Paragon: sample type
def	"The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2311. MS:1002423 Paragon: cysteine alkylation

Table 2313. Term [MS:1002423]
id	MS:1002423
name	Paragon: cysteine alkylation
def	"The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2312. MS:1002424 Paragon: instrument setting

Table 2314. Term [MS:1002424]
id	MS:1002424
name	Paragon: instrument setting
def	"The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2313. MS:1002425 Paragon: search effort

Table 2315. Term [MS:1002425]
id	MS:1002425
name	Paragon: search effort
def	"The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2314. MS:1002426 Paragon: ID focus

Table 2316. Term [MS:1002426]
id	MS:1002426
name	Paragon: ID focus
def	"A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2315. MS:1002427 Paragon: FDR analysis

Table 2317. Term [MS:1002427]
id	MS:1002427
name	Paragon: FDR analysis
def	"The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2316. MS:1002428 Paragon: quantitation

Table 2318. Term [MS:1002428]
id	MS:1002428
name	Paragon: quantitation
def	"The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2317. MS:1002429 Paragon: background correction

Table 2319. Term [MS:1002429]
id	MS:1002429
name	Paragon: background correction
def	"The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2318. MS:1002430 Paragon: bias correction

Table 2320. Term [MS:1002430]
id	MS:1002430
name	Paragon: bias correction
def	"The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2319. MS:1002431 Paragon: channel to use as denominator in ratios

Table 2321. Term [MS:1002431]
id	MS:1002431
name	Paragon: channel to use as denominator in ratios
def	"The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2320. MS:1002432 search engine specific input metadata

Table 2322. Term [MS:1002432]
id	MS:1002432
name	search engine specific input metadata
def	"Search engine specific metadata that are not user-controlled settings." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.2321. MS:1002433 Paragon: modified data dictionary or parameter translation

Table 2323. Term [MS:1002433]
id	MS:1002433
name	Paragon: modified data dictionary or parameter translation
def	"This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002432 search engine specific input metadata ! search engine specific input metadata

2.2322. MS:1002434 number of spectra searched

Table 2324. Term [MS:1002434]
id	MS:1002434
name	number of spectra searched
def	"Number of spectra in a search." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001249 search input details ! search input details

2.2323. MS:1002435 data processing start time

Table 2325. Term [MS:1002435]
id	MS:1002435
name	data processing start time
def	"The time that a data processing action was started." [PSI:MS]
xref	value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a	MS:1000630 data processing parameter ! data processing parameter

2.2324. MS:1002436 Paragon: digestion

Table 2326. Term [MS:1002436]
id	MS:1002436
name	Paragon: digestion
def	"The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001249 search input details ! search input details

2.2325. MS:1002437 number of decoy sequences

Table 2327. Term [MS:1002437]
id	MS:1002437
name	number of decoy sequences
def	"The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI]
xref	value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a	MS:1001011 search database details ! search database details

2.2326. MS:1002438 spectrum identification list result details

Table 2328. Term [MS:1002438]
id	MS:1002438
name	spectrum identification list result details
def	"Information about the list of PSMs (SpectrumIdentificationList)." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.2327. MS:1002439 final PSM list

Table 2329. Term [MS:1002439]
id	MS:1002439
name	final PSM list
def	"A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a	MS:1002438 spectrum identification list result details ! spectrum identification list result details

2.2328. MS:1002440 intermediate PSM list

Table 2330. Term [MS:1002440]
id	MS:1002440
name	intermediate PSM list
def	"A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a	MS:1002438 spectrum identification list result details ! spectrum identification list result details

2.2329. MS:1002441 Andi-MS format

Table 2331. Term [MS:1002441]
id	MS:1002441
name	Andi-MS format
def	"AIA Analytical Data Interchange file format for mass spectrometry data." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2330. MS:1002442 chromatograph file format

Table 2332. Term [MS:1002442]
id	MS:1002442
name	chromatograph file format
def	"The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:PI]
is_a	MS:1001459 file format ! file format

2.2331. MS:1002443 Andi-CHROM format

Table 2333. Term [MS:1002443]
id	MS:1002443
name	Andi-CHROM format
def	"AIA Analytical Data Interchange file format for chromatography data." [PSI:PI]
is_a	MS:1002442 chromatograph file format ! chromatograph file format

2.2332. MS:1002444 6420 Triple Quadrupole LC/MS

Table 2334. Term [MS:1002444]
id	MS:1002444
name	6420 Triple Quadrupole LC/MS
def	"The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2333. MS:1002445 6460 Triple Quadrupole LC/MS

Table 2335. Term [MS:1002445]
id	MS:1002445
name	6460 Triple Quadrupole LC/MS
def	"The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2334. MS:1002446 6490 Triple Quadrupole LC/MS

Table 2336. Term [MS:1002446]
id	MS:1002446
name	6490 Triple Quadrupole LC/MS
def	"The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2335. MS:1002447 Paragon:special factor

Table 2337. Term [MS:1002447]
id	MS:1002447
name	Paragon:special factor
def	"The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002421 Paragon input parameter ! Paragon input parameter

2.2336. MS:1002448 PEAKS:inChorusPeptideScore

Table 2338. Term [MS:1002448]
id	MS:1002448
name	PEAKS:inChorusPeptideScore
def	"The PEAKS inChorus peptide score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2337. MS:1002449 PEAKS:inChorusProteinScore

Table 2339. Term [MS:1002449]
id	MS:1002449
name	PEAKS:inChorusProteinScore
def	"The PEAKS inChorus protein score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2338. MS:1002450 param: b ion-H3PO4 DEPRECATED

Table 2340. Term [MS:1002450]
id	MS:1002450
name	param: b ion-H3PO4 DEPRECATED
def	"Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.2339. MS:1002451 param: y ion-H3PO4 DEPRECATED

Table 2341. Term [MS:1002451]
id	MS:1002451
name	param: y ion-H3PO4 DEPRECATED
def	"Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI]
is_a	MS:1001066 ions series considered in search ! ions series considered in search

2.2340. MS:1002452 Maui

Table 2342. Term [MS:1002452]
id	MS:1002452
name	Maui
def	"The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2341. MS:1002453 No fixed modifications searched

Table 2343. Term [MS:1002453]
id	MS:1002453
name	No fixed modifications searched
def	"No fixed modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI]
is_a	MS:1002094 common search engine input parameter ! common search engine input parameter

2.2342. MS:1002454 No variable modifications searched

Table 2344. Term [MS:1002454]
id	MS:1002454
name	No variable modifications searched
def	"No variable modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI]
is_a	MS:1002094 common search engine input parameter ! common search engine input parameter

2.2343. MS:1002455 H2O neutral loss

Table 2345. Term [MS:1002455]
id	MS:1002455
name	H2O neutral loss
def	"OBSOLETE Neutral loss of water." [PSI:PI]
comment	This term was obsoleted because it should be replaced by MS:1000336 with value H2O.
is_a	MS:1000336 neutral loss ! neutral loss
is_a	MS:1002473 ion series considered in search ! ion series considered in search
is_obsolete	true

2.2344. MS:1002456 NH3 neutral loss

Table 2346. Term [MS:1002456]
id	MS:1002456
name	NH3 neutral loss
def	"OBSOLETE Neutral loss of ammonia." [PSI:PI]
comment	This term was obsoleted because it should be replaced by MS:1000336 with value NH3.
is_a	MS:1000336 neutral loss ! neutral loss
is_a	MS:1002473 ion series considered in search ! ion series considered in search
is_obsolete	true

2.2345. MS:1002457 H3PO4 neutral loss

Table 2347. Term [MS:1002457]
id	MS:1002457
name	H3PO4 neutral loss
def	"OBSOLETE Neutral loss of phosphoric acid." [PSI:PI]
comment	This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4.
is_a	MS:1000336 neutral loss ! neutral loss
is_a	MS:1002473 ion series considered in search ! ion series considered in search
is_obsolete	true

2.2346. MS:1002458 PeptideShaker

Table 2348. Term [MS:1002458]
id	MS:1002458
name	PeptideShaker
def	"PeptideShaker is a software for the interpretation of proteomics identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a	MS:1001456 analysis software ! analysis software

2.2347. MS:1002459 MS Amanda csv format

Table 2349. Term [MS:1002459]
id	MS:1002459
name	MS Amanda csv format
def	"MS Amanda csv output format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.2348. MS:1002460 protein group-level global FNR

Table 2350. Term [MS:1002460]
id	MS:1002460
name	protein group-level global FNR
def	"Estimation of the global false negative rate of protein groups." [PSI:PI]
is_a	MS:1002706 protein group-level result list statistic ! protein group-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2349. MS:1002461 protein group-level confidence

Table 2351. Term [MS:1002461]
id	MS:1002461
name	protein group-level confidence
def	"Estimation of the global confidence of protein groups." [PSI:PI]
is_a	MS:1002348 protein group-level identification statistic ! protein group-level identification statistic

2.2350. MS:1002462 peptide sequence-level global FNR

Table 2352. Term [MS:1002462]
id	MS:1002462
name	peptide sequence-level global FNR
def	"Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a	MS:1002703 peptide sequence-level result list statistic ! peptide sequence-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2351. MS:1002463 peptide sequence-level global confidence

Table 2353. Term [MS:1002463]
id	MS:1002463
name	peptide sequence-level global confidence
def	"Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a	MS:1002703 peptide sequence-level result list statistic ! peptide sequence-level result list statistic

2.2352. MS:1002464 PSM-level global FNR

Table 2354. Term [MS:1002464]
id	MS:1002464
name	PSM-level global FNR
def	"Estimation of the global false negative rate of peptide spectrum matches." [PSI:PI]
is_a	MS:1002701 PSM-level result list statistic ! PSM-level result list statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2353. MS:1002465 PSM-level global confidence

Table 2355. Term [MS:1002465]
id	MS:1002465
name	PSM-level global confidence
def	"Estimation of the global confidence of peptide spectrum matches." [PSI:PI]
is_a	MS:1002701 PSM-level result list statistic ! PSM-level result list statistic

2.2354. MS:1002466 PeptideShaker PSM score

Table 2356. Term [MS:1002466]
id	MS:1002466
name	PeptideShaker PSM score
def	"The probability based PeptideShaker PSM score." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2355. MS:1002467 PeptideShaker PSM confidence

Table 2357. Term [MS:1002467]
id	MS:1002467
name	PeptideShaker PSM confidence
def	"The probability based PeptideShaker PSM confidence." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2356. MS:1002468 PeptideShaker peptide score

Table 2358. Term [MS:1002468]
id	MS:1002468
name	PeptideShaker peptide score
def	"The probability based PeptideShaker peptide score." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2357. MS:1002469 PeptideShaker peptide confidence

Table 2359. Term [MS:1002469]
id	MS:1002469
name	PeptideShaker peptide confidence
def	"The probability based PeptideShaker peptide confidence." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2358. MS:1002470 PeptideShaker protein group score

Table 2360. Term [MS:1002470]
id	MS:1002470
name	PeptideShaker protein group score
def	"The probability based PeptideShaker protein group score." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_order MS:1002108 higher score better ! higher score better

2.2359. MS:1002471 PeptideShaker protein group confidence

Table 2361. Term [MS:1002471]
id	MS:1002471
name	PeptideShaker protein group confidence
def	"The probability based PeptideShaker protein group confidence." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins
relationship	has_order MS:1002108 higher score better ! higher score better

2.2360. MS:1002472 trap-type collision-induced dissociation

Table 2362. Term [MS:1002472]
id	MS:1002472
name	trap-type collision-induced dissociation
def	"A collision-induced dissociation process that occurs in a trap-type collision cell." [PSI:PI]
is_a	MS:1000133 collision-induced dissociation ! collision-induced dissociation

2.2361. MS:1002473 ion series considered in search

Table 2363. Term [MS:1002473]
id	MS:1002473
name	ion series considered in search
def	"The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI]
is_a	MS:1001249 search input details ! search input details

2.2362. MS:1002474 ProteoAnnotator:non-canonical gene model score

Table 2364. Term [MS:1002474]
id	MS:1002474
name	ProteoAnnotator:non-canonical gene model score
def	"The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_order MS:1002108 higher score better ! higher score better

2.2363. MS:1002475 ProteoAnnotator:count alternative peptides

Table 2365. Term [MS:1002475]
id	MS:1002475
name	ProteoAnnotator:count alternative peptides
def	"The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups

2.2364. MS:1002476 ion mobility drift time

Table 2366. Term [MS:1002476]
id	MS:1002476
name	ion mobility drift time
def	"Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
is_a	MS:1002892 ion mobility attribute ! ion mobility attribute
relationship	has_units [UO:0000028] ! millisecond

2.2365. MS:1002477 mean drift time array

Table 2367. Term [MS:1002477]
id	MS:1002477
name	mean drift time array
def	"Array of drift times, averaged from a matrix of binned m/z and drift time values, corresponding to spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002893 ion mobility array ! ion mobility array
relationship	has_units [UO:0000028] ! millisecond
relationship	has_units [UO:0000010] ! second

2.2366. MS:1002478 mean charge array

Table 2368. Term [MS:1002478]
id	MS:1002478
name	mean charge array
def	"Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.2367. MS:1002479 regular expression

Table 2369. Term [MS:1002479]
id	MS:1002479
name	regular expression
def	"Regular expression." [PSI:PI]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.2368. MS:1002480 regular expression for a digital object identifier (DOI)

Table 2370. Term [MS:1002480]
id	MS:1002480
name	regular expression for a digital object identifier (DOI)
def	"(10[.][0-9]\{4,\}(?:[.])*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f]))." [PSI:PI, http://dx.doi.org/]
is_a	MS:1002479 regular expression ! regular expression

2.2369. MS:1002481 higher energy beam-type collision-induced dissociation

Table 2371. Term [MS:1002481]
id	MS:1002481
name	higher energy beam-type collision-induced dissociation
def	"A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS]
is_a	MS:1000422 beam-type collision-induced dissociation ! beam-type collision-induced dissociation

2.2370. MS:1002482 statistical threshold

Table 2372. Term [MS:1002482]
id	MS:1002482
name	statistical threshold
def	"Estimated statistical threshold." [PSI:MS]
is_a	MS:1001060 quality estimation method details ! quality estimation method details

2.2371. MS:1002483 PSM-level statistical threshold

Table 2373. Term [MS:1002483]
id	MS:1002483
name	PSM-level statistical threshold
def	"Estimated statistical threshold at PSM-level." [PSI:MS]
is_a	MS:1002573 spectrum identification statistical threshold ! spectrum identification statistical threshold

2.2372. MS:1002484 peptide-level statistical threshold

Table 2374. Term [MS:1002484]
id	MS:1002484
name	peptide-level statistical threshold
def	"Estimated statistical threshold at peptide-level." [PSI:MS]
is_a	MS:1002573 spectrum identification statistical threshold ! spectrum identification statistical threshold

2.2373. MS:1002485 protein-level statistical threshold

Table 2375. Term [MS:1002485]
id	MS:1002485
name	protein-level statistical threshold
def	"Estimated statistical threshold at protein-level." [PSI:MS]
is_a	MS:1002572 protein detection statistical threshold ! protein detection statistical threshold

2.2374. MS:1002486 protein group-level statistical threshold

Table 2376. Term [MS:1002486]
id	MS:1002486
name	protein group-level statistical threshold
def	"Estimated statistical threshold at protein group-level." [PSI:PI]
is_a	MS:1002572 protein detection statistical threshold ! protein detection statistical threshold

2.2375. MS:1002487 MassIVE dataset identifier

Table 2377. Term [MS:1002487]
id	MS:1002487
name	MassIVE dataset identifier
def	"Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2376. MS:1002488 MassIVE dataset URI

Table 2378. Term [MS:1002488]
id	MS:1002488
name	MassIVE dataset URI
def	"URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2377. MS:1002489 special processing

Table 2379. Term [MS:1002489]
id	MS:1002489
name	special processing
def	"Details describing a special processing." [PSI:PI]
is_a	MS:1001080 search type ! search type
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.2378. MS:1002490 peptide-level scoring

Table 2380. Term [MS:1002490]
id	MS:1002490
name	peptide-level scoring
def	"Peptide-level scoring performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2379. MS:1002491 modification localization scoring

Table 2381. Term [MS:1002491]
id	MS:1002491
name	modification localization scoring
def	"Modification localization scoring performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2380. MS:1002492 consensus scoring

Table 2382. Term [MS:1002492]
id	MS:1002492
name	consensus scoring
def	"Consensus multiple search engine approach performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2381. MS:1002493 sample pre-fractionation

Table 2383. Term [MS:1002493]
id	MS:1002493
name	sample pre-fractionation
def	"Sample pre-fractionation performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2382. MS:1002494 cross-linking search

Table 2384. Term [MS:1002494]
id	MS:1002494
name	cross-linking search
def	"Cross-linking search performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2383. MS:1002495 no special processing

Table 2385. Term [MS:1002495]
id	MS:1002495
name	no special processing
def	"No special processing performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2384. MS:1002496 group PSMs by sequence

Table 2386. Term [MS:1002496]
id	MS:1002496
name	group PSMs by sequence
def	"Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
is_a	MS:1002658 identification parameter ! identification parameter

2.2385. MS:1002497 group PSMs by sequence with modifications

Table 2387. Term [MS:1002497]
id	MS:1002497
name	group PSMs by sequence with modifications
def	"Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
is_a	MS:1002658 identification parameter ! identification parameter

2.2386. MS:1002498 group PSMs by sequence with modifications and charge

Table 2388. Term [MS:1002498]
id	MS:1002498
name	group PSMs by sequence with modifications and charge
def	"Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
is_a	MS:1002658 identification parameter ! identification parameter

2.2387. MS:1002499 peptide level score

Table 2389. Term [MS:1002499]
id	MS:1002499
name	peptide level score
def	"OBSOLETE Peptide level score." [PSI:PI]
comment	This term was obsoleted because it was never intended to go in the CV.
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic
is_obsolete	true

2.2388. MS:1002500 peptide passes threshold

Table 2390. Term [MS:1002500]
id	MS:1002500
name	peptide passes threshold
def	"A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2389. MS:1002501 no PSM threshold

Table 2391. Term [MS:1002501]
id	MS:1002501
name	no PSM threshold
def	"Indicating that no PSM threshold was used." [PSI:PI]
is_a	MS:1002701 PSM-level result list statistic ! PSM-level result list statistic

2.2390. MS:1002502 no peptide-level threshold

Table 2392. Term [MS:1002502]
id	MS:1002502
name	no peptide-level threshold
def	"Indicating that no peptide-level threshold was used." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2391. MS:1002503 PSM is used for peptide-level scoring

Table 2393. Term [MS:1002503]
id	MS:1002503
name	PSM is used for peptide-level scoring
def	"Flags a PSM that it is used for peptide-level scoring." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2392. MS:1002504 modification index

Table 2394. Term [MS:1002504]
id	MS:1002504
name	modification index
def	"The order of modifications to be referenced elsewhere in the document." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1001055 modification parameters ! modification parameters

2.2393. MS:1002505 regular expression for modification localization scoring

Table 2395. Term [MS:1002505]
id	MS:1002505
name	regular expression for modification localization scoring
def	"(:[0\|1]\{1\}.[:digit:][Ee]{0,1}[-]{0,1}[:digit:]*:[:digit:][\|]{1}[:digit:]+:(true\|false){1})." [PSI:PI]
is_a	MS:1002479 regular expression ! regular expression

2.2394. MS:1002506 modification position score

Table 2396. Term [MS:1002506]
id	MS:1002506
name	modification position score
def	"Modification position score." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters

2.2395. MS:1002507 modification rescoring:false localization rate

Table 2397. Term [MS:1002507]
id	MS:1002507
name	modification rescoring:false localization rate
def	"Mod position score: false localization rate." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002506 modification position score ! modification position score
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2396. MS:1002508 cross-linking attribute

Table 2398. Term [MS:1002508]
id	MS:1002508
name	cross-linking attribute
def	"Cross-linking attribute." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2397. MS:1002509 cross-link donor

Table 2399. Term [MS:1002509]
id	MS:1002509
name	cross-link donor
def	"The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002508 cross-linking attribute ! cross-linking attribute

2.2398. MS:1002510 cross-link acceptor

Table 2400. Term [MS:1002510]
id	MS:1002510
name	cross-link acceptor
def	"Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002508 cross-linking attribute ! cross-linking attribute

2.2399. MS:1002511 cross-link spectrum identification item

Table 2401. Term [MS:1002511]
id	MS:1002511
name	cross-link spectrum identification item
def	"Cross-linked spectrum identification item." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002508 cross-linking attribute ! cross-linking attribute

2.2400. MS:1002512 cross-linking score

Table 2402. Term [MS:1002512]
id	MS:1002512
name	cross-linking score
def	"Cross-linking scoring value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2401. MS:1002513 molecules per cell

Table 2403. Term [MS:1002513]
id	MS:1002513
name	molecules per cell
def	"The absolute abundance of protein in a cell." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2402. MS:1002514 absolute quantitation analysis

Table 2404. Term [MS:1002514]
id	MS:1002514
name	absolute quantitation analysis
def	"Absolute quantitation analysis." [PSI:PI]
is_a	MS:1001833 quantitation analysis summary ! quantitation analysis summary

2.2403. MS:1002515 internal peptide reference used

Table 2405. Term [MS:1002515]
id	MS:1002515
name	internal peptide reference used
def	"States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001832 quantitation software comment or customizations ! quantitation software comment or customizations

2.2404. MS:1002516 internal protein reference used

Table 2406. Term [MS:1002516]
id	MS:1002516
name	internal protein reference used
def	"States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1001832 quantitation software comment or customizations ! quantitation software comment or customizations

2.2405. MS:1002517 internal reference abundance

Table 2407. Term [MS:1002517]
id	MS:1002517
name	internal reference abundance
def	"The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2406. MS:1002518 Progenesis:protein group normalised abundance

Table 2408. Term [MS:1002518]
id	MS:1002518
name	Progenesis:protein group normalised abundance
def	"The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002739 protein group-level quantification datatype ! protein group-level quantification datatype

2.2407. MS:1002519 Progenesis:protein group raw abundance

Table 2409. Term [MS:1002519]
id	MS:1002519
name	Progenesis:protein group raw abundance
def	"The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002739 protein group-level quantification datatype ! protein group-level quantification datatype

2.2408. MS:1002520 peptide group ID

Table 2410. Term [MS:1002520]
id	MS:1002520
name	peptide group ID
def	"Peptide group identifier for peptide-level stats." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2409. MS:1002521 mass spectrometry imaging

Table 2411. Term [MS:1002521]
id	MS:1002521
name	mass spectrometry imaging
def	"A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position." [PSI:PI]
is_a	MS:1000857 run attribute ! run attribute

2.2410. MS:1002522 ProteomeDiscoverer:1. Static Terminal Modification

Table 2412. Term [MS:1002522]
id	MS:1002522
name	ProteomeDiscoverer:1. Static Terminal Modification
def	"Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2411. MS:1002523 Q Exactive HF

Table 2413. Term [MS:1002523]
id	MS:1002523
name	Q Exactive HF
def	"Thermo Scientific Q Exactive." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2412. MS:1002524 PepFinder

Table 2414. Term [MS:1002524]
id	MS:1002524
name	PepFinder
def	"Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI]
is_a	MS:1001457 data processing software ! data processing software

2.2413. MS:1002525 TSQ 8000 Evo

Table 2415. Term [MS:1002525]
id	MS:1002525
name	TSQ 8000 Evo
def	"Thermo Scientific TSQ 8000 Evo MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2414. MS:1002526 Exactive Plus

Table 2416. Term [MS:1002526]
id	MS:1002526
name	Exactive Plus
def	"Thermo Scientific Exactive Plus MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2415. MS:1002527 instrument specific scan attribute

Table 2417. Term [MS:1002527]
id	MS:1002527
name	instrument specific scan attribute
def	"Instrument specific scan properties that are associated with a value." [PSI:PI]
is_a	MS:1000503 scan attribute ! scan attribute

2.2416. MS:1002528 synchronous prefilter selection

Table 2418. Term [MS:1002528]
id	MS:1002528
name	synchronous prefilter selection
def	"Synchronous prefilter selection." [PSI:PI]
synonym	"SPS" EXACT []
is_a	MS:1002527 instrument specific scan attribute ! instrument specific scan attribute

2.2417. MS:1002529 resolution array

Table 2419. Term [MS:1002529]
id	MS:1002529
name	resolution array
def	"A data array of resolution values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.2418. MS:1002530 baseline array

Table 2420. Term [MS:1002530]
id	MS:1002530
name	baseline array
def	"A data array of signal baseline values (the signal in the absence of analytes)." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.2419. MS:1002531 UIMF format

Table 2421. Term [MS:1002531]
id	MS:1002531
name	UIMF format
def	"SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2420. MS:1002532 UIMF nativeID format

Table 2422. Term [MS:1002532]
id	MS:1002532
name	UIMF nativeID format
def	"Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.2421. MS:1002533 TripleTOF 6600

Table 2423. Term [MS:1002533]
id	MS:1002533
name	TripleTOF 6600
def	"SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2422. MS:1002534 ProLuCID:xcorr

Table 2424. Term [MS:1002534]
id	MS:1002534
name	ProLuCID:xcorr
def	"The ProLuCID result 'XCorr'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2423. MS:1002535 ProLuCID:deltacn

Table 2425. Term [MS:1002535]
id	MS:1002535
name	ProLuCID:deltacn
def	"The ProLuCID result 'DeltaCn'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2424. MS:1002536 D-Score

Table 2426. Term [MS:1002536]
id	MS:1002536
name	D-Score
def	"D-Score for PTM site location at the PSM-level." [PMID:23307401]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2425. MS:1002537 MD-Score

Table 2427. Term [MS:1002537]
id	MS:1002537
name	MD-Score
def	"MD-Score for PTM site location at the PSM-level." [PMID:21057138]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2426. MS:1002538 PTM localization confidence metric

Table 2428. Term [MS:1002538]
id	MS:1002538
name	PTM localization confidence metric
def	"Localization confidence metric for a post translational modification (PTM)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2427. MS:1002539 PeptideShaker PTM confidence type

Table 2429. Term [MS:1002539]
id	MS:1002539
name	PeptideShaker PTM confidence type
def	"PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002538 PTM localization confidence metric ! PTM localization confidence metric

2.2428. MS:1002540 PeptideShaker PSM confidence type

Table 2430. Term [MS:1002540]
id	MS:1002540
name	PeptideShaker PSM confidence type
def	"PeptideShaker quality criteria for the confidence of PSM’s." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002347 PSM-level identification statistic ! PSM-level identification statistic

2.2429. MS:1002541 PeptideShaker peptide confidence type

Table 2431. Term [MS:1002541]
id	MS:1002541
name	PeptideShaker peptide confidence type
def	"PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.2430. MS:1002542 PeptideShaker protein confidence type

Table 2432. Term [MS:1002542]
id	MS:1002542
name	PeptideShaker protein confidence type
def	"PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001116 single protein identification statistic ! single protein identification statistic

2.2431. MS:1002543 xiFDR

Table 2433. Term [MS:1002543]
id	MS:1002543
name	xiFDR
def	"Target/Decoy based FDR estimation for cross-linking peptide-identifications." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2432. MS:1002544 xi

Table 2434. Term [MS:1002544]
id	MS:1002544
name	xi
def	"Search engine for cross-linked peptides." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2433. MS:1002545 xi:score

Table 2435. Term [MS:1002545]
id	MS:1002545
name	xi:score
def	"The xi result 'Score'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2434. MS:1002546 Skyline mzQuantML converter

Table 2436. Term [MS:1002546]
id	MS:1002546
name	Skyline mzQuantML converter
def	"A software package to convert Skyline report to mzQuantML." [PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software

2.2435. MS:1002547 normalized spectral abundance factor

Table 2437. Term [MS:1002547]
id	MS:1002547
name	normalized spectral abundance factor
def	"A normalized spectral abundance factor (NSAF)." [DOI:10.1021/pr060161n, PMID:16944946]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2436. MS:1002548 distributed normalized spectral abundance factor

Table 2438. Term [MS:1002548]
id	MS:1002548
name	distributed normalized spectral abundance factor
def	"A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2437. MS:1002549 PTM localization distinct peptide-level statistic

Table 2439. Term [MS:1002549]
id	MS:1002549
name	PTM localization distinct peptide-level statistic
def	"Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence." [PSI:PI]
is_a	MS:1002689 PTM localization single result statistic ! PTM localization single result statistic

2.2438. MS:1002550 peptide:phosphoRS score

Table 2440. Term [MS:1002550]
id	MS:1002550
name	peptide:phosphoRS score
def	"phosphoRS score for PTM site location at the peptide-level." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002549 PTM localization distinct peptide-level statistic ! PTM localization distinct peptide-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2439. MS:1002551 peptide:Ascore

Table 2441. Term [MS:1002551]
id	MS:1002551
name	peptide:Ascore
def	"A-score for PTM site location at the peptide-level." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002549 PTM localization distinct peptide-level statistic ! PTM localization distinct peptide-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2440. MS:1002552 peptide:H-Score

Table 2442. Term [MS:1002552]
id	MS:1002552
name	peptide:H-Score
def	"H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002549 PTM localization distinct peptide-level statistic ! PTM localization distinct peptide-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2441. MS:1002553 peptide:D-Score

Table 2443. Term [MS:1002553]
id	MS:1002553
name	peptide:D-Score
def	"D-Score for PTM site location at the peptide-level." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002549 PTM localization distinct peptide-level statistic ! PTM localization distinct peptide-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2442. MS:1002554 peptide:MD-Score

Table 2444. Term [MS:1002554]
id	MS:1002554
name	peptide:MD-Score
def	"MD-Score for PTM site location at the peptide-level." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002549 PTM localization distinct peptide-level statistic ! PTM localization distinct peptide-level statistic
relationship	has_regexp MS:1002505 regular expression for modification localization scoring ! regular expression for modification localization scoring

2.2443. MS:1002555 PTM localization score threshold

Table 2445. Term [MS:1002555]
id	MS:1002555
name	PTM localization score threshold
def	"Threshold for PTM site location score." [PSI:PI]
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2444. MS:1002556 Ascore threshold

Table 2446. Term [MS:1002556]
id	MS:1002556
name	Ascore threshold
def	"Threshold for Ascore PTM site location score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2445. MS:1002557 D-Score threshold

Table 2447. Term [MS:1002557]
id	MS:1002557
name	D-Score threshold
def	"Threshold for D-score PTM site location score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2446. MS:1002558 MD-Score threshold

Table 2448. Term [MS:1002558]
id	MS:1002558
name	MD-Score threshold
def	"Threshold for MD-score PTM site location score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2447. MS:1002559 H-Score threshold

Table 2449. Term [MS:1002559]
id	MS:1002559
name	H-Score threshold
def	"Threshold for H-score PTM site location score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2448. MS:1002560 DeBunker:score threshold

Table 2450. Term [MS:1002560]
id	MS:1002560
name	DeBunker:score threshold
def	"Threshold for DeBunker PTM site location score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2449. MS:1002561 Mascot:PTM site assignment confidence threshold

Table 2451. Term [MS:1002561]
id	MS:1002561
name	Mascot:PTM site assignment confidence threshold
def	"Threshold for Mascot PTM site assignment confidence." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2450. MS:1002562 MSQuant:PTM-score threshold

Table 2452. Term [MS:1002562]
id	MS:1002562
name	MSQuant:PTM-score threshold
def	"Threshold for MSQuant:PTM-score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2451. MS:1002563 MaxQuant:PTM Score threshold

Table 2453. Term [MS:1002563]
id	MS:1002563
name	MaxQuant:PTM Score threshold
def	"Threshold for MaxQuant:PTM Score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2452. MS:1002564 MaxQuant:P-site localization probability threshold

Table 2454. Term [MS:1002564]
id	MS:1002564
name	MaxQuant:P-site localization probability threshold
def	"Threshold for MaxQuant:P-site localization probability." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2453. MS:1002565 MaxQuant:PTM Delta Score threshold

Table 2455. Term [MS:1002565]
id	MS:1002565
name	MaxQuant:PTM Delta Score threshold
def	"Threshold for MaxQuant:PTM Delta Score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2454. MS:1002566 MaxQuant:Phospho (STY) Probabilities threshold

Table 2456. Term [MS:1002566]
id	MS:1002566
name	MaxQuant:Phospho (STY) Probabilities threshold
def	"Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2455. MS:1002567 phosphoRS score threshold

Table 2457. Term [MS:1002567]
id	MS:1002567
name	phosphoRS score threshold
def	"Threshold for phosphoRS score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2456. MS:1002568 phosphoRS site probability threshold

Table 2458. Term [MS:1002568]
id	MS:1002568
name	phosphoRS site probability threshold
def	"Threshold for phosphoRS site probability." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2457. MS:1002569 ProteomeDiscoverer:Number of Spectra Processed At Once

Table 2459. Term [MS:1002569]
id	MS:1002569
name	ProteomeDiscoverer:Number of Spectra Processed At Once
def	"Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002101 ProteomeDiscoverer input parameter ! ProteomeDiscoverer input parameter

2.2458. MS:1002570 sequence multiply subsumable protein

Table 2460. Term [MS:1002570]
id	MS:1002570
name	sequence multiply subsumable protein
def	"A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2459. MS:1002571 spectrum multiply subsumable protein

Table 2461. Term [MS:1002571]
id	MS:1002571
name	spectrum multiply subsumable protein
def	"A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001101 protein group or subset relationship ! protein group or subset relationship

2.2460. MS:1002572 protein detection statistical threshold

Table 2462. Term [MS:1002572]
id	MS:1002572
name	protein detection statistical threshold
def	"Estimated statistical threshold used for protein detection." [PSI:MS]
is_a	MS:1002482 statistical threshold ! statistical threshold

2.2461. MS:1002573 spectrum identification statistical threshold

Table 2463. Term [MS:1002573]
id	MS:1002573
name	spectrum identification statistical threshold
def	"Estimated statistical threshold used for spectrum identification." [PSI:MS]
is_a	MS:1002482 statistical threshold ! statistical threshold

2.2462. MS:1002574 ASAPRatio

Table 2464. Term [MS:1002574]
id	MS:1002574
name	ASAPRatio
def	"A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI]
is_a	MS:1002286 Trans-Proteomic Pipeline software ! Trans-Proteomic Pipeline software

2.2463. MS:1002575 Tide

Table 2465. Term [MS:1002575]
id	MS:1002575
name	Tide
def	"Tide open-source sequence search program developed at the University of Washington." [PMID:21761931]
is_a	MS:1001456 analysis software ! analysis software

2.2464. MS:1002576 Andromeda result format

Table 2466. Term [MS:1002576]
id	MS:1002576
name	Andromeda result format
def	"Andromeda result file output format." [PSI:PI]
is_a	MS:1001040 intermediate analysis format ! intermediate analysis format

2.2465. MS:1002577 2000 QTRAP

Table 2467. Term [MS:1002577]
id	MS:1002577
name	2000 QTRAP
def	"SCIEX 2000 QTRAP." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2466. MS:1002578 2500 QTRAP

Table 2468. Term [MS:1002578]
id	MS:1002578
name	2500 QTRAP
def	"SCIEX 2500 QTRAP." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2467. MS:1002579 3500 QTRAP

Table 2469. Term [MS:1002579]
id	MS:1002579
name	3500 QTRAP
def	"SCIEX 3500 QTRAP." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2468. MS:1002580 QTRAP 4500

Table 2470. Term [MS:1002580]
id	MS:1002580
name	QTRAP 4500
def	"SCIEX QTRAP 4500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2469. MS:1002581 QTRAP 6500

Table 2471. Term [MS:1002581]
id	MS:1002581
name	QTRAP 6500
def	"SCIEX QTRAP 6500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2470. MS:1002582 QTRAP 6500+

Table 2472. Term [MS:1002582]
id	MS:1002582
name	QTRAP 6500+
def	"SCIEX QTRAP 6500+." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2471. MS:1002583 TripleTOF 4600

Table 2473. Term [MS:1002583]
id	MS:1002583
name	TripleTOF 4600
def	"SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2472. MS:1002584 TripleTOF 5600+

Table 2474. Term [MS:1002584]
id	MS:1002584
name	TripleTOF 5600+
def	"SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2473. MS:1002585 API 100

Table 2475. Term [MS:1002585]
id	MS:1002585
name	API 100
def	"Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2474. MS:1002586 API 100LC

Table 2476. Term [MS:1002586]
id	MS:1002586
name	API 100LC
def	"Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2475. MS:1002587 API 165

Table 2477. Term [MS:1002587]
id	MS:1002587
name	API 165
def	"Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2476. MS:1002588 API 300

Table 2478. Term [MS:1002588]
id	MS:1002588
name	API 300
def	"Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2477. MS:1002589 API 350

Table 2479. Term [MS:1002589]
id	MS:1002589
name	API 350
def	"Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2478. MS:1002590 API 365

Table 2480. Term [MS:1002590]
id	MS:1002590
name	API 365
def	"Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2479. MS:1002591 Triple Quad 3500

Table 2481. Term [MS:1002591]
id	MS:1002591
name	Triple Quad 3500
def	"SCIEX Triple Quad 3500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2480. MS:1002592 Triple Quad 4500

Table 2482. Term [MS:1002592]
id	MS:1002592
name	Triple Quad 4500
def	"SCIEX Triple Quad 4500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2481. MS:1002593 Triple Quad 5500

Table 2483. Term [MS:1002593]
id	MS:1002593
name	Triple Quad 5500
def	"SCIEX Triple Quad 5500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2482. MS:1002594 Triple Quad 6500

Table 2484. Term [MS:1002594]
id	MS:1002594
name	Triple Quad 6500
def	"SCIEX Triple Quad 6500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2483. MS:1002595 Triple Quad 6500+

Table 2485. Term [MS:1002595]
id	MS:1002595
name	Triple Quad 6500+
def	"SCIEX Triple Quad 6500+." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2484. MS:1002596 ProLuCID

Table 2486. Term [MS:1002596]
id	MS:1002596
name	ProLuCID
def	"The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute." [PMID:26171723]
is_a	MS:1001456 analysis software ! analysis software

2.2485. MS:1002597 MS1 format

Table 2487. Term [MS:1002597]
id	MS:1002597
name	MS1 format
def	"MS1 file format for MS1 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2486. MS:1002598 DTASelect

Table 2488. Term [MS:1002598]
id	MS:1002598
name	DTASelect
def	"Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches." [PMID:12643522, http://fields.scripps.edu/DTASelect/]
is_a	MS:1001456 analysis software ! analysis software

2.2487. MS:1002599 splash key

Table 2489. Term [MS:1002599]
id	MS:1002599
name	splash key
def	"Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2488. MS:1002600 PRIDE XML

Table 2490. Term [MS:1002600]
id	MS:1002600
name	PRIDE XML
def	"Internal data and submission format of the PRIDE database." [http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a	MS:1002130 identification file format ! identification file format
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2489. MS:1002601 mzTab

Table 2491. Term [MS:1002601]
id	MS:1002601
name	mzTab
def	"Tabular result format for proteomics and metabolomics experiments." [PMID:24980485, http://www.psidev.info/mztab/]
is_a	MS:1000914 tab delimited text format ! tab delimited text format

2.2490. MS:1002602 sample label

Table 2492. Term [MS:1002602]
id	MS:1002602
name	sample label
def	"Reagent used in labeled quantification methods." [PSI:PI]
is_a	MS:1002111 assay label attribute ! assay label attribute
is_a	MS:1000548 sample attribute ! sample attribute

2.2491. MS:1002603 ICAT reagent

Table 2493. Term [MS:1002603]
id	MS:1002603
name	ICAT reagent
def	"Isotope coded affinity tag reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2492. MS:1002604 ICAT heavy reagent

Table 2494. Term [MS:1002604]
id	MS:1002604
name	ICAT heavy reagent
def	"The name of the sample labelled with the heavy ICAT label." [PSI:PI]
is_a	MS:1002603 ICAT reagent ! ICAT reagent

2.2493. MS:1002605 ICAT light reagent

Table 2495. Term [MS:1002605]
id	MS:1002605
name	ICAT light reagent
def	"The name of the sample labelled with the light ICAT label." [PSI:PI]
is_a	MS:1002603 ICAT reagent ! ICAT reagent

2.2494. MS:1002606 ICPL reagent

Table 2496. Term [MS:1002606]
id	MS:1002606
name	ICPL reagent
def	"Isotope coded protein labeling reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2495. MS:1002607 ICPL reagent 0

Table 2497. Term [MS:1002607]
id	MS:1002607
name	ICPL reagent 0
def	"The name of the sample labelled with the ICPL reagent 0." [PSI:PI]
is_a	MS:1002606 ICPL reagent ! ICPL reagent

2.2496. MS:1002608 ICPL reagent 4

Table 2498. Term [MS:1002608]
id	MS:1002608
name	ICPL reagent 4
def	"The name of the sample labelled with the ICPL reagent 4." [PSI:PI]
is_a	MS:1002606 ICPL reagent ! ICPL reagent

2.2497. MS:1002609 ICPL reagent 6

Table 2499. Term [MS:1002609]
id	MS:1002609
name	ICPL reagent 6
def	"The name of the sample labelled with the ICPL reagent 6." [PSI:PI]
is_a	MS:1002606 ICPL reagent ! ICPL reagent

2.2498. MS:1002610 ICPL reagent 10

Table 2500. Term [MS:1002610]
id	MS:1002610
name	ICPL reagent 10
def	"The name of the sample labelled with the ICPL reagent 10." [PSI:PI]
is_a	MS:1002606 ICPL reagent ! ICPL reagent

2.2499. MS:1002611 SILAC reagent

Table 2501. Term [MS:1002611]
id	MS:1002611
name	SILAC reagent
def	"Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2500. MS:1002612 SILAC heavy reagent

Table 2502. Term [MS:1002612]
id	MS:1002612
name	SILAC heavy reagent
def	"The name of the sample labelled with the heavy SILAC label." [PSI:PI]
is_a	MS:1002611 SILAC reagent ! SILAC reagent

2.2501. MS:1002613 SILAC medium reagent

Table 2503. Term [MS:1002613]
id	MS:1002613
name	SILAC medium reagent
def	"The name of the sample labelled with the medium SILAC label." [PSI:PI]
is_a	MS:1002611 SILAC reagent ! SILAC reagent

2.2502. MS:1002614 SILAC light reagent

Table 2504. Term [MS:1002614]
id	MS:1002614
name	SILAC light reagent
def	"The name of the sample labelled with the light SILAC label." [PSI:PI]
is_a	MS:1002611 SILAC reagent ! SILAC reagent

2.2503. MS:1002615 TMT reagent

Table 2505. Term [MS:1002615]
id	MS:1002615
name	TMT reagent
def	"Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2504. MS:1002616 TMT reagent 126

Table 2506. Term [MS:1002616]
id	MS:1002616
name	TMT reagent 126
def	"The name of the sample labelled with the TMT reagent 126." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2505. MS:1002617 TMT reagent 127

Table 2507. Term [MS:1002617]
id	MS:1002617
name	TMT reagent 127
def	"The name of the sample labelled with the TMT reagent 127." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2506. MS:1002618 TMT reagent 128

Table 2508. Term [MS:1002618]
id	MS:1002618
name	TMT reagent 128
def	"The name of the sample labelled with the TMT reagent 128." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2507. MS:1002619 TMT reagent 129

Table 2509. Term [MS:1002619]
id	MS:1002619
name	TMT reagent 129
def	"The name of the sample labelled with the TMT reagent 129." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2508. MS:1002620 TMT reagent 130

Table 2510. Term [MS:1002620]
id	MS:1002620
name	TMT reagent 130
def	"The name of the sample labelled with the TMT reagent 130." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2509. MS:1002621 TMT reagent 131

Table 2511. Term [MS:1002621]
id	MS:1002621
name	TMT reagent 131
def	"The name of the sample labelled with the TMT reagent 131." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2510. MS:1002622 iTRAQ reagent

Table 2512. Term [MS:1002622]
id	MS:1002622
name	iTRAQ reagent
def	"Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2511. MS:1002623 iTRAQ reagent 113

Table 2513. Term [MS:1002623]
id	MS:1002623
name	iTRAQ reagent 113
def	"The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2512. MS:1002624 iTRAQ reagent 114

Table 2514. Term [MS:1002624]
id	MS:1002624
name	iTRAQ reagent 114
def	"The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2513. MS:1002625 iTRAQ reagent 115

Table 2515. Term [MS:1002625]
id	MS:1002625
name	iTRAQ reagent 115
def	"The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2514. MS:1002626 iTRAQ reagent 116

Table 2516. Term [MS:1002626]
id	MS:1002626
name	iTRAQ reagent 116
def	"The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2515. MS:1002627 iTRAQ reagent 117

Table 2517. Term [MS:1002627]
id	MS:1002627
name	iTRAQ reagent 117
def	"The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2516. MS:1002628 iTRAQ reagent 118

Table 2518. Term [MS:1002628]
id	MS:1002628
name	iTRAQ reagent 118
def	"The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2517. MS:1002629 iTRAQ reagent 119

Table 2519. Term [MS:1002629]
id	MS:1002629
name	iTRAQ reagent 119
def	"The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2518. MS:1002630 iTRAQ reagent 121

Table 2520. Term [MS:1002630]
id	MS:1002630
name	iTRAQ reagent 121
def	"The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI]
is_a	MS:1002622 iTRAQ reagent ! iTRAQ reagent

2.2519. MS:1002631 Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

Table 2521. Term [MS:1002631]
id	MS:1002631
name	Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def	"A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI]
synonym	"EThcD" EXACT []
is_a	MS:1000044 dissociation method ! dissociation method

2.2520. MS:1002632 jPOST dataset identifier

Table 2522. Term [MS:1002632]
id	MS:1002632
name	jPOST dataset identifier
def	"Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2521. MS:1002633 jPOST dataset URI

Table 2523. Term [MS:1002633]
id	MS:1002633
name	jPOST dataset URI
def	"URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2522. MS:1002634 Q Exactive Plus

Table 2524. Term [MS:1002634]
id	MS:1002634
name	Q Exactive Plus
def	"Thermo Scientific Q Exactive Plus." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2523. MS:1002635 proteogenomics search

Table 2525. Term [MS:1002635]
id	MS:1002635
name	proteogenomics search
def	"Proteogenomics search performed." [PSI:PI]
is_a	MS:1002489 special processing ! special processing

2.2524. MS:1002636 proteogenomics attribute

Table 2526. Term [MS:1002636]
id	MS:1002636
name	proteogenomics attribute
def	"Proteogenomics attribute." [PSI:PI]
is_a	MS:1001105 peptide sequence-level identification attribute ! peptide sequence-level identification attribute

2.2525. MS:1002637 chromosome name

Table 2527. Term [MS:1002637]
id	MS:1002637
name	chromosome name
def	"The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2526. MS:1002638 chromosome strand

Table 2528. Term [MS:1002638]
id	MS:1002638
name	chromosome strand
def	"The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2527. MS:1002639 peptide start on chromosome

Table 2529. Term [MS:1002639]
id	MS:1002639
name	peptide start on chromosome
def	"OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI]
comment	This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome.
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute
is_obsolete	true

2.2528. MS:1002640 peptide end on chromosome

Table 2530. Term [MS:1002640]
id	MS:1002640
name	peptide end on chromosome
def	"The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2529. MS:1002641 peptide exon count

Table 2531. Term [MS:1002641]
id	MS:1002641
name	peptide exon count
def	"The number of exons to which the peptide has been mapped." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2530. MS:1002642 peptide exon nucleotide sizes

Table 2532. Term [MS:1002642]
id	MS:1002642
name	peptide exon nucleotide sizes
def	"A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2531. MS:1002643 peptide start positions on chromosome

Table 2533. Term [MS:1002643]
id	MS:1002643
name	peptide start positions on chromosome
def	"A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2532. MS:1002644 genome reference version

Table 2534. Term [MS:1002644]
id	MS:1002644
name	genome reference version
def	"The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2533. MS:1002645 MSDK

Table 2535. Term [MS:1002645]
id	MS:1002645
name	MSDK
def	"Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data." [PSI:PI, http://msdk.github.io/]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2534. MS:1002646 native spectrum identifier format, combined spectra

Table 2536. Term [MS:1002646]
id	MS:1002646
name	native spectrum identifier format, combined spectra
def	"Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
synonym	"nativeID format, combined spectra" EXACT []
relationship	part_of MS:1000577 source data file ! source data file

2.2535. MS:1002647 Thermo nativeID format, combined spectra

Table 2537. Term [MS:1002647]
id	MS:1002647
name	Thermo nativeID format, combined spectra
def	"Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2536. MS:1002648 Waters nativeID format, combined spectra

Table 2538. Term [MS:1002648]
id	MS:1002648
name	Waters nativeID format, combined spectra
def	"Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2537. MS:1002649 WIFF nativeID format, combined spectra

Table 2539. Term [MS:1002649]
id	MS:1002649
name	WIFF nativeID format, combined spectra
def	"WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2538. MS:1002650 Bruker/Agilent YEP nativeID format, combined spectra

Table 2540. Term [MS:1002650]
id	MS:1002650
name	Bruker/Agilent YEP nativeID format, combined spectra
def	"Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2539. MS:1002651 Bruker BAF nativeID format, combined spectra

Table 2541. Term [MS:1002651]
id	MS:1002651
name	Bruker BAF nativeID format, combined spectra
def	"Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2540. MS:1002652 Bruker FID nativeID format, combined spectra

Table 2542. Term [MS:1002652]
id	MS:1002652
name	Bruker FID nativeID format, combined spectra
def	"Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	The nativeID must be the same as the source file ID.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2541. MS:1002653 multiple peak list nativeID format, combined spectra

Table 2543. Term [MS:1002653]
id	MS:1002653
name	multiple peak list nativeID format, combined spectra
def	"Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2542. MS:1002654 single peak list nativeID format, combined spectra

Table 2544. Term [MS:1002654]
id	MS:1002654
name	single peak list nativeID format, combined spectra
def	"Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2543. MS:1002655 scan number only nativeID format, combined spectra

Table 2545. Term [MS:1002655]
id	MS:1002655
name	scan number only nativeID format, combined spectra
def	"Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2544. MS:1002656 spectrum identifier nativeID format, combined spectra

Table 2546. Term [MS:1002656]
id	MS:1002656
name	spectrum identifier nativeID format, combined spectra
def	"Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	Used for conversion from mzData. The spectrum id attribute is referenced.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2545. MS:1002657 mzML unique identifier, combined spectra

Table 2547. Term [MS:1002657]
id	MS:1002657
name	mzML unique identifier, combined spectra
def	"Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment	A unique identifier of a spectrum stored in an mzML file.
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2546. MS:1002658 identification parameter

Table 2548. Term [MS:1002658]
id	MS:1002658
name	identification parameter
def	"Identification parameter for the search engine run." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.2547. MS:1002659 UniProtKB text sequence format

Table 2549. Term [MS:1002659]
id	MS:1002659
name	UniProtKB text sequence format
def	"Text-based format used by UniProtKB for sequence entries." [PSI:PI]
xref	SWO:http://edamontology.org/format_2187
is_a	MS:1001347 database file formats ! database file formats

2.2548. MS:1002660 UniProtKB XML sequence format

Table 2550. Term [MS:1002660]
id	MS:1002660
name	UniProtKB XML sequence format
def	"XML-based format used by UniProtKB for sequence entries." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.2549. MS:1002661 Morpheus

Table 2551. Term [MS:1002661]
id	MS:1002661
name	Morpheus
def	"Morpheus search engine." [PMID:23323968]
is_a	MS:1001456 analysis software ! analysis software

2.2550. MS:1002662 Morpheus:Morpheus score

Table 2552. Term [MS:1002662]
id	MS:1002662
name	Morpheus:Morpheus score
def	"Morpheus score for PSMs." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2551. MS:1002663 Morpheus:summed Morpheus score

Table 2553. Term [MS:1002663]
id	MS:1002663
name	Morpheus:summed Morpheus score
def	"Summed Morpheus score for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_order MS:1002108 higher score better ! higher score better

2.2552. MS:1002664 interaction score derived from cross-linking

Table 2554. Term [MS:1002664]
id	MS:1002664
name	interaction score derived from cross-linking
def	"Parent term for interaction scores derived from cross-linking." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002675 cross-linking result details ! cross-linking result details
relationship	has_regexp MS:1002665 regular expression for interaction scores derived from cross-linking ! ([.][a\|b]:[:digit:]:[:digit:][.][:digit:]([Ee][-][0-9])*:(true\|false]{1}))

2.2553. MS:1002665 regular expression for interaction scores derived from cross-linking

Table 2555. Term [MS:1002665]
id	MS:1002665
name	regular expression for interaction scores derived from cross-linking
def	"([.][a\|b]:([:digit:]\|null):[:digit:][.][:digit:]([Ee][-][0-9])*:(true\|false]{1}))." [PSI:PI]
is_a	MS:1002479 regular expression ! regular expression

2.2554. MS:1002666 impact II

Table 2556. Term [MS:1002666]
id	MS:1002666
name	impact II
def	"Bruker Daltonics' impact II." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.2555. MS:1002667 impact HD

Table 2557. Term [MS:1002667]
id	MS:1002667
name	impact HD
def	"Bruker Daltonics' impact HD." [PSI:MS]
is_a	MS:1001536 Bruker Daltonics micrOTOF series ! Bruker Daltonics micrOTOF series

2.2556. MS:1002668 frag: iTRAQ 4plex reporter ion

Table 2558. Term [MS:1002668]
id	MS:1002668
name	frag: iTRAQ 4plex reporter ion
def	"Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2557. MS:1002669 frag: iTRAQ 8plex reporter ion

Table 2559. Term [MS:1002669]
id	MS:1002669
name	frag: iTRAQ 8plex reporter ion
def	"Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2558. MS:1002670 frag: TMT reporter ion

Table 2560. Term [MS:1002670]
id	MS:1002670
name	frag: TMT reporter ion
def	"Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2559. MS:1002671 frag: TMT ETD reporter ion

Table 2561. Term [MS:1002671]
id	MS:1002671
name	frag: TMT ETD reporter ion
def	"Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2560. MS:1002672 no modification threshold

Table 2562. Term [MS:1002672]
id	MS:1002672
name	no modification threshold
def	"No statistical threshold for accepting or rejecting that a modification position." [PSI:PI]
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2561. MS:1002673 OpenXQuest

Table 2563. Term [MS:1002673]
id	MS:1002673
name	OpenXQuest
def	"Cross-Linking MS search engine." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2562. MS:1002674 X500R QTOF

Table 2564. Term [MS:1002674]
id	MS:1002674
name	X500R QTOF
def	"SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.2563. MS:1002675 cross-linking result details

Table 2565. Term [MS:1002675]
id	MS:1002675
name	cross-linking result details
def	"This subsection describes terms which can describe details of cross-linking results." [PSI:PI]
relationship	part_of MS:1001000 spectrum interpretation ! spectrum interpretation

2.2564. MS:1002676 protein-pair-level global FDR

Table 2566. Term [MS:1002676]
id	MS:1002676
name	protein-pair-level global FDR
def	"Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002664 interaction score derived from cross-linking ! interaction score derived from cross-linking
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive
relationship	has_regexp MS:1002665 regular expression for interaction scores derived from cross-linking ! ([.][a\|b]:[:digit:]:[:digit:][.][:digit:]([Ee][-][0-9])*:(true\|false]{1}))

2.2565. MS:1002677 residue-pair-level global FDR

Table 2567. Term [MS:1002677]
id	MS:1002677
name	residue-pair-level global FDR
def	"Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002664 interaction score derived from cross-linking ! interaction score derived from cross-linking
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive
relationship	has_regexp MS:1002665 regular expression for interaction scores derived from cross-linking ! ([.][a\|b]:[:digit:]:[:digit:][.][:digit:]([Ee][-][0-9])*:(true\|false]{1}))

2.2566. MS:1002678 supplemental beam-type collision-induced dissociation

Table 2568. Term [MS:1002678]
id	MS:1002678
name	supplemental beam-type collision-induced dissociation
def	"A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS]
is_a	MS:1000422 beam-type collision-induced dissociation ! beam-type collision-induced dissociation

2.2567. MS:1002679 supplemental collision-induced dissociation

Table 2569. Term [MS:1002679]
id	MS:1002679
name	supplemental collision-induced dissociation
def	"The dissociation of an ion after supplemental collisional excitation." [PSI:MS]
is_a	MS:1000133 collision-induced dissociation ! collision-induced dissociation

2.2568. MS:1002680 supplemental collision energy

Table 2570. Term [MS:1002680]
id	MS:1002680
name	supplemental collision energy
def	"Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000510 precursor activation attribute ! precursor activation attribute
relationship	has_units [UO:0000266] ! electronvolt

2.2569. MS:1002681 OpenXQuest:combined score

Table 2571. Term [MS:1002681]
id	MS:1002681
name	OpenXQuest:combined score
def	"OpenXQuest’s combined score for a cross-link spectrum match." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2570. MS:1002682 OpenXQuest:xcorr xlink

Table 2572. Term [MS:1002682]
id	MS:1002682
name	OpenXQuest:xcorr xlink
def	"OpenXQuest’s cross-correlation of cross-linked ions subscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2571. MS:1002683 OpenXQuest:xcorr common

Table 2573. Term [MS:1002683]
id	MS:1002683
name	OpenXQuest:xcorr common
def	"OpenXQuest’s cross-correlation of unlinked ions subscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2572. MS:1002684 OpenXQuest:match-odds

Table 2574. Term [MS:1002684]
id	MS:1002684
name	OpenXQuest:match-odds
def	"OpenXQuest’s match-odds subscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.2573. MS:1002685 OpenXQuest:intsum

Table 2575. Term [MS:1002685]
id	MS:1002685
name	OpenXQuest:intsum
def	"OpenXQuest’s sum of matched peak intensity subscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002306 value greater than zero ! value greater than zero

2.2574. MS:1002686 OpenXQuest:wTIC

Table 2576. Term [MS:1002686]
id	MS:1002686
name	OpenXQuest:wTIC
def	"OpenXQuest’s weighted percent of total ion current subscore." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2575. MS:1002687 analysis attribute

Table 2577. Term [MS:1002687]
id	MS:1002687
name	analysis attribute
def	"Attribute of an item in the result of mass spectrometry proteomics data analysis." [PSI:PI]
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2576. MS:1002688 PTM localization attribute

Table 2578. Term [MS:1002688]
id	MS:1002688
name	PTM localization attribute
def	"Statistic derived from a post-translational modification localization analysis." [PSI:PI]
is_a	MS:1002687 analysis attribute ! analysis attribute

2.2577. MS:1002689 PTM localization single result statistic

Table 2579. Term [MS:1002689]
id	MS:1002689
name	PTM localization single result statistic
def	"Statistic for a single item derived from a post-translational modification localization analysis." [PSI:PI]
is_a	MS:1002688 PTM localization attribute ! PTM localization attribute

2.2578. MS:1002690 PTM localization result list statistic

Table 2580. Term [MS:1002690]
id	MS:1002690
name	PTM localization result list statistic
def	"Statistic for all items derived from a post-translational modification localization analysis." [PSI:PI]
is_a	MS:1002688 PTM localization attribute ! PTM localization attribute

2.2579. MS:1002691 global FLR

Table 2581. Term [MS:1002691]
id	MS:1002691
name	global FLR
def	"Global false localization rate for all localizations in a dataset." [PSI:PI]
is_a	MS:1002690 PTM localization result list statistic ! PTM localization result list statistic

2.2580. MS:1002692 local FLR at threshold

Table 2582. Term [MS:1002692]
id	MS:1002692
name	local FLR at threshold
def	"Local false localization rate for the bottom item in list of localizations sorted from most to least confident." [PSI:PI]
is_a	MS:1002690 PTM localization result list statistic ! PTM localization result list statistic

2.2581. MS:1002693 identification attribute

Table 2583. Term [MS:1002693]
id	MS:1002693
name	identification attribute
def	"Attribute of an identification item in the result of mass spectrometry proteomics data analysis." [PSI:PI]
is_a	MS:1002687 analysis attribute ! analysis attribute

2.2582. MS:1002694 single identification result attribute

Table 2584. Term [MS:1002694]
id	MS:1002694
name	single identification result attribute
def	"Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis." [PSI:PI]
is_a	MS:1002693 identification attribute ! identification attribute

2.2583. MS:1002695 frag: isobaric label ion

Table 2585. Term [MS:1002695]
id	MS:1002695
name	frag: isobaric label ion
def	"Fragment ion corresponding to an isobaric label artifact." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2584. MS:1002697 secondary isotope peak

Table 2586. Term [MS:1002697]
id	MS:1002697
name	secondary isotope peak
def	"Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion." [PSI:PI]
is_a	MS:1002307 fragmentation ion type ! fragmentation ion type

2.2585. MS:1002698 protein cluster identification attribute

Table 2587. Term [MS:1002698]
id	MS:1002698
name	protein cluster identification attribute
def	"An attribute of the protein cluster concept as used in mzIdentML." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2586. MS:1002699 result list attribute

Table 2588. Term [MS:1002699]
id	MS:1002699
name	result list attribute
def	"General property of an entire result list." [PSI:PI]
is_a	MS:1002693 identification attribute ! identification attribute

2.2587. MS:1002700 PSM-level result list attribute

Table 2589. Term [MS:1002700]
id	MS:1002700
name	PSM-level result list attribute
def	"General property of the list of all PSMs." [PSI:PI]
is_a	MS:1002699 result list attribute ! result list attribute

2.2588. MS:1002701 PSM-level result list statistic

Table 2590. Term [MS:1002701]
id	MS:1002701
name	PSM-level result list statistic
def	"Statistic pertaining to the full list of all PSMs." [PSI:PI]
is_a	MS:1002700 PSM-level result list attribute ! PSM-level result list attribute

2.2589. MS:1002702 peptide sequence-level result list attribute

Table 2591. Term [MS:1002702]
id	MS:1002702
name	peptide sequence-level result list attribute
def	"General property of all peptide sequences in the list." [PSI:PI]
is_a	MS:1002699 result list attribute ! result list attribute

2.2590. MS:1002703 peptide sequence-level result list statistic

Table 2592. Term [MS:1002703]
id	MS:1002703
name	peptide sequence-level result list statistic
def	"Statistic pertaining to all peptide sequences in the list." [PSI:PI]
is_a	MS:1002702 peptide sequence-level result list attribute ! peptide sequence-level result list attribute

2.2591. MS:1002704 protein-level result list attribute

Table 2593. Term [MS:1002704]
id	MS:1002704
name	protein-level result list attribute
def	"Attribute of an entire protein list." [PSI:PI]
is_a	MS:1002699 result list attribute ! result list attribute

2.2592. MS:1002705 protein-level result list statistic

Table 2594. Term [MS:1002705]
id	MS:1002705
name	protein-level result list statistic
def	"A statistical metric of an entire protein list." [PSI:PI]
is_a	MS:1002704 protein-level result list attribute ! protein-level result list attribute

2.2593. MS:1002706 protein group-level result list statistic

Table 2595. Term [MS:1002706]
id	MS:1002706
name	protein group-level result list statistic
def	"Attrbiute of an entire list of protein groups." [PSI:PI]
is_a	MS:1002405 protein group-level result list attribute ! protein group-level result list attribute

2.2594. MS:1002719 Pegasus BT

Table 2596. Term [MS:1002719]
id	MS:1002719
name	Pegasus BT
def	"LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI]
is_a	MS:1001800 LECO instrument model ! LECO instrument model

2.2595. MS:1002720 MSPathFinder

Table 2597. Term [MS:1002720]
id	MS:1002720
name	MSPathFinder
def	"PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2596. MS:1002721 MSPathFinder:SpecEValue

Table 2598. Term [MS:1002721]
id	MS:1002721
name	MSPathFinder:SpecEValue
def	"MSPathFinder spectral E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2597. MS:1002722 MSPathFinder:EValue

Table 2599. Term [MS:1002722]
id	MS:1002722
name	MSPathFinder:EValue
def	"MSPathFinder E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2598. MS:1002723 MSPathFinder:QValue

Table 2600. Term [MS:1002723]
id	MS:1002723
name	MSPathFinder:QValue
def	"MSPathFinder Q-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002354 PSM-level q-value ! PSM-level q-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2599. MS:1002724 MSPathFinder:PepQValue

Table 2601. Term [MS:1002724]
id	MS:1002724
name	MSPathFinder:PepQValue
def	"MSPathFinder peptide-level Q-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2600. MS:1002725 MSPathFinder:RawScore

Table 2602. Term [MS:1002725]
id	MS:1002725
name	MSPathFinder:RawScore
def	"MSPathFinder raw score." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2601. MS:1002726 SYNAPT G2-Si

Table 2603. Term [MS:1002726]
id	MS:1002726
name	SYNAPT G2-Si
def	"Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2602. MS:1002727 MALDI SYNAPT G2-Si

Table 2604. Term [MS:1002727]
id	MS:1002727
name	MALDI SYNAPT G2-Si
def	"Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2603. MS:1002728 Vion IMS QTof

Table 2605. Term [MS:1002728]
id	MS:1002728
name	Vion IMS QTof
def	"Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2604. MS:1002729 Xevo G2 XS Tof

Table 2606. Term [MS:1002729]
id	MS:1002729
name	Xevo G2 XS Tof
def	"Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2605. MS:1002730 Xevo TQ-XS

Table 2607. Term [MS:1002730]
id	MS:1002730
name	Xevo TQ-XS
def	"Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2606. MS:1002731 Xevo TQ-S micro

Table 2608. Term [MS:1002731]
id	MS:1002731
name	Xevo TQ-S micro
def	"Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI]
is_a	MS:1000126 Waters instrument model ! Waters instrument model

2.2607. MS:1002732 Orbitrap Fusion Lumos

Table 2609. Term [MS:1002732]
id	MS:1002732
name	Orbitrap Fusion Lumos
def	"Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2608. MS:1002733 peptide-level spectral count

Table 2610. Term [MS:1002733]
id	MS:1002733
name	peptide-level spectral count
def	"The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.2609. MS:1002734 peptide ion-level spectral count

Table 2611. Term [MS:1002734]
id	MS:1002734
name	peptide ion-level spectral count
def	"The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	MS:1002737 peptide-level quantification datatype ! peptide-level quantification datatype

2.2610. MS:1002735 feature-level quantification datatype

Table 2612. Term [MS:1002735]
id	MS:1002735
name	feature-level quantification datatype
def	"The data type of the value reported in a QuantLayer for a feature." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2611. MS:1002736 PSM-level quantification datatype

Table 2613. Term [MS:1002736]
id	MS:1002736
name	PSM-level quantification datatype
def	"The data type of the value reported in a QuantLayer for a PSM." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2612. MS:1002737 peptide-level quantification datatype

Table 2614. Term [MS:1002737]
id	MS:1002737
name	peptide-level quantification datatype
def	"The data type of the value reported in a QuantLayer for a peptide." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2613. MS:1002738 protein-level quantification datatype

Table 2615. Term [MS:1002738]
id	MS:1002738
name	protein-level quantification datatype
def	"The data type of the value reported in a QuantLayer for a protein." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2614. MS:1002739 protein group-level quantification datatype

Table 2616. Term [MS:1002739]
id	MS:1002739
name	protein group-level quantification datatype
def	"The data type of the value reported in a QuantLayer for a protein group." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2615. MS:1002740 unmapped peptide

Table 2617. Term [MS:1002740]
id	MS:1002740
name	unmapped peptide
def	"Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location." [PSI:PI]
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2616. MS:1002741 unmapped protein

Table 2618. Term [MS:1002741]
id	MS:1002741
name	unmapped protein
def	"Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location." [PSI:PI]
is_a	MS:1002636 proteogenomics attribute ! proteogenomics attribute

2.2617. MS:1002742 noise array

Table 2619. Term [MS:1002742]
id	MS:1002742
name	noise array
def	"A data array of noise values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.2618. MS:1002743 sampled noise m/z array

Table 2620. Term [MS:1002743]
id	MS:1002743
name	sampled noise m/z array
def	"A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array)." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units MS:1000040 m/z ! m/z

2.2619. MS:1002744 sampled noise intensity array

Table 2621. Term [MS:1002744]
id	MS:1002744
name	sampled noise intensity array
def	"A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units MS:1000131 number of detector counts ! number of detector counts

2.2620. MS:1002745 sampled noise baseline array

Table 2622. Term [MS:1002745]
id	MS:1002745
name	sampled noise baseline array
def	"A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array

2.2621. MS:1002746 MS-Numpress linear prediction compression followed by zlib compression

Table 2623. Term [MS:1002746]
id	MS:1002746
name	MS-Numpress linear prediction compression followed by zlib compression
def	"Compression using MS-Numpress linear prediction compression and zlib." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2622. MS:1002747 MS-Numpress positive integer compression followed by zlib compression

Table 2624. Term [MS:1002747]
id	MS:1002747
name	MS-Numpress positive integer compression followed by zlib compression
def	"Compression using MS-Numpress positive integer compression and zlib." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2623. MS:1002748 MS-Numpress short logged float compression followed by zlib compression

Table 2625. Term [MS:1002748]
id	MS:1002748
name	MS-Numpress short logged float compression followed by zlib compression
def	"Compression using MS-Numpress short logged float compression and zlib." [https://github.com/ms-numpress/ms-numpress]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2624. MS:1002749 Mascot:IntegratedSpectralLibrarySearch

Table 2626. Term [MS:1002749]
id	MS:1002749
name	Mascot:IntegratedSpectralLibrarySearch
def	"Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.2625. MS:1002750 NIST MSPepSearch

Table 2627. Term [MS:1002750]
id	MS:1002750
name	NIST MSPepSearch
def	"Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2626. MS:1002751 NIST MSP format

Table 2628. Term [MS:1002751]
id	MS:1002751
name	NIST MSP format
def	"MSP text format defined by the NIST." [PSI:PI]
is_a	MS:1001347 database file formats ! database file formats

2.2627. MS:1002752 database type spectral library

Table 2629. Term [MS:1002752]
id	MS:1002752
name	database type spectral library
def	"Database containing spectra." [PSI:PI]
is_a	MS:1001073 database type amino acid ! database type amino acid

2.2628. MS:1002753 value between 0 and 1000 inclusive

Table 2630. Term [MS:1002753]
id	MS:1002753
name	value between 0 and 1000 inclusive
def	"Value range for scores." [PSI:PI]
is_a	MS:1002304 domain range ! domain range

2.2629. MS:1002754 MSPepSearch:score

Table 2631. Term [MS:1002754]
id	MS:1002754
name	MSPepSearch:score
def	"MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum." [PSI:PI]
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002753 value between 0 and 1000 inclusive ! value between 0 and 1000 inclusive

2.2630. MS:1002755 combined ms-ms + spectral library search

Table 2632. Term [MS:1002755]
id	MS:1002755
name	combined ms-ms + spectral library search
def	"A combined MS2 (with fragment ions) and spectral library search." [PSI:PI]
is_a	MS:1001080 search type ! search type

2.2631. MS:1002756 iodoTMT quantitation analysis

Table 2633. Term [MS:1002756]
id	MS:1002756
name	iodoTMT quantitation analysis
def	"Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2632. MS:1002757 glyco-TMT quantitation analysis

Table 2634. Term [MS:1002757]
id	MS:1002757
name	glyco-TMT quantitation analysis
def	"Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, PMID:22455665]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2633. MS:1002758 aminoxyTMT quantitation analysis

Table 2635. Term [MS:1002758]
id	MS:1002758
name	aminoxyTMT quantitation analysis
def	"Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, PMID:25337643]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2634. MS:1002759 hydrazideTMT quantitation analysis

Table 2636. Term [MS:1002759]
id	MS:1002759
name	hydrazideTMT quantitation analysis
def	"Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, PMID:25337643]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2635. MS:1002760 iTRAQH quantitation analysis

Table 2637. Term [MS:1002760]
id	MS:1002760
name	iTRAQH quantitation analysis
def	"Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow." [PSI:PI, PMID:22926130]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2636. MS:1002761 DiART quantitation analysis

Table 2638. Term [MS:1002761]
id	MS:1002761
name	DiART quantitation analysis
def	"Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, PMID:20715779]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2637. MS:1002762 DiLeu quantitation analysis

Table 2639. Term [MS:1002762]
id	MS:1002762
name	DiLeu quantitation analysis
def	"Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a	MS:1002009 isobaric label quantitation analysis ! isobaric label quantitation analysis

2.2638. MS:1002763 TMT reagent 127N

Table 2640. Term [MS:1002763]
id	MS:1002763
name	TMT reagent 127N
def	"The name of the sample labelled with the TMT reagent 127N." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2639. MS:1002764 TMT reagent 127C

Table 2641. Term [MS:1002764]
id	MS:1002764
name	TMT reagent 127C
def	"The name of the sample labelled with the TMT reagent 127C." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2640. MS:1002765 TMT reagent 128N

Table 2642. Term [MS:1002765]
id	MS:1002765
name	TMT reagent 128N
def	"The name of the sample labelled with the TMT reagent 128N." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2641. MS:1002766 TMT reagent 128C

Table 2643. Term [MS:1002766]
id	MS:1002766
name	TMT reagent 128C
def	"The name of the sample labelled with the TMT reagent 128C." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2642. MS:1002767 TMT reagent 129N

Table 2644. Term [MS:1002767]
id	MS:1002767
name	TMT reagent 129N
def	"The name of the sample labelled with the TMT reagent 129N." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2643. MS:1002768 TMT reagent 129C

Table 2645. Term [MS:1002768]
id	MS:1002768
name	TMT reagent 129C
def	"The name of the sample labelled with the TMT reagent 129C." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2644. MS:1002769 TMT reagent 130N

Table 2646. Term [MS:1002769]
id	MS:1002769
name	TMT reagent 130N
def	"The name of the sample labelled with the TMT reagent 130N." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2645. MS:1002770 TMT reagent 130C

Table 2647. Term [MS:1002770]
id	MS:1002770
name	TMT reagent 130C
def	"The name of the sample labelled with the TMT reagent 130C." [PSI:PI]
is_a	MS:1002615 TMT reagent ! TMT reagent

2.2646. MS:1002771 DiART reagent

Table 2648. Term [MS:1002771]
id	MS:1002771
name	DiART reagent
def	"Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2647. MS:1002772 DiART reagent 114

Table 2649. Term [MS:1002772]
id	MS:1002772
name	DiART reagent 114
def	"The name of the sample labelled with the DiART reagent 114." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2648. MS:1002773 DiART reagent 115

Table 2650. Term [MS:1002773]
id	MS:1002773
name	DiART reagent 115
def	"The name of the sample labelled with the DiART reagent 115." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2649. MS:1002774 DiART reagent 116

Table 2651. Term [MS:1002774]
id	MS:1002774
name	DiART reagent 116
def	"The name of the sample labelled with the DiART reagent 116." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2650. MS:1002775 DiART reagent 117

Table 2652. Term [MS:1002775]
id	MS:1002775
name	DiART reagent 117
def	"The name of the sample labelled with the DiART reagent 117." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2651. MS:1002776 DiART reagent 118

Table 2653. Term [MS:1002776]
id	MS:1002776
name	DiART reagent 118
def	"The name of the sample labelled with the DiART reagent 118." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2652. MS:1002777 DiART reagent 119

Table 2654. Term [MS:1002777]
id	MS:1002777
name	DiART reagent 119
def	"The name of the sample labelled with the DiART reagent 119." [PSI:PI]
is_a	MS:1002771 DiART reagent ! DiART reagent

2.2653. MS:1002778 DiLeu reagent

Table 2655. Term [MS:1002778]
id	MS:1002778
name	DiLeu reagent
def	"Dimethyl leucine labeling reagent." [PSI:PI]
is_a	MS:1002602 sample label ! sample label

2.2654. MS:1002779 DiLeu reagent 115

Table 2656. Term [MS:1002779]
id	MS:1002779
name	DiLeu reagent 115
def	"The name of the sample labelled with the DiLeu reagent 115." [PSI:PI]
is_a	MS:1002778 DiLeu reagent ! DiLeu reagent

2.2655. MS:1002780 DiLeu reagent 116

Table 2657. Term [MS:1002780]
id	MS:1002780
name	DiLeu reagent 116
def	"The name of the sample labelled with the DiLeu reagent 116." [PSI:PI]
is_a	MS:1002778 DiLeu reagent ! DiLeu reagent

2.2656. MS:1002781 DiLeu reagent 117

Table 2658. Term [MS:1002781]
id	MS:1002781
name	DiLeu reagent 117
def	"The name of the sample labelled with the DiLeu reagent 117." [PSI:PI]
is_a	MS:1002778 DiLeu reagent ! DiLeu reagent

2.2657. MS:1002782 DiLeu reagent 118

Table 2659. Term [MS:1002782]
id	MS:1002782
name	DiLeu reagent 118
def	"The name of the sample labelled with the DiLeu reagent 118." [PSI:PI]
is_a	MS:1002778 DiLeu reagent ! DiLeu reagent

2.2658. MS:1002783 6550 iFunnel Q-TOF LC/MS

Table 2660. Term [MS:1002783]
id	MS:1002783
name	6550 iFunnel Q-TOF LC/MS
def	"The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2659. MS:1002784 6550A iFunnel Q-TOF LC/MS

Table 2661. Term [MS:1002784]
id	MS:1002784
name	6550A iFunnel Q-TOF LC/MS
def	"The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2660. MS:1002785 6520B Q-TOF LC/MS

Table 2662. Term [MS:1002785]
id	MS:1002785
name	6520B Q-TOF LC/MS
def	"The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2661. MS:1002786 6530A Q-TOF LC/MS

Table 2663. Term [MS:1002786]
id	MS:1002786
name	6530A Q-TOF LC/MS
def	"The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2662. MS:1002787 6530B Q-TOF LC/MS

Table 2664. Term [MS:1002787]
id	MS:1002787
name	6530B Q-TOF LC/MS
def	"The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2663. MS:1002788 6538 Q-TOF LC/MS

Table 2665. Term [MS:1002788]
id	MS:1002788
name	6538 Q-TOF LC/MS
def	"The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2664. MS:1002789 6540 Q-TOF LC/MS

Table 2666. Term [MS:1002789]
id	MS:1002789
name	6540 Q-TOF LC/MS
def	"The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2665. MS:1002790 6542 Q-TOF LC/MS

Table 2667. Term [MS:1002790]
id	MS:1002790
name	6542 Q-TOF LC/MS
def	"The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2666. MS:1002791 6545 Q-TOF LC/MS

Table 2668. Term [MS:1002791]
id	MS:1002791
name	6545 Q-TOF LC/MS
def	"The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2667. MS:1002792 6560 Q-TOF LC/MS

Table 2669. Term [MS:1002792]
id	MS:1002792
name	6560 Q-TOF LC/MS
def	"The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2668. MS:1002793 6570 Q-TOF LC/MS

Table 2670. Term [MS:1002793]
id	MS:1002793
name	6570 Q-TOF LC/MS
def	"The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2669. MS:1002794 6120B Quadrupole LC/MS

Table 2671. Term [MS:1002794]
id	MS:1002794
name	6120B Quadrupole LC/MS
def	"The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2670. MS:1002795 6150 Quadrupole LC/MS

Table 2672. Term [MS:1002795]
id	MS:1002795
name	6150 Quadrupole LC/MS
def	"The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2671. MS:1002796 6224 Time-of-Flight LC/MS

Table 2673. Term [MS:1002796]
id	MS:1002796
name	6224 Time-of-Flight LC/MS
def	"The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2672. MS:1002797 6230A Time-of-Flight LC/MS

Table 2674. Term [MS:1002797]
id	MS:1002797
name	6230A Time-of-Flight LC/MS
def	"The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2673. MS:1002798 6230B Time-of-Flight LC/MS

Table 2675. Term [MS:1002798]
id	MS:1002798
name	6230B Time-of-Flight LC/MS
def	"The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2674. MS:1002799 6430 Triple Quadrupole LC/MS

Table 2676. Term [MS:1002799]
id	MS:1002799
name	6430 Triple Quadrupole LC/MS
def	"The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2675. MS:1002800 6495A Triple Quadrupole LC/MS

Table 2677. Term [MS:1002800]
id	MS:1002800
name	6495A Triple Quadrupole LC/MS
def	"The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2676. MS:1002801 6495B Triple Quadrupole LC/MS

Table 2678. Term [MS:1002801]
id	MS:1002801
name	6495B Triple Quadrupole LC/MS
def	"The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2677. MS:1002802 7000A Triple Quadrupole GC/MS

Table 2679. Term [MS:1002802]
id	MS:1002802
name	7000A Triple Quadrupole GC/MS
def	"The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2678. MS:1002803 7000B Triple Quadrupole GC/MS

Table 2680. Term [MS:1002803]
id	MS:1002803
name	7000B Triple Quadrupole GC/MS
def	"The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2679. MS:1002804 7800 Quadrupole ICP-MS

Table 2681. Term [MS:1002804]
id	MS:1002804
name	7800 Quadrupole ICP-MS
def	"The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2680. MS:1002805 8800 Triple Quadrupole ICP-MS

Table 2682. Term [MS:1002805]
id	MS:1002805
name	8800 Triple Quadrupole ICP-MS
def	"The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS]
is_a	MS:1000490 Agilent instrument model ! Agilent instrument model

2.2681. MS:1002806 ion

Table 2683. Term [MS:1002806]
id	MS:1002806
name	ion
def	"Molecular entity having a net positive or negative electric charge." [PSI:MS]
is_a	MS:1000881 molecular entity ! molecular entity

2.2682. MS:1002807 positive mode adduct ion

Table 2684. Term [MS:1002807]
id	MS:1002807
name	positive mode adduct ion
def	"Adduct ion with positive ionization." [PSI:MS]
is_a	MS:1000353 adduct ion ! adduct ion

2.2683. MS:1002808 negative mode adduct ion

Table 2685. Term [MS:1002808]
id	MS:1002808
name	negative mode adduct ion
def	"Adduct ion with negative ionization." [PSI:MS]
is_a	MS:1000353 adduct ion ! adduct ion

2.2684. MS:1002809 adduct ion attribute

Table 2686. Term [MS:1002809]
id	MS:1002809
name	adduct ion attribute
def	"Nonphysical characteristic attributed to an adduct ion." [PSI:MS]
relationship	part_of MS:1000353 adduct ion ! adduct ion

2.2685. MS:1002810 adduct ion X m/z

Table 2687. Term [MS:1002810]
id	MS:1002810
name	adduct ion X m/z
def	"Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003056 adduct ion property ! adduct ion property

2.2686. MS:1002811 adduct ion isotope

Table 2688. Term [MS:1002811]
id	MS:1002811
name	adduct ion isotope
def	"Isotope of the matrix molecule M of an adduct formation." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1003056 adduct ion property ! adduct ion property

2.2687. MS:1002812 Regular expression for adduct ion formula

Table 2689. Term [MS:1002812]
id	MS:1002812
name	Regular expression for adduct ion formula
def	"(\[[:digit:]{0,1}M([][:digit:]{0,1}(H\|K\|(Na)\|(Li)\|(Cl)\|(Br)\|(NH3)\|(NH4)\|(CH3OH)\|(IsoProp)\|(DMSO)\|(FA)\|(Hac)\|(TFA)\|(NaCOOH)\|(HCOOH)\|(CF3COOH)\|(ACN))){0,}([-][:digit:]{0,1}(H\|(H2O)\|(CH2)\|(CH4)\|(NH3)\|(CO)\|(CO2)\|(COCH2)\|(HCOOH)\|(C2H4)\|(C4H8)\|(C3H2O3)\|(C5H8O4)\|(C6H10O4)\|(C6H10O5)\|(C6H8O6))){0,}\][:digit:]{0,1}[-])." [PSI:PI]
is_a	MS:1002479 regular expression ! regular expression

2.2688. MS:1002813 adduct ion formula

Table 2690. Term [MS:1002813]
id	MS:1002813
name	adduct ion formula
def	"Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002809 adduct ion attribute ! adduct ion attribute
relationship	has_regexp MS:1002812 Regular expression for adduct ion formula ! (\[[:digit:]{0,1}M([][:digit:]{0,1}(H\|K\|(Na)\|(Li)\|(Cl)\|(Br)\|(NH3)\|(NH4)\|(CH3OH)\|(IsoProp)\|(DMSO)\|(FA)\|(Hac)\|(TFA)\|(NaCOOH)\|(HCOOH)\|(CF3COOH)\|(ACN))){0,}([-][:digit:]{0,1}(H\|(H2O)\|(CH2)\|(CH4)\|(NH3)\|(CO)\|(CO2)\|(COCH2)\|(HCOOH)\|(C2H4)\|(C4H8)\|(C3H2O3)\|(C5H8O4)\|(C6H10O4)\|(C6H10O5)\|(C6H8O6))){0,}\][:digit:]{0,1}[-])

2.2689. MS:1002814 volt-second per square centimeter

Table 2691. Term [MS:1002814]
id	MS:1002814
name	volt-second per square centimeter
def	"An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI]
synonym	"Vs/cm^2" EXACT []
is_a	[UO:0000000] ! unit

2.2690. MS:1002815 inverse reduced ion mobility

Table 2692. Term [MS:1002815]
id	MS:1002815
name	inverse reduced ion mobility
def	"Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1000455 ion selection attribute ! ion selection attribute
is_a	MS:1002892 ion mobility attribute ! ion mobility attribute
relationship	has_units MS:1002814 volt-second per square centimeter ! volt-second per square centimeter

2.2691. MS:1002816 mean ion mobility array

Table 2693. Term [MS:1002816]
id	MS:1002816
name	mean ion mobility array
def	"Array of drift times, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002893 ion mobility array ! ion mobility array
relationship	has_units [UO:0000028] ! millisecond
relationship	has_units [UO:0000010] ! second

2.2692. MS:1002817 Bruker TDF format

Table 2694. Term [MS:1002817]
id	MS:1002817
name	Bruker TDF format
def	"Bruker TDF raw file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2693. MS:1002818 Bruker TDF nativeID format

Table 2695. Term [MS:1002818]
id	MS:1002818
name	Bruker TDF nativeID format
def	"Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.2694. MS:1002819 Bruker TDF nativeID format, combined spectra

Table 2696. Term [MS:1002819]
id	MS:1002819
name	Bruker TDF nativeID format, combined spectra
def	"Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002646 native spectrum identifier format, combined spectra ! native spectrum identifier format, combined spectra

2.2695. MS:1002820 M+H ion

Table 2697. Term [MS:1002820]
id	MS:1002820
name	M+H ion
def	"Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton." [PSI:MS]
property_value	ionMass: "M + 1.007276" xsd:string
is_a	MS:1002807 positive mode adduct ion ! positive mode adduct ion

2.2696. MS:1002821 M-H ion

Table 2698. Term [MS:1002821]
id	MS:1002821
name	M-H ion
def	"Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M." [PSI:MS]
property_value	ionMass: "M - 1.007276" xsd:string
is_a	MS:1002808 negative mode adduct ion ! negative mode adduct ion

2.2697. MS:1002822 OpenMS file format

Table 2699. Term [MS:1002822]
id	MS:1002822
name	OpenMS file format
def	"File format developed by the OpenMS team." [PMID:27575624]
is_a	MS:1001459 file format ! file format

2.2698. MS:1002823 idXML

Table 2700. Term [MS:1002823]
id	MS:1002823
name	idXML
def	"OpenMS intermediate identification format." [PSI:PI]
is_a	MS:1002822 OpenMS file format ! OpenMS file format

2.2699. MS:1002824 featureXML

Table 2701. Term [MS:1002824]
id	MS:1002824
name	featureXML
def	"OpenMS feature file format." [PSI:PI]
is_a	MS:1002822 OpenMS file format ! OpenMS file format

2.2700. MS:1002825 consensusXML

Table 2702. Term [MS:1002825]
id	MS:1002825
name	consensusXML
def	"OpenMS consensus map format." [PSI:PI]
is_a	MS:1002822 OpenMS file format ! OpenMS file format

2.2701. MS:1002826 MetaMorpheus

Table 2703. Term [MS:1002826]
id	MS:1002826
name	MetaMorpheus
def	"MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus]
is_a	MS:1001456 analysis software ! analysis software

2.2702. MS:1002827 MetaMorpheus:score

Table 2704. Term [MS:1002827]
id	MS:1002827
name	MetaMorpheus:score
def	"MetaMorpheus score for PSMs." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2703. MS:1002828 MetaMorpheus:protein score

Table 2705. Term [MS:1002828]
id	MS:1002828
name	MetaMorpheus:protein score
def	"MetaMorpheus score for protein groups." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups
relationship	has_order MS:1002108 higher score better ! higher score better

2.2704. MS:1002829 XCMS:into

Table 2706. Term [MS:1002829]
id	MS:1002829
name	XCMS:into
def	"Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.2705. MS:1002830 XCMS:intf

Table 2707. Term [MS:1002830]
id	MS:1002830
name	XCMS:intf
def	"Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.2706. MS:1002831 XCMS:maxo

Table 2708. Term [MS:1002831]
id	MS:1002831
name	XCMS:maxo
def	"Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.2707. MS:1002832 XCMS:area

Table 2709. Term [MS:1002832]
id	MS:1002832
name	XCMS:area
def	"Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002735 feature-level quantification datatype ! feature-level quantification datatype

2.2708. MS:1002833 alternating polarity mode

Table 2710. Term [MS:1002833]
id	MS:1002833
name	alternating polarity mode
def	"Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI]
is_a	MS:1000857 run attribute ! run attribute

2.2709. MS:1002834 ProteomeDiscoverer:Delta Score

Table 2711. Term [MS:1002834]
id	MS:1002834
name	ProteomeDiscoverer:Delta Score
def	"The Delta Score reported by Proteome Discoverer version 2." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2710. MS:1002835 LTQ Orbitrap Classic

Table 2712. Term [MS:1002835]
id	MS:1002835
name	LTQ Orbitrap Classic
def	"Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2711. MS:1002836 iProX dataset identifier

Table 2713. Term [MS:1002836]
id	MS:1002836
name	iProX dataset identifier
def	"Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2712. MS:1002837 iProX dataset URI

Table 2714. Term [MS:1002837]
id	MS:1002837
name	iProX dataset URI
def	"URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2713. MS:1002838 mzMLb format

Table 2715. Term [MS:1002838]
id	MS:1002838
name	mzMLb format
def	"mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2714. MS:1002839 Conversion to mzMLb

Table 2716. Term [MS:1002839]
id	MS:1002839
name	Conversion to mzMLb
def	"Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI]
is_a	MS:1000530 file format conversion ! file format conversion

2.2715. MS:1002840 external reference data

Table 2717. Term [MS:1002840]
id	MS:1002840
name	external reference data
def	"Data belonging to an external reference." [PSI:MS]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.2716. MS:1002841 external HDF5 dataset

Table 2718. Term [MS:1002841]
id	MS:1002841
name	external HDF5 dataset
def	"The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002840 external reference data ! external reference data

2.2717. MS:1002842 external offset

Table 2719. Term [MS:1002842]
id	MS:1002842
name	external offset
def	"The position in the external data where the array begins." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship	has_units [UO:0000189] ! Count
is_a	MS:1002840 external reference data ! external reference data

2.2718. MS:1002843 external array length

Table 2720. Term [MS:1002843]
id	MS:1002843
name	external array length
def	"Describes how many fields an array contains." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship	has_units [UO:0000189] ! Count
is_a	MS:1002840 external reference data ! external reference data

2.2719. MS:1002844 Experiment additional parameter

Table 2721. Term [MS:1002844]
id	MS:1002844
name	Experiment additional parameter
def	"Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI]
is_a	MS:1001458 spectrum generation information ! spectrum generation information

2.2720. MS:1002845 Associated file URI

Table 2722. Term [MS:1002845]
id	MS:1002845
name	Associated file URI
def	"URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2721. MS:1002846 Associated raw file URI

Table 2723. Term [MS:1002846]
id	MS:1002846
name	Associated raw file URI
def	"URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2722. MS:1002847 ProteomeCentral dataset URI

Table 2724. Term [MS:1002847]
id	MS:1002847
name	ProteomeCentral dataset URI
def	"URI associated to one PX submission in ProteomeCentral." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2723. MS:1002848 Result file URI

Table 2725. Term [MS:1002848]
id	MS:1002848
name	Result file URI
def	"URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2724. MS:1002849 Search engine output file URI

Table 2726. Term [MS:1002849]
id	MS:1002849
name	Search engine output file URI
def	"URI of one search engine output file associated to one PX submission." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2725. MS:1002850 Peak list file URI

Table 2727. Term [MS:1002850]
id	MS:1002850
name	Peak list file URI
def	"URI of one of one search engine output file associated to one PX submission." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2726. MS:1002851 Other type file URI

Table 2728. Term [MS:1002851]
id	MS:1002851
name	Other type file URI
def	"URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2727. MS:1002852 Dataset FTP location

Table 2729. Term [MS:1002852]
id	MS:1002852
name	Dataset FTP location
def	"FTP location of one entire PX data set." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2728. MS:1002853 Dataset with no associated published manuscript

Table 2730. Term [MS:1002853]
id	MS:1002853
name	Dataset with no associated published manuscript
def	"A dataset which does not have an associated published manuscript." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2729. MS:1002854 Peer-reviewed dataset

Table 2731. Term [MS:1002854]
id	MS:1002854
name	Peer-reviewed dataset
def	"Dataset has been peer-reviewed somehow." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2730. MS:1002855 Non peer-reviewed dataset

Table 2732. Term [MS:1002855]
id	MS:1002855
name	Non peer-reviewed dataset
def	"Dataset that has not been peer-reviewed by any means." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2731. MS:1002856 Supported dataset by repository

Table 2733. Term [MS:1002856]
id	MS:1002856
name	Supported dataset by repository
def	"Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2732. MS:1002857 Unsupported dataset by repository

Table 2734. Term [MS:1002857]
id	MS:1002857
name	Unsupported dataset by repository
def	"Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2733. MS:1002858 Dataset with its publication pending

Table 2735. Term [MS:1002858]
id	MS:1002858
name	Dataset with its publication pending
def	"A dataset which has an associated manuscript pending for publication." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2734. MS:1002859 Additional associated raw file URI

Table 2736. Term [MS:1002859]
id	MS:1002859
name	Additional associated raw file URI
def	"Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2735. MS:1002860 Gel image file URI

Table 2737. Term [MS:1002860]
id	MS:1002860
name	Gel image file URI
def	"URI of one gel image file associated to one PX submission." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002845 Associated file URI ! Associated file URI

2.2736. MS:1002861 Reprocessed complete dataset

Table 2738. Term [MS:1002861]
id	MS:1002861
name	Reprocessed complete dataset
def	"All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2737. MS:1002862 Reprocessed subset dataset

Table 2739. Term [MS:1002862]
id	MS:1002862
name	Reprocessed subset dataset
def	"A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2738. MS:1002863 Data derived from previous dataset

Table 2740. Term [MS:1002863]
id	MS:1002863
name	Data derived from previous dataset
def	"One dataset is a reanalysis of previously published data." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2739. MS:1002864 No PTMs are included in the dataset

Table 2741. Term [MS:1002864]
id	MS:1002864
name	No PTMs are included in the dataset
def	"No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2740. MS:1002865 Accepted manuscript

Table 2742. Term [MS:1002865]
id	MS:1002865
name	Accepted manuscript
def	"A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2741. MS:1002866 Reference

Table 2743. Term [MS:1002866]
id	MS:1002866
name	Reference
def	"Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2742. MS:1002867 Experimental information has been refined since this experiment was originally made publicly available

Table 2744. Term [MS:1002867]
id	MS:1002867
name	Experimental information has been refined since this experiment was originally made publicly available
def	"This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2743. MS:1002868 Original data

Table 2745. Term [MS:1002868]
id	MS:1002868
name	Original data
def	"One dataset is not a reanalysis of previously published data." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2744. MS:1002869 mzR

Table 2746. Term [MS:1002869]
id	MS:1002869
name	mzR
def	"Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2745. MS:1002870 MSnbase

Table 2747. Term [MS:1002870]
id	MS:1002870
name	MSnbase
def	"Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2746. MS:1002871 CAMERA

Table 2748. Term [MS:1002871]
id	MS:1002871
name	CAMERA
def	"Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2747. MS:1002872 Panorama Public dataset identifier

Table 2749. Term [MS:1002872]
id	MS:1002872
name	Panorama Public dataset identifier
def	"Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2748. MS:1002873 Panorama Public dataset URI

Table 2750. Term [MS:1002873]
id	MS:1002873
name	Panorama Public dataset URI
def	"URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref	value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2749. MS:1002874 TSQ Altis

Table 2751. Term [MS:1002874]
id	MS:1002874
name	TSQ Altis
def	"Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2750. MS:1002875 TSQ Quantis

Table 2752. Term [MS:1002875]
id	MS:1002875
name	TSQ Quantis
def	"Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2751. MS:1002876 TSQ 9000

Table 2753. Term [MS:1002876]
id	MS:1002876
name	TSQ 9000
def	"Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2752. MS:1002877 Q Exactive HF-X

Table 2754. Term [MS:1002877]
id	MS:1002877
name	Q Exactive HF-X
def	"Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2753. MS:1002878 small molecule analysis software

Table 2755. Term [MS:1002878]
id	MS:1002878
name	small molecule analysis software
def	"Software for the analysis of small molecules." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2754. MS:1002879 Progenesis QI

Table 2756. Term [MS:1002879]
id	MS:1002879
name	Progenesis QI
def	"Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI]
is_a	MS:1002878 small molecule analysis software ! small molecule analysis software

2.2755. MS:1002880 Compound Discoverer

Table 2757. Term [MS:1002880]
id	MS:1002880
name	Compound Discoverer
def	"Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI]
is_a	MS:1002878 small molecule analysis software ! small molecule analysis software

2.2756. MS:1002881 MyCompoundID

Table 2758. Term [MS:1002881]
id	MS:1002881
name	MyCompoundID
def	"Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753]
is_a	MS:1002878 small molecule analysis software ! small molecule analysis software

2.2757. MS:1002882 study variable average function

Table 2759. Term [MS:1002882]
id	MS:1002882
name	study variable average function
def	"Function used to calculate the study variable quantification value." [PSI:PI]
is_a	MS:1001184 search statistics ! search statistics

2.2758. MS:1002883 median

Table 2760. Term [MS:1002883]
id	MS:1002883
name	median
def	"Median function." [PSI:PI]
is_a	MS:1002882 study variable average function ! study variable average function

2.2759. MS:1002884 study variable variation function

Table 2761. Term [MS:1002884]
id	MS:1002884
name	study variable variation function
def	"Function used to calculate the study variable quantification variation value." [PSI:PI]
is_a	MS:1001184 search statistics ! search statistics

2.2760. MS:1002885 standard error

Table 2762. Term [MS:1002885]
id	MS:1002885
name	standard error
def	"Standard error function." [PSI:PI]
is_a	MS:1002884 study variable variation function ! study variable variation function

2.2761. MS:1002886 small molecule quantification datatype

Table 2763. Term [MS:1002886]
id	MS:1002886
name	small molecule quantification datatype
def	"The value reported in a small molecule quantification." [PSI:PI]
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2762. MS:1002887 Progenesis QI normalised abundance

Table 2764. Term [MS:1002887]
id	MS:1002887
name	Progenesis QI normalised abundance
def	"The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002886 small molecule quantification datatype ! small molecule quantification datatype

2.2763. MS:1002888 small molecule confidence measure

Table 2765. Term [MS:1002888]
id	MS:1002888
name	small molecule confidence measure
def	"The confidence score produced by a small molecule analysis software." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2764. MS:1002889 Progenesis MetaScope score

Table 2766. Term [MS:1002889]
id	MS:1002889
name	Progenesis MetaScope score
def	"The confidence score produced by Progenesis QI." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002888 small molecule confidence measure ! small molecule confidence measure

2.2765. MS:1002890 fragmentation score

Table 2767. Term [MS:1002890]
id	MS:1002890
name	fragmentation score
def	"The fragmentation confidence score." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002888 small molecule confidence measure ! small molecule confidence measure

2.2766. MS:1002891 isotopic fit score

Table 2768. Term [MS:1002891]
id	MS:1002891
name	isotopic fit score
def	"The isotopic fit confidence score." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002888 small molecule confidence measure ! small molecule confidence measure

2.2767. MS:1002892 ion mobility attribute

Table 2769. Term [MS:1002892]
id	MS:1002892
name	ion mobility attribute
def	"An attribute describing ion mobility searches." [PSI:PI]
is_a	MS:1000503 scan attribute ! scan attribute
is_a	MS:1002345 PSM-level attribute ! PSM-level attribute

2.2768. MS:1002893 ion mobility array

Table 2770. Term [MS:1002893]
id	MS:1002893
name	ion mobility array
def	"An array of ion mobility data." [PSI:PI]
is_a	MS:1000513 binary data array ! binary data array

2.2769. MS:1002894 InChIKey

Table 2771. Term [MS:1002894]
id	MS:1002894
name	InChIKey
def	"Unique chemical structure identifier for chemical compounds." [PMID:273343401]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001405 spectrum identification result details ! spectrum identification result details

2.2770. MS:1002895 small molecule identification attribute

Table 2772. Term [MS:1002895]
id	MS:1002895
name	small molecule identification attribute
def	"Compound identification information." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2771. MS:1002896 compound identification confidence level

Table 2773. Term [MS:1002896]
id	MS:1002896
name	compound identification confidence level
def	"Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002895 small molecule identification attribute ! small molecule identification attribute

2.2772. MS:1002897 isotopomer peak

Table 2774. Term [MS:1002897]
id	MS:1002897
name	isotopomer peak
def	"OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI]
comment	This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
xref	value-type:xsd:string "The allowed value-type for this CV term."
is_a	MS:1000231 peak ! peak
is_obsolete	true

2.2773. MS:1002898 Shimadzu Biotech QTOF nativeID format

Table 2775. Term [MS:1002898]
id	MS:1002898
name	Shimadzu Biotech QTOF nativeID format
def	"Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI]
is_a	MS:1000767 native spectrum identifier format ! native spectrum identifier format

2.2774. MS:1002899 msalign format

Table 2776. Term [MS:1002899]
id	MS:1002899
name	msalign format
def	"msalign file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2775. MS:1002900 feature format

Table 2777. Term [MS:1002900]
id	MS:1002900
name	feature format
def	"TopFD feature file format." [PSI:MS]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2776. MS:1002901 TopPIC

Table 2778. Term [MS:1002901]
id	MS:1002901
name	TopPIC
def	"TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a	MS:1001456 analysis software ! analysis software

2.2777. MS:1002902 TopFD

Table 2779. Term [MS:1002902]
id	MS:1002902
name	TopFD
def	"Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a	MS:1001456 analysis software ! analysis software

2.2778. MS:1002903 TopMG

Table 2780. Term [MS:1002903]
id	MS:1002903
name	TopMG
def	"A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html]
is_a	MS:1001456 analysis software ! analysis software

2.2779. MS:1002904 proteoform-level identification attribute

Table 2781. Term [MS:1002904]
id	MS:1002904
name	proteoform-level identification attribute
def	"Proteoform level information." [PSI:PI]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.2780. MS:1002905 proteoform-level identification statistic

Table 2782. Term [MS:1002905]
id	MS:1002905
name	proteoform-level identification statistic
def	"Identification confidence metric for a proteoform." [PSI:PI]
is_a	MS:1002904 proteoform-level identification attribute ! proteoform-level identification attribute

2.2781. MS:1002906 search engine specific score for proteoforms

Table 2783. Term [MS:1002906]
id	MS:1002906
name	search engine specific score for proteoforms
def	"Search engine specific proteoform scores." [PSI:PI]
is_a	MS:1002905 proteoform-level identification statistic ! proteoform-level identification statistic

2.2782. MS:1002907 proteoform-level global FDR

Table 2784. Term [MS:1002907]
id	MS:1002907
name	proteoform-level global FDR
def	"Estimation of the global false discovery rate of proteoforms." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002905 proteoform-level identification statistic ! proteoform-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2783. MS:1002908 proteoform-level local FDR

Table 2785. Term [MS:1002908]
id	MS:1002908
name	proteoform-level local FDR
def	"Estimation of the local false discovery rate of proteoforms." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002905 proteoform-level identification statistic ! proteoform-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2784. MS:1002909 proteoform-level statistical threshold

Table 2786. Term [MS:1002909]
id	MS:1002909
name	proteoform-level statistical threshold
def	"Estimated statistical threshold at proteoform-level." [PSI:PI]
is_a	MS:1002573 spectrum identification statistical threshold ! spectrum identification statistical threshold

2.2785. MS:1002910 proteoform-level global FDR threshold

Table 2787. Term [MS:1002910]
id	MS:1002910
name	proteoform-level global FDR threshold
def	"Threshold for the global false discovery rate of proteoforms." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002909 proteoform-level statistical threshold ! proteoform-level statistical threshold

2.2786. MS:1002911 proteoform-level local FDR threshold

Table 2788. Term [MS:1002911]
id	MS:1002911
name	proteoform-level local FDR threshold
def	"Threshold for the local false discovery rate of proteoforms." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002909 proteoform-level statistical threshold ! proteoform-level statistical threshold

2.2787. MS:1002912 TopPIC input parameter

Table 2789. Term [MS:1002912]
id	MS:1002912
name	TopPIC input parameter
def	"Search engine input parameters specific to TopPIC." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.2788. MS:1002913 TopPIC:fixed modification

Table 2790. Term [MS:1002913]
id	MS:1002913
name	TopPIC:fixed modification
def	"Fixed modifications for TopPIC searching." [PSI:PI]
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2789. MS:1002914 TopPIC:N-term form

Table 2791. Term [MS:1002914]
id	MS:1002914
name	TopPIC:N-term form
def	"N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI]
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2790. MS:1002915 TopPIC:error tolerance

Table 2792. Term [MS:1002915]
id	MS:1002915
name	TopPIC:error tolerance
def	"Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2791. MS:1002916 TopPIC:max shift

Table 2793. Term [MS:1002916]
id	MS:1002916
name	TopPIC:max shift
def	"Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2792. MS:1002917 TopPIC:min shift

Table 2794. Term [MS:1002917]
id	MS:1002917
name	TopPIC:min shift
def	"Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2793. MS:1002918 TopPIC:shift num

Table 2795. Term [MS:1002918]
id	MS:1002918
name	TopPIC:shift num
def	"Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2794. MS:1002919 TopPIC:spectral cutoff type

Table 2796. Term [MS:1002919]
id	MS:1002919
name	TopPIC:spectral cutoff type
def	"Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2795. MS:1002920 TopPIC:spectral cutoff value

Table 2797. Term [MS:1002920]
id	MS:1002920
name	TopPIC:spectral cutoff value
def	"Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2796. MS:1002921 TopPIC:proteoform-level cutoff type

Table 2798. Term [MS:1002921]
id	MS:1002921
name	TopPIC:proteoform-level cutoff type
def	"Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2797. MS:1002922 TopPIC:proteoform-level cutoff value

Table 2799. Term [MS:1002922]
id	MS:1002922
name	TopPIC:proteoform-level cutoff value
def	"Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2798. MS:1002923 TopPIC:generating function

Table 2800. Term [MS:1002923]
id	MS:1002923
name	TopPIC:generating function
def	"P-value and E-value estimation using generating function." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2799. MS:1002924 TopPIC:combined spectrum number

Table 2801. Term [MS:1002924]
id	MS:1002924
name	TopPIC:combined spectrum number
def	"Number of combined spectra." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2800. MS:1002925 TopPIC:mod file

Table 2802. Term [MS:1002925]
id	MS:1002925
name	TopPIC:mod file
def	"The text file containing the information of common PTMs." [PSI:PI]
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2801. MS:1002926 TopPIC:thread number

Table 2803. Term [MS:1002926]
id	MS:1002926
name	TopPIC:thread number
def	"Number of threads used in TopPIC." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2802. MS:1002927 TopPIC:use TopFD feature

Table 2804. Term [MS:1002927]
id	MS:1002927
name	TopPIC:use TopFD feature
def	"Proteoform identification using TopFD feature file." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002912 TopPIC input parameter ! TopPIC input parameter

2.2803. MS:1002928 TopPIC:spectral E-value

Table 2805. Term [MS:1002928]
id	MS:1002928
name	TopPIC:spectral E-value
def	"TopPIC spectrum-level E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
relationship	has_order MS:1002109 lower score better ! lower score better

2.2804. MS:1002929 TopPIC:spectral FDR

Table 2806. Term [MS:1002929]
id	MS:1002929
name	TopPIC:spectral FDR
def	"TopPIC spectrum-level FDR." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002351 PSM-level local FDR ! PSM-level local FDR

2.2805. MS:1002930 TopPIC:proteoform-level FDR

Table 2807. Term [MS:1002930]
id	MS:1002930
name	TopPIC:proteoform-level FDR
def	"TopPIC proteoform-level FDR." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002908 proteoform-level local FDR ! proteoform-level local FDR
is_a	MS:1002906 search engine specific score for proteoforms ! search engine specific score for proteoforms

2.2806. MS:1002931 TopPIC:spectral p-value

Table 2808. Term [MS:1002931]
id	MS:1002931
name	TopPIC:spectral p-value
def	"TopPIC spectrum-level p-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1002352 PSM-level p-value ! PSM-level p-value

2.2807. MS:1002932 TopPIC:MIScore

Table 2809. Term [MS:1002932]
id	MS:1002932
name	TopPIC:MIScore
def	"Modification identification score." [PMID:27291504]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001968 PTM localization PSM-level statistic ! PTM localization PSM-level statistic

2.2808. MS:1002933 TopPIC:MIScore threshold

Table 2810. Term [MS:1002933]
id	MS:1002933
name	TopPIC:MIScore threshold
def	"TopPIC:MIScore threshold." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002555 PTM localization score threshold ! PTM localization score threshold

2.2809. MS:1002934 TopMG input parameter

Table 2811. Term [MS:1002934]
id	MS:1002934
name	TopMG input parameter
def	"Search engine input parameters specific to TopMG." [PSI:PI]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.2810. MS:1002935 TopMG:fixed modification

Table 2812. Term [MS:1002935]
id	MS:1002935
name	TopMG:fixed modification
def	"Fixed modifications for TopMG searching." [PSI:PI]
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2811. MS:1002936 TopMG:N-term form

Table 2813. Term [MS:1002936]
id	MS:1002936
name	TopMG:N-term form
def	"N-terminal forms of proteins allowed in TopMG searching." [PSI:PI]
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2812. MS:1002937 TopMG:error tolerance

Table 2814. Term [MS:1002937]
id	MS:1002937
name	TopMG:error tolerance
def	"Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2813. MS:1002938 TopMG:max shift

Table 2815. Term [MS:1002938]
id	MS:1002938
name	TopMG:max shift
def	"Maximum value of the mass shift (in Dalton)." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2814. MS:1002939 TopMG:spectral cutoff type

Table 2816. Term [MS:1002939]
id	MS:1002939
name	TopMG:spectral cutoff type
def	"Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2815. MS:1002940 TopMG:spectral cutoff value

Table 2817. Term [MS:1002940]
id	MS:1002940
name	TopMG:spectral cutoff value
def	"Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2816. MS:1002941 TopMG:proteoform-level cutoff type

Table 2818. Term [MS:1002941]
id	MS:1002941
name	TopMG:proteoform-level cutoff type
def	"Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2817. MS:1002942 TopMG:proteoform-level cutoff value

Table 2819. Term [MS:1002942]
id	MS:1002942
name	TopMG:proteoform-level cutoff value
def	"Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2818. MS:1002943 TopMG:mod file

Table 2820. Term [MS:1002943]
id	MS:1002943
name	TopMG:mod file
def	"The text file containing the information of common PTMs." [PSI:PI]
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2819. MS:1002944 TopMG:thread number

Table 2821. Term [MS:1002944]
id	MS:1002944
name	TopMG:thread number
def	"Number of threads used in TopMG." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2820. MS:1002945 TopMG:use TopFD feature

Table 2822. Term [MS:1002945]
id	MS:1002945
name	TopMG:use TopFD feature
def	"Proteoform identification using TopFD feature file." [PSI:PI]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2821. MS:1002946 TopMG:proteoform graph gap size

Table 2823. Term [MS:1002946]
id	MS:1002946
name	TopMG:proteoform graph gap size
def	"Gap size in constructing proteoform graph." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2822. MS:1002947 TopMG:variable PTM number

Table 2824. Term [MS:1002947]
id	MS:1002947
name	TopMG:variable PTM number
def	"Maximum number of variable PTMs." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2823. MS:1002948 TopMG:variable PTM number in proteoform graph gap

Table 2825. Term [MS:1002948]
id	MS:1002948
name	TopMG:variable PTM number in proteoform graph gap
def	"Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI]
xref	value-type:xsd\:integer "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2824. MS:1002949 TopMG:use ASF-DIAGONAL

Table 2826. Term [MS:1002949]
id	MS:1002949
name	TopMG:use ASF-DIAGONAL
def	"Protein filtering using ASF-DIAGONAL method." [PMID:29327814]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1002934 TopMG input parameter ! TopMG input parameter

2.2825. MS:1002950 TopMG:spectral E-value

Table 2827. Term [MS:1002950]
id	MS:1002950
name	TopMG:spectral E-value
def	"TopMG spectrum-level E-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2826. MS:1002951 TopMG:spectral FDR

Table 2828. Term [MS:1002951]
id	MS:1002951
name	TopMG:spectral FDR
def	"TopMG spectrum-level FDR." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002351 PSM-level local FDR ! PSM-level local FDR
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2827. MS:1002952 TopMG:proteoform-level FDR

Table 2829. Term [MS:1002952]
id	MS:1002952
name	TopMG:proteoform-level FDR
def	"TopMG proteoform-level FDR." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002908 proteoform-level local FDR ! proteoform-level local FDR
is_a	MS:1002906 search engine specific score for proteoforms ! search engine specific score for proteoforms

2.2828. MS:1002953 TopMG:spectral p-value

Table 2830. Term [MS:1002953]
id	MS:1002953
name	TopMG:spectral p-value
def	"TopMG spectrum-level p-value." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002352 PSM-level p-value ! PSM-level p-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2829. MS:1002954 collisional cross sectional area

Table 2831. Term [MS:1002954]
id	MS:1002954
name	collisional cross sectional area
def	"Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1000861 molecular entity property ! molecular entity property
relationship	has_units [UO:0000324] ! square angstrom

2.2830. MS:1002955 hr-ms compound identification confidence level

Table 2832. Term [MS:1002955]
id	MS:1002955
name	hr-ms compound identification confidence level
def	"Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
xref	value-type:xsd:string "The allowed value-type for this CV term."
is_a	MS:1002895 small molecule identification attribute ! small molecule identification attribute

2.2831. MS:1002956 isotopic ion MS peak

Table 2833. Term [MS:1002956]
id	MS:1002956
name	isotopic ion MS peak
def	"A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000231 peak ! peak

2.2832. MS:1002957 isotopomer MS peak

Table 2834. Term [MS:1002957]
id	MS:1002957
name	isotopomer MS peak
def	"The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002956 isotopic ion MS peak ! isotopic ion MS peak

2.2833. MS:1002958 isotopologue MS peak

Table 2835. Term [MS:1002958]
id	MS:1002958
name	isotopologue MS peak
def	"The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002956 isotopic ion MS peak ! isotopic ion MS peak

2.2834. MS:1002959 isomer

Table 2836. Term [MS:1002959]
id	MS:1002959
name	isomer
def	"One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000859 molecule ! molecule

2.2835. MS:1002960 isotopomer

Table 2837. Term [MS:1002960]
id	MS:1002960
name	isotopomer
def	"An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002959 isomer ! isomer

2.2836. MS:1002961 isotopologue

Table 2838. Term [MS:1002961]
id	MS:1002961
name	isotopologue
def	"A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002959 isomer ! isomer

2.2837. MS:1002962 mean

Table 2839. Term [MS:1002962]
id	MS:1002962
name	mean
def	"The arithmetic mean." [PSI:PI]
is_a	MS:1002882 study variable average function ! study variable average function

2.2838. MS:1002963 variation coefficient

Table 2840. Term [MS:1002963]
id	MS:1002963
name	variation coefficient
def	"The coefficient of variation." [PSI:PI]
is_a	MS:1002884 study variable variation function ! study variable variation function

2.2839. MS:1002964 lipidomics analysis software

Table 2841. Term [MS:1002964]
id	MS:1002964
name	lipidomics analysis software
def	"Lipidomics analysis software." [PSI:PI]
is_a	MS:1002878 small molecule analysis software ! small molecule analysis software

2.2840. MS:1002965 Lipid Data Analyzer

Table 2842. Term [MS:1002965]
id	MS:1002965
name	Lipid Data Analyzer
def	"Lipid Data Analyzer software for lipid quantification." [PMID:29058722]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2841. MS:1002966 chrom format

Table 2843. Term [MS:1002966]
id	MS:1002966
name	chrom format
def	"The Lipid Data Analyzer native chrom format." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2842. MS:1002967 LipidHunter

Table 2844. Term [MS:1002967]
id	MS:1002967
name	LipidHunter
def	"Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2843. MS:1002968 LipidXplorer

Table 2845. Term [MS:1002968]
id	MS:1002968
name	LipidXplorer
def	"Software for consensual cross-platform lipidomics." [PMID:22272252]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2844. MS:1002969 LipidMatch

Table 2846. Term [MS:1002969]
id	MS:1002969
name	LipidMatch
def	"An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data." [PMID:28693421]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2845. MS:1002970 Greazy

Table 2847. Term [MS:1002970]
id	MS:1002970
name	Greazy
def	"Open-source software for automated phospholipid tandem mass spectrometry identification." [PMID:27186799]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2846. MS:1002971 LipidBlast

Table 2848. Term [MS:1002971]
id	MS:1002971
name	LipidBlast
def	"LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library." [PMID:28660581]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2847. MS:1002972 Lipid-Pro

Table 2849. Term [MS:1002972]
id	MS:1002972
name	Lipid-Pro
def	"A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms." [PMID:25433698]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2848. MS:1002973 LipidFinder

Table 2850. Term [MS:1002973]
id	MS:1002973
name	LipidFinder
def	"A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets." [PMID:28405621]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2849. MS:1002974 LipiDex

Table 2851. Term [MS:1002974]
id	MS:1002974
name	LipiDex
def	"An integrated software package for high-confidence lipid identification." [PMID:29705063]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2850. MS:1002975 LIQUID

Table 2852. Term [MS:1002975]
id	MS:1002975
name	LIQUID
def	"An-open source software for identifying lipids in LC-MS/MS-based lipidomics data." [PMID:28158427]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2851. MS:1002976 ALEX

Table 2853. Term [MS:1002976]
id	MS:1002976
name	ALEX
def	"Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)." [PMID:24244551]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2852. MS:1002977 ALEX123

Table 2854. Term [MS:1002977]
id	MS:1002977
name	ALEX123
def	"Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level." [PMID:29786091]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2853. MS:1002978 LIMSA

Table 2855. Term [MS:1002978]
id	MS:1002978
name	LIMSA
def	"Software tool for the quantitative analysis of mass spectrometric lipidome data." [PMID:17165823]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2854. MS:1002979 LOBSTAHS

Table 2856. Term [MS:1002979]
id	MS:1002979
name	LOBSTAHS
def	"Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers." [PMID:27322848]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2855. MS:1002980 LipidQA

Table 2857. Term [MS:1002980]
id	MS:1002980
name	LipidQA
def	"Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species." [PMID:17720531]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2856. MS:1002981 Proline

Table 2858. Term [MS:1002981]
id	MS:1002981
name	Proline
def	"The Proline software suite for mass spectrometry based proteomics." [http://www.profiproteomics.fr/proline/]
is_a	MS:1001456 analysis software ! analysis software

2.2857. MS:1002982 PepNovo

Table 2859. Term [MS:1002982]
id	MS:1002982
name	PepNovo
def	"PepNovo tool for de novo peptide sequencing." [PMID:15858974]
is_a	MS:1001456 analysis software ! analysis software

2.2858. MS:1002983 pNovo

Table 2860. Term [MS:1002983]
id	MS:1002983
name	pNovo
def	"pNovo tool for de novo peptide sequencing and identification using HCD spectra." [PMID:20329752]
is_a	MS:1001456 analysis software ! analysis software

2.2859. MS:1002984 Novor

Table 2861. Term [MS:1002984]
id	MS:1002984
name	Novor
def	"Novor real-time peptide de novo sequencing software tool." [PMID:26122521]
is_a	MS:1001456 analysis software ! analysis software

2.2860. MS:1002985 in-gel digestion

Table 2862. Term [MS:1002985]
id	MS:1002985
name	in-gel digestion
def	"Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a	MS:1000831 sample preparation ! sample preparation

2.2861. MS:1002986 in-solution digestion

Table 2863. Term [MS:1002986]
id	MS:1002986
name	in-solution digestion
def	"Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a	MS:1000831 sample preparation ! sample preparation

2.2862. MS:1002987 IdentiPy

Table 2864. Term [MS:1002987]
id	MS:1002987
name	IdentiPy
def	"IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy]
is_a	MS:1001456 analysis software ! analysis software

2.2863. MS:1002988 IdentiPy:RHNS

Table 2865. Term [MS:1002988]
id	MS:1002988
name	IdentiPy:RHNS
def	"The IdentiPy result 'RHNS'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2864. MS:1002989 IdentiPy:hyperscore

Table 2866. Term [MS:1002989]
id	MS:1002989
name	IdentiPy:hyperscore
def	"The IdentiPy result 'hyperscore'." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2865. MS:1002990 ms_deisotope

Table 2867. Term [MS:1002990]
id	MS:1002990
name	ms_deisotope
def	"ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra." [https://github.com/mobiusklein/ms_deisotope]
is_a	MS:1001457 data processing software ! data processing software

2.2866. MS:1002991 python-psims

Table 2868. Term [MS:1002991]
id	MS:1002991
name	python-psims
def	"python-psims, a library for generating mzML and mzIdentML." [https://github.com/mobiusklein/psims]
is_a	MS:1002333 conversion software ! conversion software

2.2867. MS:1002995 Andromeda:PEP

Table 2869. Term [MS:1002995]
id	MS:1002995
name	Andromeda:PEP
def	"Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive
relationship	has_order MS:1002108 higher score better ! higher score better

2.2868. MS:1002996 Andromeda:apl file format

Table 2870. Term [MS:1002996]
id	MS:1002996
name	Andromeda:apl file format
def	"Peak list file format of the Andromeda search engine." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2869. MS:1002997 ProteomeXchange dataset identifier reanalysis number

Table 2871. Term [MS:1002997]
id	MS:1002997
name	ProteomeXchange dataset identifier reanalysis number
def	"Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2870. MS:1002998 LCMS-9030

Table 2872. Term [MS:1002998]
id	MS:1002998
name	LCMS-9030
def	"Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2871. MS:1002999 LCMS-8060

Table 2873. Term [MS:1002999]
id	MS:1002999
name	LCMS-8060
def	"Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2872. MS:1003000 LCMS-8050

Table 2874. Term [MS:1003000]
id	MS:1003000
name	LCMS-8050
def	"Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2873. MS:1003001 LCMS-8045

Table 2875. Term [MS:1003001]
id	MS:1003001
name	LCMS-8045
def	"Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2874. MS:1003002 LCMS-8040

Table 2876. Term [MS:1003002]
id	MS:1003002
name	LCMS-8040
def	"Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2875. MS:1003003 LCMS-2020

Table 2877. Term [MS:1003003]
id	MS:1003003
name	LCMS-2020
def	"Shimadzu Scientific Instruments LCMS-2020." [PSI:MS]
is_a	MS:1000603 Shimadzu Scientific Instruments instrument model ! Shimadzu Scientific Instruments instrument model

2.2876. MS:1003004 maXis II

Table 2878. Term [MS:1003004]
id	MS:1003004
name	maXis II
def	"Bruker Daltonics' maXis II." [PSI:MS]
is_a	MS:1001547 Bruker Daltonics maXis series ! Bruker Daltonics maXis series

2.2877. MS:1003005 timsTOF Pro

Table 2879. Term [MS:1003005]
id	MS:1003005
name	timsTOF Pro
def	"Bruker Daltonics' timsTOF Pro." [PSI:MS]
is_a	MS:1003123 Bruker Daltonics timsTOF series ! Bruker Daltonics timsTOF series

2.2878. MS:1003006 mean inverse reduced ion mobility array

Table 2880. Term [MS:1003006]
id	MS:1003006
name	mean inverse reduced ion mobility array
def	"Array of inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002893 ion mobility array ! ion mobility array
relationship	has_units MS:1002814 volt-second per square centimeter ! volt-second per square centimeter

2.2879. MS:1003007 raw ion mobility array

Table 2881. Term [MS:1003007]
id	MS:1003007
name	raw ion mobility array
def	"Array of raw drift times." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002893 ion mobility array ! ion mobility array
relationship	has_units [UO:0000028] ! millisecond
relationship	has_units [UO:0000010] ! second

2.2880. MS:1003008 raw inverse reduced ion mobility array

Table 2882. Term [MS:1003008]
id	MS:1003008
name	raw inverse reduced ion mobility array
def	"Array of raw inverse reduced ion mobilities." [PSI:MS]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002893 ion mobility array ! ion mobility array
relationship	has_units MS:1002814 volt-second per square centimeter ! volt-second per square centimeter

2.2881. MS:1003009 Shimadzu Biotech LCD format

Table 2883. Term [MS:1003009]
id	MS:1003009
name	Shimadzu Biotech LCD format
def	"Shimadzu Biotech LCD file format." [PSI:PI]
is_a	MS:1000560 mass spectrometer file format ! mass spectrometer file format

2.2882. MS:1003010 LPPtiger

Table 2884. Term [MS:1003010]
id	MS:1003010
name	LPPtiger
def	"Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." [PMID:29123162]
is_a	MS:1002964 lipidomics analysis software ! lipidomics analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2883. MS:1003011 pFind

Table 2885. Term [MS:1003011]
id	MS:1003011
name	pFind
def	"Sequence-tag-based search engine pFind." [PMID:30295672]
is_a	MS:1001456 analysis software ! analysis software

2.2884. MS:1003012 KSDP score

Table 2886. Term [MS:1003012]
id	MS:1003012
name	KSDP score
def	"Kernel mass spectral dot product scoring function." [PMID:15044235]
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2885. MS:1003013 i3tms

Table 2887. Term [MS:1003013]
id	MS:1003013
name	i3tms
def	"i3-tms search engine and data-analysis software." [PSI:PI]
is_a	MS:1001456 analysis software ! analysis software

2.2886. MS:1003014 MSFragger

Table 2888. Term [MS:1003014]
id	MS:1003014
name	MSFragger
def	"A database search-based peptide identification tool." [PMID:28394336]
is_a	MS:1001456 analysis software ! analysis software

2.2887. MS:1003015 razor peptide

Table 2889. Term [MS:1003015]
id	MS:1003015
name	razor peptide
def	"Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:MS]
is_a	MS:1000860 peptide ! peptide

2.2888. MS:1003016 ProteinProphet:peptide weight

Table 2890. Term [MS:1003016]
id	MS:1003016
name	ProteinProphet:peptide weight
def	"Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002490 peptide-level scoring ! peptide-level scoring
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2889. MS:1003017 ProteinProphet:peptide group weight

Table 2891. Term [MS:1003017]
id	MS:1003017
name	ProteinProphet:peptide group weight
def	"Fraction of peptide evidence attributable to a group of proteins." [PSI:PI]
xref	value-type:xsd\:float "The allowed value-type for this CV term."
is_a	MS:1002490 peptide-level scoring ! peptide-level scoring
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.2890. MS:1003018 Philosopher

Table 2892. Term [MS:1003018]
id	MS:1003018
name	Philosopher
def	"General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/]
is_a	MS:1001456 analysis software ! analysis software

2.2891. MS:1003019 pressure chromatogram

Table 2893. Term [MS:1003019]
id	MS:1003019
name	pressure chromatogram
def	"Representation of chromatographic pressure versus time." [PSI:MS]
is_a	MS:1000626 chromatogram type ! chromatogram type

2.2892. MS:1003020 flow rate chromatogram

Table 2894. Term [MS:1003020]
id	MS:1003020
name	flow rate chromatogram
def	"Representation of the chromatographic flow rate versus time." [PSI:MS]
is_a	MS:1000626 chromatogram type ! chromatogram type

2.2893. MS:1003021 Fixed modification

Table 2895. Term [MS:1003021]
id	MS:1003021
name	Fixed modification
def	"Post-translational modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters
is_a	MS:1003026 named element in mzIdentML ! named element in mzIdentML

2.2894. MS:1003022 Variable modification

Table 2896. Term [MS:1003022]
id	MS:1003022
name	Variable modification
def	"Post-translational modification which may or may not be present at a residue type." [PSI:PI]
is_a	MS:1001055 modification parameters ! modification parameters
is_a	MS:1003026 named element in mzIdentML ! named element in mzIdentML

2.2895. MS:1003023 OpenPepXL

Table 2897. Term [MS:1003023]
id	MS:1003023
name	OpenPepXL
def	"Cross-Linking MS search engine." [PSI:PI]
is_a	MS:1000752 TOPP software ! TOPP software

2.2896. MS:1003024 OpenPepXL:score

Table 2898. Term [MS:1003024]
id	MS:1003024
name	OpenPepXL:score
def	"The OpenPepXL score for a cross-link spectrum match." [PSI:PI]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
is_a	MS:1001153 search engine specific score ! search engine specific score
relationship	has_order MS:1002108 higher score better ! higher score better

2.2897. MS:1003025 named element

Table 2899. Term [MS:1003025]
id	MS:1003025
name	named element
def	"A named element that is an attribute in a proteomics standards file." [PSI:PI]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.2898. MS:1003026 named element in mzIdentML

Table 2900. Term [MS:1003026]
id	MS:1003026
name	named element in mzIdentML
def	"A named element that is an attribute in a mzIdentML file." [PSI:PI]
is_a	MS:1003025 named element ! named element

2.2899. MS:1003027 named element in mzML

Table 2901. Term [MS:1003027]
id	MS:1003027
name	named element in mzML
def	"A named element that is an attribute in a mzML file." [PSI:PI]
is_a	MS:1003025 named element ! named element

2.2900. MS:1003028 Orbitrap Exploris 480

Table 2902. Term [MS:1003028]
id	MS:1003028
name	Orbitrap Exploris 480
def	"Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2901. MS:1003029 Orbitrap Eclipse

Table 2903. Term [MS:1003029]
id	MS:1003029
name	Orbitrap Eclipse
def	"Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2902. MS:1003030 Mascot:MinNumSigUniqueSeqs

Table 2904. Term [MS:1003030]
id	MS:1003030
name	Mascot:MinNumSigUniqueSeqs
def	"Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI]
xref	value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a	MS:1002095 Mascot input parameter ! Mascot input parameter

2.2903. MS:1003031 CPTAC accession number

Table 2905. Term [MS:1003031]
id	MS:1003031
name	CPTAC accession number
def	"Main identifier of a CPTAC dataset." [PSI:PI]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000878 external reference identifier ! external reference identifier

2.2904. MS:1003032 compound identification confidence code in MS-DIAL

Table 2906. Term [MS:1003032]
id	MS:1003032
name	compound identification confidence code in MS-DIAL
def	"The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1002895 small molecule identification attribute ! small molecule identification attribute

2.2905. MS:1003033 molecular entity attribute

Table 2907. Term [MS:1003033]
id	MS:1003033
name	molecular entity attribute
def	"Non-inherent characteristic attributed to a molecular entity." [PSI:PI]
relationship	part_of MS:1000881 molecular entity ! molecular entity

2.2906. MS:1003034 atom

Table 2908. Term [MS:1003034]
id	MS:1003034
name	atom
def	"Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a	MS:1000881 molecular entity ! molecular entity

2.2907. MS:1003035 small molecule

Table 2909. Term [MS:1003035]
id	MS:1003035
name	small molecule
def	"Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule]
is_a	MS:1000859 molecule ! molecule

2.2908. MS:1003036 metabolite

Table 2910. Term [MS:1003036]
id	MS:1003036
name	metabolite
def	"Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a	MS:1003035 small molecule ! small molecule

2.2909. MS:1003037 ribonucleotide

Table 2911. Term [MS:1003037]
id	MS:1003037
name	ribonucleotide
def	"Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide]
is_a	MS:1003035 small molecule ! small molecule

2.2910. MS:1003038 deoxyribonucleotide

Table 2912. Term [MS:1003038]
id	MS:1003038
name	deoxyribonucleotide
def	"Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a	MS:1003035 small molecule ! small molecule

2.2911. MS:1003039 amino acid

Table 2913. Term [MS:1003039]
id	MS:1003039
name	amino acid
def	"Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a	MS:1003035 small molecule ! small molecule

2.2912. MS:1003040 monosaccharide

Table 2914. Term [MS:1003040]
id	MS:1003040
name	monosaccharide
def	"Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide]
is_a	MS:1003035 small molecule ! small molecule

2.2913. MS:1003041 nucleic acid

Table 2915. Term [MS:1003041]
id	MS:1003041
name	nucleic acid
def	"Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid]
is_a	MS:1000859 molecule ! molecule

2.2914. MS:1003042 polysaccharide

Table 2916. Term [MS:1003042]
id	MS:1003042
name	polysaccharide
def	"Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide]
is_a	MS:1000859 molecule ! molecule

2.2915. MS:1003043 number of residues

Table 2917. Term [MS:1003043]
id	MS:1003043
name	number of residues
def	"Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI]
is_a	MS:1000887 peptide attribute ! peptide attribute

2.2916. MS:1003044 number of missed cleavages

Table 2918. Term [MS:1003044]
id	MS:1003044
name	number of missed cleavages
def	"Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI]
is_a	MS:1000887 peptide attribute ! peptide attribute

2.2917. MS:1003045 peptide-to-protein mapping

Table 2919. Term [MS:1003045]
id	MS:1003045
name	peptide-to-protein mapping
def	"Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a	MS:1000887 peptide attribute ! peptide attribute

2.2918. MS:1003046 peptide-to-protein mapping attribute

Table 2920. Term [MS:1003046]
id	MS:1003046
name	peptide-to-protein mapping attribute
def	"Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI]
is_a	MS:1003045 peptide-to-protein mapping ! peptide-to-protein mapping

2.2919. MS:1003047 protein sequence offset

Table 2921. Term [MS:1003047]
id	MS:1003047
name	protein sequence offset
def	"Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI]
is_a	MS:1003046 peptide-to-protein mapping attribute ! peptide-to-protein mapping attribute

2.2920. MS:1003048 number of enzymatic termini

Table 2922. Term [MS:1003048]
id	MS:1003048
name	number of enzymatic termini
def	"Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI]
is_a	MS:1003046 peptide-to-protein mapping attribute ! peptide-to-protein mapping attribute

2.2921. MS:1003049 peptidoform

Table 2923. Term [MS:1003049]
id	MS:1003049
name	peptidoform
def	"Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI]
is_a	MS:1000860 peptide ! peptide

2.2922. MS:1003050 peptidoform attribute

Table 2924. Term [MS:1003050]
id	MS:1003050
name	peptidoform attribute
def	"Non-inherent characteristic attributed to a peptidoform." [PSI:PI]
relationship	part_of MS:1003049 peptidoform ! peptidoform

2.2923. MS:1003051 peptidoform ion

Table 2925. Term [MS:1003051]
id	MS:1003051
name	peptidoform ion
def	"Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a	MS:1003049 peptidoform ! peptidoform
synonym	"precursor" RELATED []
synonym	"precursor ion" RELATED []
synonym	"parent ion" RELATED []

2.2924. MS:1003052 peptidoform ion property

Table 2926. Term [MS:1003052]
id	MS:1003052
name	peptidoform ion property
def	"Inherent or measurable characteristic of a peptidoform ion." [PSI:PI]
relationship	part_of MS:1003051 peptidoform ion ! peptidoform ion

2.2925. MS:1003053 theoretical monoisotopic m/z

Table 2927. Term [MS:1003053]
id	MS:1003053
name	theoretical monoisotopic m/z
def	"Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI]
is_a	MS:1003052 peptidoform ion property ! peptidoform ion property

2.2926. MS:1003054 theoretical average m/z

Table 2928. Term [MS:1003054]
id	MS:1003054
name	theoretical average m/z
def	"Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI]
is_a	MS:1003052 peptidoform ion property ! peptidoform ion property

2.2927. MS:1003055 adduct

Table 2929. Term [MS:1003055]
id	MS:1003055
name	adduct
def	"Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct]
is_a	MS:1000859 molecule ! molecule

2.2928. MS:1003056 adduct ion property

Table 2930. Term [MS:1003056]
id	MS:1003056
name	adduct ion property
def	"Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship	part_of MS:1000353 adduct ion ! adduct ion

2.2929. MS:1003057 scan number

Table 2931. Term [MS:1003057]
id	MS:1003057
name	scan number
def	"Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI]
is_a	MS:1000503 scan attribute ! scan attribute

2.2930. MS:1003058 spectrum property

Table 2932. Term [MS:1003058]
id	MS:1003058
name	spectrum property
def	"Inherent or measurable characteristic of a spectrum." [PSI:PI]
relationship	part_of MS:1000442 spectrum ! spectrum

2.2931. MS:1003059 number of peaks

Table 2933. Term [MS:1003059]
id	MS:1003059
name	number of peaks
def	"Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI]
is_a	MS:1003058 spectrum property ! spectrum property

2.2932. MS:1003060 number of data points

Table 2934. Term [MS:1003060]
id	MS:1003060
name	number of data points
def	"Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI]
is_a	MS:1003058 spectrum property ! spectrum property

2.2933. MS:1003061 spectrum name

Table 2935. Term [MS:1003061]
id	MS:1003061
name	spectrum name
def	"Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2934. MS:1003062 spectrum index

Table 2936. Term [MS:1003062]
id	MS:1003062
name	spectrum index
def	"Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI]
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2935. MS:1003063 universal spectrum identifier

Table 2937. Term [MS:1003063]
id	MS:1003063
name	universal spectrum identifier
def	"PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI]
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2936. MS:1003064 spectrum aggregation attribute

Table 2938. Term [MS:1003064]
id	MS:1003064
name	spectrum aggregation attribute
def	"Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI]
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2937. MS:1003065 spectrum aggregation type

Table 2939. Term [MS:1003065]
id	MS:1003065
name	spectrum aggregation type
def	"Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI]
is_a	MS:1003064 spectrum aggregation attribute ! spectrum aggregation attribute

2.2938. MS:1003066 singleton spectrum

Table 2940. Term [MS:1003066]
id	MS:1003066
name	singleton spectrum
def	"Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a	MS:1003065 spectrum aggregation type ! spectrum aggregation type

2.2939. MS:1003067 consensus spectrum

Table 2941. Term [MS:1003067]
id	MS:1003067
name	consensus spectrum
def	"Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI]
is_a	MS:1003065 spectrum aggregation type ! spectrum aggregation type

2.2940. MS:1003068 best replicate spectrum

Table 2942. Term [MS:1003068]
id	MS:1003068
name	best replicate spectrum
def	"Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI]
is_a	MS:1003065 spectrum aggregation type ! spectrum aggregation type

2.2941. MS:1003069 number of replicate spectra available

Table 2943. Term [MS:1003069]
id	MS:1003069
name	number of replicate spectra available
def	"Number of replicate spectra available for use during the aggregation process." [PSI:PI]
is_a	MS:1003064 spectrum aggregation attribute ! spectrum aggregation attribute

2.2942. MS:1003070 number of replicate spectra used

Table 2944. Term [MS:1003070]
id	MS:1003070
name	number of replicate spectra used
def	"Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI]
is_a	MS:1003064 spectrum aggregation attribute ! spectrum aggregation attribute

2.2943. MS:1003071 spectrum origin attribute

Table 2945. Term [MS:1003071]
id	MS:1003071
name	spectrum origin attribute
def	"Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI]
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2944. MS:1003072 spectrum origin type

Table 2946. Term [MS:1003072]
id	MS:1003072
name	spectrum origin type
def	"Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI]
is_a	MS:1003071 spectrum origin attribute ! spectrum origin attribute

2.2945. MS:1003073 observed spectrum

Table 2947. Term [MS:1003073]
id	MS:1003073
name	observed spectrum
def	"Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI]
is_a	MS:1003072 spectrum origin type ! spectrum origin type

2.2946. MS:1003074 predicted spectrum

Table 2948. Term [MS:1003074]
id	MS:1003074
name	predicted spectrum
def	"Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI]
is_a	MS:1003072 spectrum origin type ! spectrum origin type

2.2947. MS:1003075 demultiplexed spectrum

Table 2949. Term [MS:1003075]
id	MS:1003075
name	demultiplexed spectrum
def	"Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI]
is_a	MS:1003072 spectrum origin type ! spectrum origin type

2.2948. MS:1003076 uninterpreted spectrum

Table 2950. Term [MS:1003076]
id	MS:1003076
name	uninterpreted spectrum
def	"Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI]
is_a	MS:1000442 spectrum ! spectrum

2.2949. MS:1003077 interpreted spectrum

Table 2951. Term [MS:1003077]
id	MS:1003077
name	interpreted spectrum
def	"Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI]
is_a	MS:1000442 spectrum ! spectrum

2.2950. MS:1003078 interpreted spectrum attribute

Table 2952. Term [MS:1003078]
id	MS:1003078
name	interpreted spectrum attribute
def	"Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI]
relationship	part_of MS:1003077 interpreted spectrum ! interpreted spectrum

2.2951. MS:1003079 total unassigned intensity fraction

Table 2953. Term [MS:1003079]
id	MS:1003079
name	total unassigned intensity fraction
def	"Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a	MS:1003078 interpreted spectrum attribute ! interpreted spectrum attribute

2.2952. MS:1003080 top 20 peak unassigned intensity fraction

Table 2954. Term [MS:1003080]
id	MS:1003080
name	top 20 peak unassigned intensity fraction
def	"Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI]
is_a	MS:1003078 interpreted spectrum attribute ! interpreted spectrum attribute

2.2953. MS:1003081 unidentified modification monoisotopic mass delta

Table 2955. Term [MS:1003081]
id	MS:1003081
name	unidentified modification monoisotopic mass delta
def	"Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML." [PSI:PI]
is_a	MS:1001471 peptide modification details ! peptide modification details
xref	value-type:xsd\:double "The allowed value-type for this CV term."
relationship	has_units [UO:0000221] ! dalton

2.2954. MS:1003082 MS-DIAL

Table 2956. Term [MS:1003082]
id	MS:1003082
name	MS-DIAL
def	"Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372]
is_a	MS:1002878 small molecule analysis software ! small molecule analysis software
is_a	MS:1001457 data processing software ! data processing software

2.2955. MS:1003083 raw data file

Table 2957. Term [MS:1003083]
id	MS:1003083
name	raw data file
def	"Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS]
is_a	MS:1000577 source data file ! source data file

2.2956. MS:1003084 processed data file

Table 2958. Term [MS:1003084]
id	MS:1003084
name	processed data file
def	"File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000577 source data file ! source data file

2.2957. MS:1003085 previous MSn-1 scan precursor intensity

Table 2959. Term [MS:1003085]
id	MS:1003085
name	previous MSn-1 scan precursor intensity
def	"Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001141 intensity of precursor ion ! intensity of precursor ion
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2958. MS:1003086 precursor apex intensity

Table 2960. Term [MS:1003086]
id	MS:1003086
name	precursor apex intensity
def	"Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1001141 intensity of precursor ion ! intensity of precursor ion
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2959. MS:1003087 supported by repository but incomplete data and/or metadata

Table 2961. Term [MS:1003087]
id	MS:1003087
name	supported by repository but incomplete data and/or metadata
def	"Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI]
is_a	MS:1002844 Experiment additional parameter ! Experiment additional parameter

2.2960. MS:1003088 truncation and zlib compression

Table 2962. Term [MS:1003088]
id	MS:1003088
name	truncation and zlib compression
def	"Data array compression using mantissa bit truncation followed by zlib compression." [https://github.com/biospi/pwiz]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2961. MS:1003089 truncation, delta prediction and zlib compression

Table 2963. Term [MS:1003089]
id	MS:1003089
name	truncation, delta prediction and zlib compression
def	"Data array compression using mantissa bit truncation, delta prediction and zlib compression." [https://github.com/biospi/pwiz]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2962. MS:1003090 truncation, linear prediction and zlib compression

Table 2964. Term [MS:1003090]
id	MS:1003090
name	truncation, linear prediction and zlib compression
def	"Data array compression using mantissa bit truncation, linear prediction and zlib compression." [https://github.com/biospi/pwiz]
is_a	MS:1000572 binary data compression type ! binary data compression type

2.2963. MS:1003091 binary data compression parameter

Table 2965. Term [MS:1003091]
id	MS:1003091
name	binary data compression parameter
def	"Settable parameter for a binary data compression event." [PSI:MS]
relationship	part_of MS:1000442 spectrum ! spectrum
relationship	part_of MS:1000625 chromatogram ! chromatogram

2.2964. MS:1003092 number of mantissa bits truncated

Table 2966. Term [MS:1003092]
id	MS:1003092
name	number of mantissa bits truncated
def	"Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS]
xref	value-type:xsd\:positiveInteger "Number of mantissa bits truncated."
is_a	MS:1003091 binary data compression parameter ! binary data compression parameter

2.2965. MS:1003093 Lys-N

Table 2967. Term [MS:1003093]
id	MS:1003093
name	Lys-N
def	"Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues." [https://en.wikipedia.org/wiki/Lys-N]
is_a	MS:1001045 cleavage agent name ! cleavage agent name
relationship	has_regexp MS:1001335 (?⇐K)(?\!P) ! (?=K)

2.2966. MS:1003094 Orbitrap Exploris 240

Table 2968. Term [MS:1003094]
id	MS:1003094
name	Orbitrap Exploris 240
def	"Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2967. MS:1003095 Orbitrap Exploris 120

Table 2969. Term [MS:1003095]
id	MS:1003095
name	Orbitrap Exploris 120
def	"Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2968. MS:1003096 LTQ Orbitrap Velos Pro

Table 2970. Term [MS:1003096]
id	MS:1003096
name	LTQ Orbitrap Velos Pro
def	"Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2969. MS:1003097 MaxQuant protein group-level score

Table 2971. Term [MS:1003097]
id	MS:1003097
name	MaxQuant protein group-level score
def	"The probability based MaxQuant protein group score." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002368 search engine specific score for protein groups ! search engine specific score for protein groups

2.2970. MS:1003098 Andromeda peptide PEP

Table 2972. Term [MS:1003098]
id	MS:1003098
name	Andromeda peptide PEP
def	"Peptide probability from Andromeda." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.2971. MS:1003099 MaxQuant-DIA peptide PEP

Table 2973. Term [MS:1003099]
id	MS:1003099
name	MaxQuant-DIA peptide PEP
def	"Peptide probability from MaxQuant-DIA algorithm." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.2972. MS:1003100 MaxQuant-DIA score

Table 2974. Term [MS:1003100]
id	MS:1003100
name	MaxQuant-DIA score
def	"PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2973. MS:1003101 MaxQuant-DIA PEP

Table 2975. Term [MS:1003101]
id	MS:1003101
name	MaxQuant-DIA PEP
def	"PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2974. MS:1003102 NIST msp comment

Table 2976. Term [MS:1003102]
id	MS:1003102
name	NIST msp comment
def	"Term for a comment field withing the NIST msp file format" [PSI:MS]
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_a	MS:1000499 spectrum attribute ! spectrum attribute

2.2975. MS:1003103 ion interpretation format

Table 2977. Term [MS:1003103]
id	MS:1003103
name	ion interpretation format
def	"Interpretation format used for annotating individual spectrum ion peaks." [PSI:MS]
is_a	MS:1003078 interpreted spectrum attribute ! interpreted spectrum attribute

2.2976. MS:1003104 peptide ion interpretation format

Table 2978. Term [MS:1003104]
id	MS:1003104
name	peptide ion interpretation format
def	"Interpretation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS]
is_a	MS:1003103 ion interpretation format ! ion interpretation format

2.2977. MS:1003105 cross-linked peptide ion interpretation format

Table 2979. Term [MS:1003105]
id	MS:1003105
name	cross-linked peptide ion interpretation format
def	"Interpretation format designed specifically for cross-linked peptide ion peaks." [PSI:MS]
is_a	MS:1003103 ion interpretation format ! ion interpretation format

2.2978. MS:1003106 glycan ion interpretation format

Table 2980. Term [MS:1003106]
id	MS:1003106
name	glycan ion interpretation format
def	"Interpretation format designed specifically for glycan ion peaks." [PSI:MS]
is_a	MS:1003103 ion interpretation format ! ion interpretation format

2.2979. MS:1003107 lipid ion interpretation format

Table 2981. Term [MS:1003107]
id	MS:1003107
name	lipid ion interpretation format
def	"Interpretation format designed specifically for lipid ion peaks." [PSI:MS]
is_a	MS:1003103 ion interpretation format ! ion interpretation format

2.2980. MS:1003108 PatternLab

Table 2982. Term [MS:1003108]
id	MS:1003108
name	PatternLab
def	"PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data." [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name
is_a	MS:1001456 analysis software ! analysis software

2.2981. MS:1003109 SIM-XL

Table 2983. Term [MS:1003109]
id	MS:1003109
name	SIM-XL
def	"Identifying cross-linked peptides in complex protein mixtures" [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.2982. MS:1003110 SIM-XL score

Table 2984. Term [MS:1003110]
id	MS:1003110
name	SIM-XL score
def	"SIM-XL identification search engine score" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.2983. MS:1003111 QUIN-XL

Table 2985. Term [MS:1003111]
id	MS:1003111
name	QUIN-XL
def	"Quantification of cross-linked peptides in complex protein mixtures" [PSI:MS]
is_a	MS:1001139 quantitation software name ! quantitation software name

2.2984. MS:1003112 Orbitrap ID-X

Table 2986. Term [MS:1003112]
id	MS:1003112
name	Orbitrap ID-X
def	"Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS]
is_a	MS:1000494 Thermo Scientific instrument model ! Thermo Scientific instrument model

2.2985. MS:1003113 OpenMS:ConsensusID PEP

Table 2987. Term [MS:1003113]
id	MS:1003113
name	OpenMS:ConsensusID PEP
def	"The OpenMS ConsesusID tool posterior error probability" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2986. MS:1003114 OpenMS:Best PSM Score

Table 2988. Term [MS:1003114]
id	MS:1003114
name	OpenMS:Best PSM Score
def	"The score of the best PSM selected by the underlying identification tool" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.2987. MS:1003115 OpenMS:Target-decoy PSM q-value

Table 2989. Term [MS:1003115]
id	MS:1003115
name	OpenMS:Target-decoy PSM q-value
def	"The OpenMS Target-decoy q-values at PSM level" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic

2.2988. MS:1003116 OpenMS:Target-decoy peptide q-value

Table 2990. Term [MS:1003116]
id	MS:1003116
name	OpenMS:Target-decoy peptide q-value
def	"The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002358 search engine specific peptide sequence-level identification statistic ! search engine specific peptide sequence-level identification statistic

2.2989. MS:1003117 OpenMS:Target-decoy protein q-value

Table 2991. Term [MS:1003117]
id	MS:1003117
name	OpenMS:Target-decoy protein q-value
def	"The OpenMS Target-decoy q-values at protein level" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2990. MS:1003118 EPIFANY

Table 2992. Term [MS:1003118]
id	MS:1003118
name	EPIFANY
def	"A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework" [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software
is_a	MS:1000752 TOPP software ! TOPP software

2.2991. MS:1003119 EPIFANY:Protein posterior probability

Table 2993. Term [MS:1003119]
id	MS:1003119
name	EPIFANY:Protein posterior probability
def	"Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002363 search engine specific score for proteins ! search engine specific score for proteins

2.2992. MS:1003120 OpenMS:LFQ intensity

Table 2994. Term [MS:1003120]
id	MS:1003120
name	OpenMS:LFQ intensity
def	"The data type LFQ intensity produced by OpenMS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2993. MS:1003121 OpenMS:LFQ spectral count

Table 2995. Term [MS:1003121]
id	MS:1003121
name	OpenMS:LFQ spectral count
def	"The data type LFQ spectral count produced by OpenMS." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001805 quantification datatype ! quantification datatype

2.2994. MS:1003122 rapifleX

Table 2996. Term [MS:1003122]
id	MS:1003122
name	rapifleX
def	"Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS]
is_a	MS:1001534 Bruker Daltonics flex series ! Bruker Daltonics flex series

2.2995. MS:1003123 Bruker Daltonics timsTOF series

Table 2997. Term [MS:1003123]
id	MS:1003123
name	Bruker Daltonics timsTOF series
def	"Bruker Daltonics timsTOF series" [PSI:MS]
is_a	MS:1000122 Bruker Daltonics instrument model ! Bruker Daltonics instrument model

2.2996. MS:1003124 timsTOF fleX

Table 2998. Term [MS:1003124]
id	MS:1003124
name	timsTOF fleX
def	"Bruker Daltonics' timsTOF fleX" [PSI:MS]
is_a	MS:1003123 Bruker Daltonics timsTOF series ! Bruker Daltonics timsTOF series

2.2997. MS:1003125 ProSight:spectral Q-value

Table 2999. Term [MS:1003125]
id	MS:1003125
name	ProSight:spectral Q-value
def	"ProSight spectrum-level Q-value." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002354 PSM-level q-value ! PSM-level q-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2998. MS:1003126 ProSight:spectral P-score

Table 3000. Term [MS:1003126]
id	MS:1003126
name	ProSight:spectral P-score
def	"ProSight spectrum-level P-score." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.2999. MS:1003127 ProSight:spectral E-value

Table 3001. Term [MS:1003127]
id	MS:1003127
name	ProSight:spectral E-value
def	"ProSight spectrum-level E-value." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002353 PSM-level e-value ! PSM-level e-value
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002109 lower score better ! lower score better

2.3000. MS:1003128 ProSight:spectral C-score

Table 3002. Term [MS:1003128]
id	MS:1003128
name	ProSight:spectral C-score
def	"ProSight spectrum-level C-score." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001143 PSM-level search engine specific statistic ! PSM-level search engine specific statistic
relationship	has_order MS:1002108 higher score better ! higher score better

2.3001. MS:1003129 proteoform-level Q-value

Table 3003. Term [MS:1003129]
id	MS:1003129
name	proteoform-level Q-value
def	"Estimation of the Q-value for proteoforms." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1002905 proteoform-level identification statistic ! proteoform-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive
relationship	has_order MS:1002109 lower score better ! lower score better

2.3002. MS:1003130 ProSight:proteoform Q-value

Table 3004. Term [MS:1003130]
id	MS:1003130
name	ProSight:proteoform Q-value
def	"ProSight proteoform-level Q-value." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1003129 proteoform-level Q-value ! proteoform-level Q-value
relationship	has_order MS:1002109 lower score better ! lower score better

2.3003. MS:1003131 isoform-level identification attribute

Table 3005. Term [MS:1003131]
id	MS:1003131
name	isoform-level identification attribute
def	"Isoform level information." [PSI:MS]
is_a	MS:1002694 single identification result attribute ! single identification result attribute

2.3004. MS:1003132 isoform-level identification statistic

Table 3006. Term [MS:1003132]
id	MS:1003132
name	isoform-level identification statistic
def	"Identification confidence metric for a isoform." [PSI:MS]
is_a	MS:1003131 isoform-level identification attribute ! isoform-level identification attribute

2.3005. MS:1003133 isoform-level Q-value

Table 3007. Term [MS:1003133]
id	MS:1003133
name	isoform-level Q-value
def	"Estimation of the Q-value for isoforms." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1003132 isoform-level identification statistic ! isoform-level identification statistic
relationship	has_domain MS:1002305 value between 0 and 1 inclusive ! value between 0 and 1 inclusive

2.3006. MS:1003134 ProSight:isoform Q-value

Table 3008. Term [MS:1003134]
id	MS:1003134
name	ProSight:isoform Q-value
def	"ProSight isoform-level Q-value." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1003133 isoform-level Q-value ! isoform-level Q-value
relationship	has_order MS:1002109 lower score better ! lower score better

2.3007. MS:1003135 ProSight:protein Q-value

Table 3009. Term [MS:1003135]
id	MS:1003135
name	ProSight:protein Q-value
def	"ProSight protein-level Q-value." [PSI:MS]
xref	value-type:xsd\:double "The allowed value-type for this CV term."
is_a	MS:1001869 protein-level q-value ! protein-level q-value
relationship	has_order MS:1002109 lower score better ! lower score better

2.3008. MS:1003136 ProSight input parameter

Table 3010. Term [MS:1003136]
id	MS:1003136
name	ProSight input parameter
def	"Search engine input parameters specific to ProSight." [PSI:MS]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.3009. MS:1003137 TDPortal input parameter

Table 3011. Term [MS:1003137]
id	MS:1003137
name	TDPortal input parameter
def	"Search engine input parameters specific to TDPortal." [PSI:MS]
is_a	MS:1001302 search engine specific input parameter ! search engine specific input parameter

2.3010. MS:1003138 ProSight:Run delta m mode

Table 3012. Term [MS:1003138]
id	MS:1003138
name	ProSight:Run delta m mode
def	"If true, runs delta m mode in ProSight." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1003136 ProSight input parameter ! ProSight input parameter
is_a	MS:1003137 TDPortal input parameter ! TDPortal input parameter

2.3011. MS:1003139 ProSight:Run Subsequence Search mode

Table 3013. Term [MS:1003139]
id	MS:1003139
name	ProSight:Run Subsequence Search mode
def	"If true, runs Subsequence Search mode in ProSight." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1003136 ProSight input parameter ! ProSight input parameter
is_a	MS:1003137 TDPortal input parameter ! TDPortal input parameter

2.3012. MS:1003140 ProSight:Run Annotated Proteoform Search mode

Table 3014. Term [MS:1003140]
id	MS:1003140
name	ProSight:Run Annotated Proteoform Search mode
def	"If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS]
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a	MS:1003136 ProSight input parameter ! ProSight input parameter
is_a	MS:1003137 TDPortal input parameter ! TDPortal input parameter

2.3013. MS:1003141 ProSight

Table 3015. Term [MS:1003141]
id	MS:1003141
name	ProSight
def	"ProSight: Database search engine for top-down proteomics." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.3014. MS:1003142 TDPortal

Table 3016. Term [MS:1003142]
id	MS:1003142
name	TDPortal
def	"TDPortal: Database search engine for top-down proteomics." [PSI:MS]
is_a	MS:1001456 analysis software ! analysis software

2.3015. MS:1003143 mass array

Table 3017. Term [MS:1003143]
id	MS:1003143
name	mass array
def	"A data array of mass values." [PSI:MS]
xref	binary-data-type:MS\:1000521 "32-bit float"
xref	binary-data-type:MS\:1000523 "64-bit float"
is_a	MS:1000513 binary data array ! binary data array
relationship	has_units [UO:0000221] ! dalton

2.3016. MS:1003144 Triple Quad 7500

Table 3018. Term [MS:1003144]
id	MS:1003144
name	Triple Quad 7500
def	"SCIEX Triple Quad 7500." [PSI:MS]
is_a	MS:1000121 SCIEX instrument model ! SCIEX instrument model

2.3017. MS:1003145 ThermoRawFileParser

Table 3019. Term [MS:1003145]
id	MS:1003145
name	ThermoRawFileParser
def	"Cross-platform software to convert Thermo RAW files to a number of open formats." [DOI:10.1021/acs.jproteome.9b00328, PMID:31755270]
is_a	MS:1001457 data processing software ! data processing software

2.3018. MS:1003146 pyteomics

Table 3020. Term [MS:1003146]
id	MS:1003146
name	pyteomics
def	"Python module that helps handling various proteomics data analysis tasks." [DOI:10.1021/acs.jproteome.8b00717, PMID:30576148]
is_a	MS:1001456 analysis software ! analysis software

2.3019. PEFF:0000001 PEFF CV term

Table 3021. Term [PEFF:0000001]
id	PEFF:0000001
name	PEFF CV term
def	"PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF]
relationship	part_of MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.3020. PEFF:0000002 PEFF file header section term

Table 3022. Term [PEFF:0000002]
id	PEFF:0000002
name	PEFF file header section term
def	"CV term that may appear in a PEFF file header section." [PSI:PEFF]
is_a	PEFF:0000001 PEFF CV term ! PEFF CV term

2.3021. PEFF:0000003 PEFF file sequence entry term

Table 3023. Term [PEFF:0000003]
id	PEFF:0000003
name	PEFF file sequence entry term
def	"CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF]
is_a	PEFF:0000001 PEFF CV term ! PEFF CV term

2.3022. PEFF:0000008 DbName

Table 3024. Term [PEFF:0000008]
id	PEFF:0000008
name	DbName
def	"PEFF keyword for the sequence database name." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3023. PEFF:0000009 Prefix

Table 3025. Term [PEFF:0000009]
id	PEFF:0000009
name	Prefix
def	"PEFF keyword for the sequence database prefix." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3024. PEFF:0000010 DbDescription

Table 3026. Term [PEFF:0000010]
id	PEFF:0000010
name	DbDescription
def	"PEFF keyword for the sequence database short description." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3025. PEFF:0000011 Decoy

Table 3027. Term [PEFF:0000011]
id	PEFF:0000011
name	Decoy
def	"PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:boolean "The allowed value-type for this CV term."

2.3026. PEFF:0000012 DbSource

Table 3028. Term [PEFF:0000012]
id	PEFF:0000012
name	DbSource
def	"PEFF keyword for the source of the database file." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3027. PEFF:0000013 DbVersion

Table 3029. Term [PEFF:0000013]
id	PEFF:0000013
name	DbVersion
def	"PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3028. PEFF:0000014 DbDate

Table 3030. Term [PEFF:0000014]
id	PEFF:0000014
name	DbDate
def	"OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF]
comment	This term was obsoleted.
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
is_obsolete	true

2.3029. PEFF:0000015 NumberOfEntries

Table 3031. Term [PEFF:0000015]
id	PEFF:0000015
name	NumberOfEntries
def	"PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:integer "The allowed value-type for this CV term."

2.3030. PEFF:0000016 Conversion

Table 3032. Term [PEFF:0000016]
id	PEFF:0000016
name	Conversion
def	"PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3031. PEFF:0000017 SequenceType

Table 3033. Term [PEFF:0000017]
id	PEFF:0000017
name	SequenceType
def	"PEFF keyword for the molecular type of the sequences." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002002 regular expression for PEFF molecular sequence type ! regular expression for PEFF molecular sequence type

2.3032. PEFF:0000018 SpecificKey

Table 3034. Term [PEFF:0000018]
id	PEFF:0000018
name	SpecificKey
def	"PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3033. PEFF:0000019 SpecificValue

Table 3035. Term [PEFF:0000019]
id	PEFF:0000019
name	SpecificValue
def	"PEFF keyword for the specific values for a custom key." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3034. PEFF:0000020 DatabaseDescription

Table 3036. Term [PEFF:0000020]
id	PEFF:0000020
name	DatabaseDescription
def	"PEFF keyword for the short description of the PEFF file." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3035. PEFF:0000021 GeneralComment

Table 3037. Term [PEFF:0000021]
id	PEFF:0000021
name	GeneralComment
def	"PEFF keyword for a general comment." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3036. PEFF:0000022 ProteoformDb

Table 3038. Term [PEFF:0000022]
id	PEFF:0000022
name	ProteoformDb
def	"PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3037. PEFF:0000023 OptionalTagDef

Table 3039. Term [PEFF:0000023]
id	PEFF:0000023
name	OptionalTagDef
def	"PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3038. PEFF:0000024 HasAnnotationIdentifiers

Table 3040. Term [PEFF:0000024]
id	PEFF:0000024
name	HasAnnotationIdentifiers
def	"PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF]
is_a	PEFF:0000002 PEFF file header section term ! PEFF file header section term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3039. PEFF:0001001 DbUniqueId

Table 3041. Term [PEFF:0001001]
id	PEFF:0001001
name	DbUniqueId
def	"OBSOLETE Sequence database unique identifier." [PSI:PEFF]
comment	This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant.
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
is_obsolete	true

2.3040. PEFF:0001002 PName

Table 3042. Term [PEFF:0001002]
id	PEFF:0001002
name	PName
def	"PEFF keyword for the protein full name." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3041. PEFF:0001003 NcbiTaxId

Table 3043. Term [PEFF:0001003]
id	PEFF:0001003
name	NcbiTaxId
def	"PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:int "The allowed value-type for this CV term."

2.3042. PEFF:0001004 TaxName

Table 3044. Term [PEFF:0001004]
id	PEFF:0001004
name	TaxName
def	"PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3043. PEFF:0001005 GName

Table 3045. Term [PEFF:0001005]
id	PEFF:0001005
name	GName
def	"PEFF keyword for the gene name." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3044. PEFF:0001006 Length

Table 3046. Term [PEFF:0001006]
id	PEFF:0001006
name	Length
def	"PEFF keyword for the sequence length." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:int "The allowed value-type for this CV term."

2.3045. PEFF:0001007 SV

Table 3047. Term [PEFF:0001007]
id	PEFF:0001007
name	SV
def	"PEFF keyword for the sequence version." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3046. PEFF:0001008 EV

Table 3048. Term [PEFF:0001008]
id	PEFF:0001008
name	EV
def	"PEFF keyword for the entry version." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3047. PEFF:0001009 PE

Table 3049. Term [PEFF:0001009]
id	PEFF:0001009
name	PE
def	"PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:int "The allowed value-type for this CV term."

2.3048. PEFF:0001010 Processed

Table 3050. Term [PEFF:0001010]
id	PEFF:0001010
name	Processed
def	"PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3049. PEFF:0001011 Variant

Table 3051. Term [PEFF:0001011]
id	PEFF:0001011
name	Variant
def	"OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF]
comment	This term was made obsolete in favor of VariantSimple and VariantComplex.
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
is_obsolete	true

2.3050. PEFF:0001012 ModResPsi

Table 3052. Term [PEFF:0001012]
id	PEFF:0001012
name	ModResPsi
def	"PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3051. PEFF:0001013 ModRes

Table 3053. Term [PEFF:0001013]
id	PEFF:0001013
name	ModRes
def	"PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3052. PEFF:0001014 AltAC

Table 3054. Term [PEFF:0001014]
id	PEFF:0001014
name	AltAC
def	"PEFF keyword for the Alternative Accession Code." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3053. PEFF:0001015 SeqStatus

Table 3055. Term [PEFF:0001015]
id	PEFF:0001015
name	SeqStatus
def	"PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002003 regular expression for PEFF sequence status ! regular expression for PEFF sequence status

2.3054. PEFF:0001016 CC

Table 3056. Term [PEFF:0001016]
id	PEFF:0001016
name	CC
def	"PEFF keyword for the entry associated comment." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3055. PEFF:0001017 KW

Table 3057. Term [PEFF:0001017]
id	PEFF:0001017
name	KW
def	"PEFF keyword for the entry associated keyword(s)." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3056. PEFF:0001018 GO

Table 3058. Term [PEFF:0001018]
id	PEFF:0001018
name	GO
def	"PEFF keyword for the Gene Ontology code." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3057. PEFF:0001019 XRef

Table 3059. Term [PEFF:0001019]
id	PEFF:0001019
name	XRef
def	"PEFF keyword for the cross-reference to an external resource." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3058. PEFF:0001020 mature protein

Table 3060. Term [PEFF:0001020]
id	PEFF:0001020
name	mature protein
def	"Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF]
is_a	PEFF:0001032 PEFF molecule processing keyword ! PEFF molecule processing keyword
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3059. PEFF:0001021 signal peptide

Table 3061. Term [PEFF:0001021]
id	PEFF:0001021
name	signal peptide
def	"Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF]
is_a	PEFF:0001032 PEFF molecule processing keyword ! PEFF molecule processing keyword
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3060. PEFF:0001022 transit peptide

Table 3062. Term [PEFF:0001022]
id	PEFF:0001022
name	transit peptide
def	"Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF]
is_a	PEFF:0001032 PEFF molecule processing keyword ! PEFF molecule processing keyword
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3061. PEFF:0001023 Conflict

Table 3063. Term [PEFF:0001023]
id	PEFF:0001023
name	Conflict
def	"PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3062. PEFF:0001024 Crc64

Table 3064. Term [PEFF:0001024]
id	PEFF:0001024
name	Crc64
def	"PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3063. PEFF:0001025 Domain

Table 3065. Term [PEFF:0001025]
id	PEFF:0001025
name	Domain
def	"PEFF keyword for the sequence range of a domain." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3064. PEFF:0001026 ID

Table 3066. Term [PEFF:0001026]
id	PEFF:0001026
name	ID
def	"PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3065. PEFF:0001027 ModResUnimod

Table 3067. Term [PEFF:0001027]
id	PEFF:0001027
name	ModResUnimod
def	"PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3066. PEFF:0001028 VariantSimple

Table 3068. Term [PEFF:0001028]
id	PEFF:0001028
name	VariantSimple
def	"PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3067. PEFF:0001029 VariantComplex

Table 3069. Term [PEFF:0001029]
id	PEFF:0001029
name	VariantComplex
def	"PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3068. PEFF:0001030 Proteoform

Table 3070. Term [PEFF:0001030]
id	PEFF:0001030
name	Proteoform
def	"PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3069. PEFF:0001031 DisulfideBond

Table 3071. Term [PEFF:0001031]
id	PEFF:0001031
name	DisulfideBond
def	"PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3070. PEFF:0001032 PEFF molecule processing keyword

Table 3072. Term [PEFF:0001032]
id	PEFF:0001032
name	PEFF molecule processing keyword
def	"PEFF keyword describing the type of processing event being described." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term

2.3071. PEFF:0001033 Comment

Table 3073. Term [PEFF:0001033]
id	PEFF:0001033
name	Comment
def	"PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF]
is_a	PEFF:0000003 PEFF file sequence entry term ! PEFF file sequence entry term
xref	value-type:xsd\:string "The allowed value-type for this CV term."

2.3072. PEFF:0001034 propeptide

Table 3074. Term [PEFF:0001034]
id	PEFF:0001034
name	propeptide
def	"Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF]
is_a	PEFF:0001032 PEFF molecule processing keyword ! PEFF molecule processing keyword
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3073. PEFF:0001035 initiator methionine

Table 3075. Term [PEFF:0001035]
id	PEFF:0001035
name	initiator methionine
def	"N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF]
is_a	PEFF:0001032 PEFF molecule processing keyword ! PEFF molecule processing keyword
xref	value-type:xsd\:string "The allowed value-type for this CV term."
relationship	has_regexp PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

2.3074. PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment

Table 3076. Term [PEFF:1002001]
id	PEFF:1002001
name	regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
def	"(\|[A-Z*](\|.)?)." [PSI:PEFF]
is_a	MS:1002479 regular expression ! regular expression

2.3075. PEFF:1002002 regular expression for PEFF molecular sequence type

Table 3077. Term [PEFF:1002002]
id	PEFF:1002002
name	regular expression for PEFF molecular sequence type
def	"(AA\|NA\|DNA\|cDNA\|RNA\|RNAi\|tRNA\|rRNA\|siRNA\|mDNA\|mRNA\|snoRNA\|ncRNA\|EST\|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a	MS:1002479 regular expression ! regular expression

2.3076. PEFF:1002003 regular expression for PEFF sequence status

Table 3078. Term [PEFF:1002003]
id	PEFF:1002003
name	regular expression for PEFF sequence status
def	"(Complete\|Fragment\|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a	MS:1002479 regular expression ! regular expression

psi-ms Ontology

1. Document Metadata

2. Definitions and Terms

2.1. has_units has_units

2.2. part_of part_of

2.3. has_order has_order

2.4. has_domain has_domain

2.5. MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies

2.6. MS:1000001 sample number

2.7. MS:1000002 sample name

2.8. MS:1000003 sample state

2.9. MS:1000004 sample mass

2.10. MS:1000005 sample volume

2.11. MS:1000006 sample concentration

2.12. MS:1000007 inlet type

2.13. MS:1000008 ionization type

2.14. MS:1000009 ionization mode

2.15. MS:1000010 analyzer type

2.16. MS:1000011 mass resolution

2.17. MS:1000012 resolution measurement method

2.18. MS:1000013 resolution type

2.19. MS:1000014 accuracy

2.20. MS:1000015 scan rate

2.21. MS:1000016 scan start time

2.22. MS:1000017 Scan Function

2.23. MS:1000018 scan direction

2.24. MS:1000019 scan law

2.25. MS:1000020 scanning method

2.26. MS:1000021 reflectron state

2.27. MS:1000022 TOF Total Path Length

2.28. MS:1000023 isolation width

2.29. MS:1000024 final MS exponent

2.30. MS:1000025 magnetic field strength

2.31. MS:1000026 detector type

2.32. MS:1000027 detector acquisition mode

2.33. MS:1000028 detector resolution

2.34. MS:1000029 sampling frequency

2.35. MS:1000030 vendor

2.36. MS:1000031 instrument model

2.37. MS:1000032 customization

2.38. MS:1000033 deisotoping

2.39. MS:1000034 charge deconvolution

2.40. MS:1000035 peak picking

2.41. MS:1000036 scan mode

2.42. MS:1000037 polarity

2.43. MS:1000038 minute

2.44. MS:1000039 second

2.45. MS:1000040 m/z

2.46. MS:1000041 charge state

2.47. MS:1000042 peak intensity

2.48. MS:1000043 intensity unit

2.49. MS:1000044 dissociation method

2.50. MS:1000045 collision energy

2.51. MS:1000046 energy unit

2.52. MS:1000047 emulsion

2.53. MS:1000048 gaseous sample state

2.54. MS:1000049 liquid sample state

2.55. MS:1000050 solid sample state

2.56. MS:1000051 solution

2.57. MS:1000052 suspension

2.58. MS:1000053 sample batch

2.59. MS:1000054 chromatography

2.60. MS:1000055 continuous flow fast atom bombardment

2.61. MS:1000056 direct inlet

2.62. MS:1000057 electrospray inlet

2.63. MS:1000058 flow injection analysis

2.64. MS:1000059 inductively coupled plasma

2.65. MS:1000060 infusion

2.66. MS:1000061 jet separator

2.67. MS:1000062 membrane separator

2.68. MS:1000063 moving belt

2.69. MS:1000064 moving wire

2.70. MS:1000065 open split

2.71. MS:1000066 particle beam

2.72. MS:1000067 reservoir

2.73. MS:1000068 septum

2.74. MS:1000069 thermospray inlet

2.75. MS:1000070 atmospheric pressure chemical ionization

2.76. MS:1000071 chemical ionization

2.77. MS:1000072 Electronic Ionization