qc-cv Ontology

Table 1. Metadata
format-version	1.2
data-version	0.1.2
date	14:01:2020 10:28
saved-by	julianu
default-namespace	QC
namespace-id-rule	* MS:$sequence(7,0,9999999)$
namespace-id-rule	* QC:$sequence(7,0,9999999)$
remark	coverage: Mass spectrometer quality control metrics
remark	creator: Chris Bielow <chris.bielow ←at→ fu-berlin.de>
remark	creator: Julian Uszkoreit <julian.uszkoreit ←at→ ruhr-uni-bochum.de>
remark	creator: Martin Eisenacher <martin.eisenacher ←at→ ruhr-uni-bochum.de>
remark	creator: Mathias Walzer <walzer ←at→ ebi.ac.uk>
remark	namespace: MS
remark	namespace: QC
import	http://ontologies.berkeleybop.org/uo.obo
import	https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
import	https://github.com/obi-ontology/obi/blob/master/views/obi.obo
import	https://github.com/ISA-tools/stato/blob/dev/releases/1.4/stato.obo
ontology	qc

Table 2. Typedef [has_relation]
id	has_relation
name	has_relation

2.1. has_type has_type

Table 3. Typedef [has_type]
id	has_type
name	has_type

2.2. has_column has_column

Table 4. Typedef [has_column]
id	has_column
name	has_column

2.3. has_optional_column has_optional_column

Table 5. Typedef [has_optional_column]
id	has_optional_column
name	has_optional_column

2.4. has_tuple has_tuple

Table 6. Typedef [has_tuple]
id	has_tuple
name	has_tuple

2.5. has_units has_units

Table 7. Typedef [has_units]
id	has_units
name	has_units

2.6. MS:1009001 quality control metrics generating software

| | null .Term [MS:1009001]

id

MS:1009001

name

quality control metrics generating software

def

"Quality control metrics generating softwares are special types of analysis softwares, which are capable of generating QC metrics." [PSI:PI]

is_a

[MS:1001456] ! analysis software

2.7. MS:1009002 QuaMeter IDFree

Table 8. Term [MS:1009002]
id	MS:1009002
name	QuaMeter IDFree
def	"QuaMeter IDFree is a QC metrics generating software." [PSI:PI]
is_a	MS:1009001 quality control metrics generating software ! quality control metrics generating software

2.8. MS:1009003 iMonDB

Table 9. Term [MS:1009003]
id	MS:1009003
name	iMonDB
def	"iMonDB is a QC metrics generating software." [PSI:PI]
is_a	MS:1009001 quality control metrics generating software ! quality control metrics generating software

2.9. QC:4000001 QC metric

Table 10. Term [QC:4000001]
id	QC:4000001
name	QC metric
def	"Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:QC]

2.10. QC:4000002 QC metric value type

Table 11. Term [QC:4000002]
id	QC:4000002
name	QC metric value type
def	"The QC metric type describes what type the respective metric is, like e.g. single value, n-tuple or table" [PSI:QC]

2.11. QC:4000003 single value

Table 12. Term [QC:4000003]
id	QC:4000003
name	single value
def	"Metrics consisting of a single value (in contrast to n-tuple or table). The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median, or OBI:0001442 ! q-value)." [PSI:QC]
is_a	QC:4000002 QC metric value type ! QC metric value type

2.12. QC:4000004 n-tuple

Table 13. Term [QC:4000004]
id	QC:4000004
name	n-tuple
def	"Metrics consisting of 'n' values (in contrast to single_value or table), where 'n' is implicitly specified by length of the JSON array, e.g. n=4 for quartiles. All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median, or OBI:0001442 ! q-value). All values in the n-tuple must have the same unit and type (if given)." [PSI:QC]
xref	value-type:xsd\:int "The allowed value-type for this CV term."
is_a	QC:4000002 QC metric value type ! QC metric value type

2.13. QC:4000006 table

Table 14. Term [QC:4000006]
id	QC:4000006
name	table
def	"Metrics consisting of a table or data frame (in contrast to single_value or n-tuple), the values of the table may have different types in each column (in contrast to a matrix). The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median, or OBI:0001442 ! q-value)." [PSI:QC]
is_a	QC:4000002 QC metric value type ! QC metric value type

2.14. QC:4000007 matrix

Table 15. Term [QC:4000007]
id	QC:4000007
name	matrix
def	"A matrix is a rectangular array of values of the same type (in contrast to a table). The actual structure of the matrix is defined in the mzQC specification document. In short: All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median, or OBI:0001442 ! q-value). All values in the matrix must have the same unit and type (if given)." [PSI:QC]
is_a	QC:4000002 QC metric value type ! QC metric value type

2.15. QC:4000008 QC metric basis

Table 16. Term [QC:4000008]
id	QC:4000008
name	QC metric basis
def	"The basis for this QC metric, like ID based, ID free, quant based…" [PSI:QC]

2.16. QC:4000009 ID based

Table 17. Term [QC:4000009]
id	QC:4000009
name	ID based
def	"Metrics based on a previous identification run (in contrast to ID_free, Quant_based)" [PSI:QC]
is_a	QC:4000008 QC metric basis ! QC metric basis

2.17. QC:4000010 ID free

Table 18. Term [QC:4000010]
id	QC:4000010
name	ID free
def	"Metrics not based on a previous identification run (in contrast to ID_based, quant_based)" [PSI:QC]
is_a	QC:4000008 QC metric basis ! QC metric basis

2.18. QC:4000011 quantification based

Table 19. Term [QC:4000011]
id	QC:4000011
name	quantification based
def	"Metrics based on a previous quantification run (in contrast to ID_free, ID_based)" [PSI:QC]
is_a	QC:4000008 QC metric basis ! QC metric basis

2.19. QC:4000012 QC metric relation

Table 20. Term [QC:4000012]
id	QC:4000012
name	QC metric relation
def	"A QC metric describes the basis for the metric calculation like \"one MS run\" or \"one spectrum\"" [PSI:QC]

2.20. QC:4000013 QC metric relation: single run

Table 21. Term [QC:4000013]
id	QC:4000013
name	QC metric relation: single run
def	"Describes a metric that is calculated from a single run (e.g. one .raw file)" [PSI:QC]
is_a	QC:4000012 QC metric relation ! QC metric relation

2.21. QC:4000014 QC metric relation: multiple runs

Table 22. Term [QC:4000014]
id	QC:4000014
name	QC metric relation: multiple runs
def	"A metric which is calculated on multiple runs / a set of runs (e.g. multiple .raw files)" [PSI:QC]
is_a	QC:4000012 QC metric relation ! QC metric relation

2.22. QC:4000015 QC metric relation: one spectrum

Table 23. Term [QC:4000015]
id	QC:4000015
name	QC metric relation: one spectrum
def	"A metric which is calculated on one spectrum" [PSI:QC]
is_a	QC:4000012 QC metric relation ! QC metric relation

2.23. QC:4000016 QC metric relation: multiple spectra

Table 24. Term [QC:4000016]
id	QC:4000016
name	QC metric relation: multiple spectra
def	"A metric which is calculated on multiple spectra" [PSI:QC]
is_a	QC:4000012 QC metric relation ! QC metric relation

2.24. QC:4000020 XIC metric

Table 25. Term [QC:4000020]
id	QC:4000020
name	XIC metric
def	"A metric based on extracted ion chromatograms" [PSI:QC]
is_a	QC:4000022 chromatogram metric ! chromatogram metric

2.25. QC:4000021 retention time metric

Table 26. Term [QC:4000021]
id	QC:4000021
name	retention time metric
def	"A metric based on retention time" [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric

2.26. QC:4000022 chromatogram metric

Table 27. Term [QC:4000022]
id	QC:4000022
name	chromatogram metric
def	"A metric based on a chromatogram" [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric

2.27. QC:4000023 MS1 metric

Table 28. Term [QC:4000023]
id	QC:4000023
name	MS1 metric
def	"a metric based on MS1 events" [PSI:QC]
is_a	QC:4000028 MS metric ! MS metric

2.28. QC:4000024 MS2 metric

Table 29. Term [QC:4000024]
id	QC:4000024
name	MS2 metric
def	"a metric based on MS2 events" [PSI:QC]
is_a	QC:4000028 MS metric ! MS metric

2.29. QC:4000025 ion source metric

Table 30. Term [QC:4000025]
id	QC:4000025
name	ion source metric
def	"A metric related to events in the ion source" [PSI:QC]
is_a	QC:4000028 MS metric ! MS metric

2.30. QC:4000026 environment metric

Table 31. Term [QC:4000026]
id	QC:4000026
name	environment metric
def	"A metric related to measurements of the environment/laboratory/room." [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric

2.31. QC:4000027 sample preparation metric

Table 32. Term [QC:4000027]
id	QC:4000027
name	sample preparation metric
is_a	QC:4000001 QC metric ! QC metric

2.32. QC:4000028 MS metric

Table 33. Term [QC:4000028]
id	QC:4000028
name	MS metric
is_a	QC:4000001 QC metric ! QC metric

2.33. QC:4000050 XIC-WideFrac

Table 34. Term [QC:4000050]
id	QC:4000050
name	XIC-WideFrac
def	"The fraction of precursor ions accounting for the top half of all peak widths" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000020 XIC metric ! XIC metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run

2.34. QC:4000051 XIC-FWHM quantiles

Table 35. Term [QC:4000051]
id	QC:4000051
name	XIC-FWHM quantiles
def	"The first to n-th quantile of peak widths for the wide XICs." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000020 XIC metric ! XIC metric
relationship	has_relation [MS:1000086] ! full width at half-maximum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"XIC-FWHM-Q1" RELATED []
synonym	"XIC-FWHM-Q2" RELATED []
synonym	"XIC-FWHM-Q3" RELATED []

2.35. QC:4000052 XIC-Height quantiles ratio to Q1

Table 36. Term [QC:4000052]
id	QC:4000052
name	XIC-Height quantiles ratio to Q1
def	"The log ratio for the second to n-th quantile of wide XIC heights over previous quantile of heights. For the boundary elements min/max are used." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000020 XIC metric ! XIC metric
relationship	has_relation [MS:1000042] ! peak intensity
relationship	has_relation [MS:1000627] ! selected ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"XIC-Height-Q2" RELATED []
synonym	"XIC-Height-Q3" RELATED []
synonym	"XIC-Height-Q4" RELATED []

2.36. QC:4000053 RT duration

Table 37. Term [QC:4000053]
id	QC:4000053
name	RT duration
def	"The retention time duration of the MS run in seconds, similar to the highest scan time minus the lowest scan time." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000021 retention time metric ! retention time metric
relationship	has_relation [MS:1000016] ! scan start time
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"RT-Duration" EXACT []

2.37. QC:4000054 RT over TIC quantile

Table 38. Term [QC:4000054]
id	QC:4000054
name	RT over TIC quantile
def	"The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of quantiles observed is given by the size of the tuple." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000021 retention time metric ! retention time metric
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"RT-TIC-Q1" RELATED []
synonym	"RT-TIC-Q2" RELATED []
synonym	"RT-TIC-Q3" RELATED []
synonym	"RT-TIC-Q4" RELATED []
property_value	has_units UO:0000191

2.38. QC:4000055 MS1 quantiles RT fraction

Table 39. Term [QC:4000055]
id	QC:4000055
name	MS1 quantiles RT fraction
def	"The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by RT-Duration." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000021 retention time metric ! retention time metric
is_a	QC:4000023 MS1 metric ! MS1 metric
relationship	has_relation [MS:1000016] ! scan start time
relationship	has_relation [MS:1000579] ! MS1 spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"RT-MS-Q1" RELATED []
synonym	"RT-MS-Q2" RELATED []
synonym	"RT-MS-Q3" RELATED []
synonym	"RT-MS-Q4" RELATED []
property_value	has_units UO:0000191

2.39. QC:4000056 MS2 quantiles RT fraction

Table 40. Term [QC:4000056]
id	QC:4000056
name	MS2 quantiles RT fraction
def	"The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by RT-Duration." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000021 retention time metric ! retention time metric
is_a	QC:4000024 MS2 metric ! MS2 metric
relationship	has_relation [MS:1000016] ! scan start time
relationship	has_relation [MS:1000580] ! MSn spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_units UO:0000191
synonym	"RT-MSMS-Q1" RELATED []
synonym	"RT-MSMS-Q2" RELATED []
synonym	"RT-MSMS-Q3" RELATED []
synonym	"RT-MSMS-Q4" RELATED []

2.40. QC:4000057 MS1 quantile TIC change ratio to Q1

Table 41. Term [QC:4000057]
id	QC:4000057
name	MS1 quantile TIC change ratio to Q1
def	"The log ratio for the second to n-th quantile of TIC changes over first quantile of TIC changes." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
is_a	QC:4000023 MS1 metric ! MS1 metric
relationship	has_relation [MS:1000016] ! scan start time
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"MS1-TIC-Change-Q2" RELATED []
synonym	"MS1-TIC-Change-Q3" RELATED []
synonym	"MS1-TIC-Change-Q4" RELATED []

2.41. QC:4000058 MS1 quantile TIC ratio to Q1

Table 42. Term [QC:4000058]
id	QC:4000058
name	MS1 quantile TIC ratio to Q1
def	"The log ratio for the second to n-th quantile of TIC over the previous quantile of TIC. For the boundary elements min/max are used." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
is_a	QC:4000023 MS1 metric ! MS1 metric
relationship	has_relation [MS:1000016] ! scan start time
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"MS1-TIC-Q2" RELATED []
synonym	"MS1-TIC-Q3" RELATED []
synonym	"MS1-TIC-Q4" RELATED []

2.42. QC:4000059 Number of MS1 spectra

Table 43. Term [QC:4000059]
id	QC:4000059
name	Number of MS1 spectra
def	"The number of MS1 events in the run." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000023 MS1 metric ! MS1 metric
comment	A lower number of MS1 spectra acquired during one sample run compared to similar runs can indicate mismatched instrument settings or issues with the instrumentation or issues with sample amounts.
relationship	has_relation [MS:1000579] ! MS1 spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_units UO:0000189
synonym	"MS1-Count" EXACT []

2.43. QC:4000060 Number of MS2 spectra

Table 44. Term [QC:4000060]
id	QC:4000060
name	Number of MS2 spectra
def	"The number of MS2 events in the run." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000024 MS2 metric ! MS2 metric
comment	A lower number of MS2 spectra acquired during one sample run compared to similar runs can indicate mismatched instrument settings or issues with the instrumentation or unusual low levels of ions collectable for MS/MS.
relationship	has_relation [MS:1000580] ! MSn spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_units UO:0000189
synonym	"MS2-Count" EXACT []

2.44. QC:4000061 Maximal MS2 frequency

Table 45. Term [QC:4000061]
id	QC:4000061
name	Maximal MS2 frequency
def	"The fastest frequency for MS/MS collection in any minute over the complete run" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000024 MS2 metric ! MS2 metric
relationship	has_relation [MS:1000029] ! sampling frequency
relationship	has_relation [MS:1000580] ! MSn spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_units UO:0000106
synonym	"MS2-Freq-Max" EXACT []

2.45. QC:4000062 MS2 density per quantile

Table 46. Term [QC:4000062]
id	QC:4000062
name	MS2 density per quantile
def	"The first to n-th quantile of MS2 scan peak counts." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000024 MS2 metric ! MS2 metric
relationship	has_relation [MS:1000035] ! peak picking
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
synonym	"MS2-Density-Q1" RELATED []
synonym	"MS2-Density-Q2" RELATED []
synonym	"MS2-Density-Q3" RELATED []

2.46. QC:4000063 MS2 known precursor charges fractions

Table 47. Term [QC:4000063]
id	QC:4000063
name	MS2 known precursor charges fractions
def	"The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. " [PSI:QC]
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000024 MS2 metric ! MS2 metric
is_a	QC:4000025 ion source metric ! ion source metric
relationship	has_relation [MS:1000041] ! charge state
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_column: QC:4000238 ! Charge state
property_value	has_column: QC:4000239 ! Fraction
synonym	"MS2-PrecZ-1" RELATED []
synonym	"MS2-PrecZ-2" RELATED []
synonym	"MS2-PrecZ-3" RELATED []
synonym	"MS2-PrecZ-4" RELATED []
synonym	"MS2-PrecZ-5" RELATED []
synonym	"MS2-PrecZ-more" RELATED []

2.47. QC:4000064 MS2 unknown and likely precursor charges fractions

Table 48. Term [QC:4000064]
id	QC:4000064
name	MS2 unknown and likely precursor charges fractions
def	"The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states." [PSI:QC]
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000024 MS2 metric ! MS2 metric
is_a	QC:4000025 ion source metric ! ion source metric
is_a	QC:4000006 table ! table
relationship	has_relation [MS:1000041] ! charge state
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_column: QC:4000238 ! Charge state
property_value	has_column: QC:4000239 ! Fraction
synonym	"MS2-PrecZ-likely-1" RELATED []
synonym	"MS2-PrecZ-likely-multi" RELATED []

2.48. QC:4000065 Precursor median m/z for IDs

Table 49. Term [QC:4000065]
id	QC:4000065
name	Precursor median m/z for IDs
def	"Median m/z value for all identified peptides (unique ions) after FDR." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000023 MS1 metric ! MS1 metric
is_a	QC:4000025 ion source metric ! ion source metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run

2.49. QC:4000066 Fraction of MS2 identified at different MS1 quantiles

Table 50. Term [QC:4000066]
id	QC:4000066
name	Fraction of MS2 identified at different MS1 quantiles
def	"Fraction of total MS2 scans identified after FDR in the respective quantile of peptides sorted by MS1 maximum intensity." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000023 MS1 metric ! MS1 metric
is_a	QC:4000024 MS2 metric ! MS2 metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run

2.50. QC:4000067 Total ion current chromatogram

Table 51. Term [QC:4000067]
id	QC:4000067
name	Total ion current chromatogram
def	"The total ion current chromatogram. The first column contains the retention time values in second, the second column the corresponding relative intensities." [PSI:QC]
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000109 ! Relative intensity

2.51. QC:4000068 Ambient humidity

Table 52. Term [QC:4000068]
id	QC:4000068
name	Ambient humidity
def	"The ambient relative humidity in percent (0,100) over one or more time points. The first column contains is the ambient humidity value(s). The second contains the respective retention time. A negative RT implies that the exact time of measurement is unknown." [PSI:QC]
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000026 environment metric ! environment metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000260 ! Percent

2.52. QC:4000069 MS1 Total ion current chromatogram

Table 53. Term [QC:4000069]
id	QC:4000069
name	MS1 Total ion current chromatogram
def	"The total ion current chromatogram of MS1 measurements. The first column contains the retention time values in seconds, the second column the corresponding relative intensities." [PSI:QC]
comment	The metric enables to check visually e.g. MS1 TIC stability along the retention time and its absolute value compared to MS2 total ion chromatogram or other analyses MS1 TICs. TIC drops caused by e.g. spray stability issues or bubbles presence can be detected here.
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
is_a	QC:4000023 MS1 metric ! MS1 metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
relationship	has_relation QC:4000067 Total ion current chromatogram ! Total ion current chromatogram
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000109 ! Relative intensity

2.53. QC:4000070 MS2 Total ion current chromatogram

Table 54. Term [QC:4000070]
id	QC:4000070
name	MS2 Total ion current chromatogram
def	"The total ion current chromatogram of MS2 measurements. The first column contains the retention time values in second, the second column the corresponding relative intensities." [PSI:QC]
comment	The metric enables to check visually e.g. MS2 TIC absolute value compared to MS1 total ion chromatogram or other analyses MS2 TICs.
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
is_a	QC:4000024 MS2 metric ! MS2 metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: single run
relationship	has_relation QC:4000067 Total ion current chromatogram ! Total ion current chromatogram
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000109 ! Relative intensity

2.54. QC:4000071 Fraction of peptide IDs around max MS1

Table 55. Term [QC:4000071]
id	QC:4000071
name	Fraction of peptide IDs around max MS1
def	"Fraction of all peptides identified at least X minutes earlier or later than the most intense MS1 signal of the identification. The first column contains the time in minute-wise steps of seconds, the other comlumn the fraction of identified. Negative time values indicate minutes before and positive after maximum MS1." [PSI:QC]
comment	Estimates very early peak broadening.
is_a	QC:4000006 table ! table
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000239 ! Fraction

2.55. QC:4000072 Interquartile RT period for peptide identifications

Table 56. Term [QC:4000072]
id	QC:4000072
name	Interquartile RT period for peptide identifications
def	"The interquartile retention time period, in seconds, for all peptide identifications over the complete run." [PSI:QC]
comment	Longer times indicate better chromatographic separation.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.56. QC:4000073 Peptide identification rate of the interquartile RT period

Table 57. Term [QC:4000073]
id	QC:4000073
name	Peptide identification rate of the interquartile RT period
def	"The identification rate of peptides for the interquartile retention time period, in peptides per second." [PSI:QC]
comment	Higher rates indicate efficient sampling and identification.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
relationship	has_relation QC:4000072 Interquartile RT period for peptide identifications ! Interquartile RT period for peptide identifications

2.57. QC:4000074 Median MS1 peak FWHM for peptides

Table 58. Term [QC:4000074]
id	QC:4000074
name	Median MS1 peak FWHM for peptides
def	"Median of all MS1 peak widths at half maximum (FWHM) for all identified peptides, in seconds" [PSI:QC]
comment	Sharper peak widths (i.e. smaller values) indicate better chromatographic resolution.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000086] ! full width at half-maximum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.58. QC:4000075 Interquartile distance of MS1 peak FWHM for identifications

Table 59. Term [QC:4000075]
id	QC:4000075
name	Interquartile distance of MS1 peak FWHM for identifications
def	"Interquartile distance of all MS1 peak widths at half maximum (FWHM) for all identifications, in seconds" [PSI:QC]
comment	Tighter distributions indicate better consistency.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000086] ! full width at half-maximum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.59. QC:4000076 Median MS1 peak FWHM for peptides in RT quantile

Table 60. Term [QC:4000076]
id	QC:4000076
name	Median MS1 peak FWHM for peptides in RT quantile
def	"Median of all MS1 peak widths at half maximum (FWHM) for all identified peptide, in seconds, in the respective identifications' quantiles ordered by retention time. The data is given in a tuple defining the quantiles, 4-tuple represents quartiles, 10-tuple deciles, etc." [PSI:QC]
comment	Sharper peak widths (i.e. smaller values) indicate better chromatographic resolution in the given quantile.
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000086] ! full width at half-maximum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.60. QC:4000077 Area under TIC

Table 61. Term [QC:4000077]
id	QC:4000077
name	Area under TIC
def	"The area under the total ion chromatogram." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.61. QC:4000078 Area under TIC RT quantiles

Table 62. Term [QC:4000078]
id	QC:4000078
name	Area under TIC RT quantiles
def	"The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1000235] ! total ion current chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run

2.62. QC:4000079 Pump pressure chromatogram

Table 63. Term [QC:4000079]
id	QC:4000079
name	Pump pressure chromatogram
def	"Representation of chromatographic pressure versus time. The first column contains the retention time points in seconds, the second column the corresponding pressures in pascal." [PSI:QC]
is_a	QC:4000006 table ! table
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation [MS:1003019] ! pressure chromatogram
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
property_value	has_column: QC:4000108 ! Retention time
property_value	has_column: QC:4000261 ! Pressure

2.63. QC:4000080 Peptide elution order trailing

Table 64. Term [QC:4000080]
id	QC:4000080
name	Peptide elution order trailing
def	"N(a, b) are the peptides common in the run and a reference run. N(a,b)_i to N(a,b)_j are the first to last eluting common peptides in the run ordered by retention time. This metric is the maximum of ('elution rank' of peptide N(a,b)_t in run) - ('elution_rank' of peptide N(a,b)_t in reference) for the first tenth of common peptides ordered by retention time. The metric is finally normalised with dividing by the number of (identified) peptides in the run." [PSI:QC]
comment	The elution rank difference gives you a measure of how many peptides are eluting early.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation QC:4000014 QC metric relation: multiple runs ! QC metric relation: multiple runs

2.64. QC:4000081 Peptide elution order preceding

Table 65. Term [QC:4000081]
id	QC:4000081
name	Peptide elution order preceding
def	"N(a, b) are the peptides common in the run and a reference run. N(a,b)_i to N(a,b)_j are the first to last eluting common peptides in the run ordered by retention time. This metric is the maximum of ('elution rank' of peptide N(a,b)_t in run) - ('elution_rank' of peptide N(a,b)_t in reference) for the last tenth of common peptides ordered by retention time. The metric is finally normalised with dividing by the number of (identified) peptides in the run." [PSI:QC]
comment	The elution rank difference gives you a measure of how many peptides are eluting late.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000022 chromatogram metric ! chromatogram metric
relationship	has_relation QC:4000014 QC metric relation: multiple runs ! QC metric relation: multiple runs

2.65. QC:4000107 Column type

Table 66. Term [QC:4000107]
id	QC:4000107
name	Column type
def	"The parent to the group of column definitions for name, content, and units for table type." [PSI:QC]
relationship	has_relation QC:4000006 table ! table

2.66. QC:4000108 Retention time

Table 67. Term [QC:4000108]
id	QC:4000108
name	Retention time
def	"The column contains retention time points in seconds." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000010

2.67. QC:4000109 Relative intensity

Table 68. Term [QC:4000109]
id	QC:4000109
name	Relative intensity
def	"The column contains relative intensity values of one type." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units MS:1000043

2.68. QC:4000110 Sequence coverage

Table 69. Term [QC:4000110]
id	QC:4000110
name	Sequence coverage
def	"The column contains sequence coverage values in percent, e.g. from proteins." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000187
property_value	has_type NCIT:C68811

2.69. QC:4000111 Protein accession

Table 70. Term [QC:4000111]
id	QC:4000111
name	Protein accession
def	"The column contains protein accessions." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_types MS:1000885

2.70. QC:4000112 Length value

Table 71. Term [QC:4000112]
id	QC:4000112
name	Length value
def	"The column contains length values of sequences, i.e. the count of items within the sequences, e.g. total length of proteins." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000189

2.71. QC:4000113 Target or decoy designation

Table 72. Term [QC:4000113]
id	QC:4000113
name	Target or decoy designation
def	"The column contains designations of the type 'target', 'decoy', or 'target+decoy'." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_types NCIT:C45253

2.72. QC:4000114 Sample rate

Table 73. Term [QC:4000114]
id	QC:4000114
name	Sample rate
def	"The column contains sample rate values as number of occurrences." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units PATO:0000161

2.73. QC:4000115 Count

Table 74. Term [QC:4000115]
id	QC:4000115
name	Count
def	"The column contains counts of occurrences of a common type." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000189

2.74. QC:4000116 Peptide sequence

Table 75. Term [QC:4000116]
id	QC:4000116
name	Peptide sequence
def	"The column contains peptide sequences; multiple peptides are separated by space." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_types NCIT:C45253

2.75. QC:4000117 Outliers below

Table 76. Term [QC:4000117]
id	QC:4000117
name	Outliers below
def	"The outlier values below 1.5 * IQR." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type NCIT:C79083

2.76. QC:4000118 Outliers above

Table 77. Term [QC:4000118]
id	QC:4000118
name	Outliers above
def	"The outlier values above 1.5 * IQR." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type NCIT:C79083

2.77. QC:4000119 Protein coverage

Table 78. Term [QC:4000119]
id	QC:4000119
name	Protein coverage
def	"The coverage of protein sequences from the peptide sequences identified. The table records the coverage itself (in percent), the protein accession (SHOULD correspond to the accession used in fasta document used for Sequence DB based identification), Length of the protein(, and optionally if it is 'target' or 'decoy' entry.)" [PSI:QC]
comment	The protein coverage can provide insight into the sensitivity of the instrument/identification/protocols used.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column QC:4000110
property_value	has_column QC:4000111
property_value	has_column QC:4000112
property_value	has_optional_column QC:4000113

2.78. QC:4000120 Sampling rates

Table 79. Term [QC:4000120]
id	QC:4000120
name	Sampling rates
def	"The sampling rates of identified peptides and their respective frequency (accumulated by the sampling rate, i.e. how often peptides were sampled n times and how many peptides were resampled at that rate. Optionally, which peptides were sampled at that rate, space separated)" [PSI:QC]
comment	The sampling rate may give insights to peptide separation, dynamic exclusion settings and gradient efficiency.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column QC:4000114
property_value	has_column QC:4000115
property_value	has_optional_column QC:4000116

2.79. QC:4000121 Explained precursor intensity first quarter

Table 80. Term [QC:4000121]
id	QC:4000121
name	Explained precursor intensity first quarter
def	"Fraction of identified MS2 in the first quarter of MS2 sorted by precursor intensity." [PSI:QC]
comment	Higher fractions of identified MS2 spectra indicate the efficiency of detection and sampling
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"MS2-4A" NARROW []

2.80. QC:4000122 Explained precursor intensity second quarter

Table 81. Term [QC:4000122]
id	QC:4000122
name	Explained precursor intensity second quarter
def	"Fraction of identified MS2 in the second quarter of MS2 sorted by precursor intensity." [PSI:QC]
comment	Higher fractions of identified MS2 spectra indicate the efficiency of detection and sampling
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"MS2-4B" NARROW []

2.81. QC:4000123 Explained precursor intensity third quarter

Table 82. Term [QC:4000123]
id	QC:4000123
name	Explained precursor intensity third quarter
def	"Fraction of identified MS2 in the third quarter of MS2 sorted by precursor intensity." [PSI:QC]
comment	Higher fractions of identified MS2 spectra indicate the efficiency of detection and sampling
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"MS2-4C" NARROW []

2.82. QC:4000124 Explained precursor intensity fourth quarter

Table 83. Term [QC:4000124]
id	QC:4000124
name	Explained precursor intensity fourth quarter
def	"Fraction of identified MS2 in the fourth quarter of MS2 sorted by precursor intensity." [PSI:QC]
comment	Higher fractions of identified MS2 spectra indicate the efficiency of detection and sampling
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"MS2-4D" NARROW []

2.83. QC:4000125 Extent of identified precursor intensity

Table 84. Term [QC:4000125]
id	QC:4000125
name	Extent of identified precursor intensity
def	"Ratio of 95th over 5th percentile of precursor intensity for identified peptides" [PSI:QC]
comment	Can be used to approximate the dynamic range of signal
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000300
synonym	"MS1-3A" NARROW []

2.84. QC:4000126 Precursor intensity range of identified MS2

Table 85. Term [QC:4000126]
id	QC:4000126
name	Precursor intensity range of identified MS2
def	"Minimum and maximum precursor intensity recorded and identified." [PSI:QC]
comment	The intensity range of the identified precursors informs about the dynamic range of the acquisition.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units MS:1003085

2.85. QC:4000127 Precursor intensity of identified MS2 Q1, Q2, Q3

Table 86. Term [QC:4000127]
id	QC:4000127
name	Precursor intensity of identified MS2 Q1, Q2, Q3
def	"From the distribution of precursor intensity of identified MS2, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The (un)identified precursor intensity distribution can aid the interpretation of overall identification success.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.86. QC:4000128 Precursor intensity of unidentified MS2 Q1, Q2, Q3

Table 87. Term [QC:4000128]
id	QC:4000128
name	Precursor intensity of unidentified MS2 Q1, Q2, Q3
def	"From the distribution of precursor intensity of unidentified MS2, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The (un)identified precursor intensity distribution can aid the interpretation of overall identification success.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.87. QC:4000129 Median S/N for MS1 spectra in RT range in which half of the identified spectra are identified

Table 88. Term [QC:4000129]
id	QC:4000129
name	Median S/N for MS1 spectra in RT range in which half of the identified spectra are identified
def	"Median S/N for MS1 spectra whose RT is between Q1-Q3 of identified MS2 spectra. This will be half of the identified MS2 spectra." [PSI:QC]
comment	Higher MS1 S/N may correlate with higher signal discrimination
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000300
synonym	"MS1-2A" NARROW []

2.88. QC:4000130 Median of TIC values in the RT range in which the middle half of peptides are identified

Table 89. Term [QC:4000130]
id	QC:4000130
name	Median of TIC values in the RT range in which the middle half of peptides are identified
def	"Median of TIC values in the RT range in which half of peptides are identified (RT values of Q1 to Q3 of identifications)" [PSI:QC]
comment	Estimates the total absolute signal for peptides (may vary significantly between instruments)
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"MS1-2B" NARROW []

2.89. QC:4000131 Median S/N for MS1 spectra in the shortest RT range in which half of the peptides are identified

Table 90. Term [QC:4000131]
id	QC:4000131
name	Median S/N for MS1 spectra in the shortest RT range in which half of the peptides are identified
def	"Median S/N for MS1 spectra in the shortest RT range in which half of the peptides are identified" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric

2.90. QC:4000132 Median of TIC values in the shortest RT range in which half of the peptides are identified

Table 91. Term [QC:4000132]
id	QC:4000132
name	Median of TIC values in the shortest RT range in which half of the peptides are identified
def	"Median of TIC values in the shortest RT range in which half of the peptides are identified" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric

2.91. QC:4000133 Explained base peak intensity median

Table 92. Term [QC:4000133]
id	QC:4000133
name	Explained base peak intensity median
def	"Median of the ratio of 'max survey scan intensity' over 'sampled precursor intensity' for all peptides identified" [PSI:QC]
comment	Gives insight into the amount of overall explained signal and whether the amount of signal could be increased by a better sampling strategy.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000574

2.92. QC:4000134 Explained base peak intensity median from least intense 50% base peaks

Table 93. Term [QC:4000134]
id	QC:4000134
name	Explained base peak intensity median from least intense 50% base peaks
def	"Ratios of 'max survey scan intensity' over sampled precursor intensity for the bottom half (by MS1 max) of MS2" [PSI:QC]
comment	Gives insight into the amount of explained signal and whether the sampling strategy is interfering with the sampling of low abundant peaks.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric

2.93. QC:4000135 Number of chromatograms

Table 94. Term [QC:4000135]
id	QC:4000135
name	Number of chromatograms
def	"Number of chromatograms" [PSI:QC]
comment	A lower number of chromatograms acquired during one sample run compared to similar runs can indicate mismatched instrument settings or issues with the instrumentation.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.94. QC:4000138 MZ acquisition range

Table 95. Term [QC:4000138]
id	QC:4000138
name	MZ acquisition range
def	"Upper and lower limit of m/z values at which spectra are recorded." [PSI:QC]
comment	Acquisition levels can be used as a criterion to assess the comparability of instrument settings between runs.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units MS:1000040

2.95. QC:4000139 RT acquisition range

Table 96. Term [QC:4000139]
id	QC:4000139
name	RT acquisition range
def	"Upper and lower limit of time at which spectra are recorded." [PSI:QC]
comment	Acquisition levels can be used as a criterion to assess the comparability of instrument settings between runs.
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units UO:0000010

2.96. QC:4000140 Fastest frequency for MS level 1 collection

Table 97. Term [QC:4000140]
id	QC:4000140
name	Fastest frequency for MS level 1 collection
def	"Fastest frequency for MS level 1 collection" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000106

2.97. QC:4000141 Fastest frequency for MS level 2 collection

Table 98. Term [QC:4000141]
id	QC:4000141
name	Fastest frequency for MS level 2 collection
def	"Fastest frequency for MS level 2 collection" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000106

2.98. QC:4000142 Slowest frequency for MS level 1 collection

Table 99. Term [QC:4000142]
id	QC:4000142
name	Slowest frequency for MS level 1 collection
def	"Slowest frequency for MS level 1 collection" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000106

2.99. QC:4000143 Slowest frequency for MS level 2 collection

Table 100. Term [QC:4000143]
id	QC:4000143
name	Slowest frequency for MS level 2 collection
def	"Slowest frequency for MS level 2 collection" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000106

2.100. QC:4000144 Precursor intensity range

Table 101. Term [QC:4000144]
id	QC:4000144
name	Precursor intensity range
def	"Minimum and maximum precursor intensity recorded." [PSI:QC]
comment	The intensity range of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units MS:1003085

2.101. QC:4000145 MS1 frequency in RT quarters

Table 102. Term [QC:4000145]
id	QC:4000145
name	MS1 frequency in RT quarters
def	"MS1 frequency in RT 1st quarter, 2nd quarter, 3rd quarter, 4th quarter" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units UO:0000106

2.102. QC:4000146 MS2 frequency in RT quarters

Table 103. Term [QC:4000146]
id	QC:4000146
name	MS2 frequency in RT quarters
def	"MS2 frequency in RT 1st quarter, 2nd quarter, 3rd quarter, 4th quarter" [PSI:QC]
comment	Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units UO:0000106

2.103. QC:4000147 MS1 ion collection time Q1, Q2, Q3

Table 104. Term [QC:4000147]
id	QC:4000147
name	MS1 ion collection time Q1, Q2, Q3
def	"From the distribution of ion injection times (MS:1000927) for MS1, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.104. QC:4000148 MS1 ion collection time mean

Table 105. Term [QC:4000148]
id	QC:4000148
name	MS1 ion collection time mean
def	"From the distribution of ion injection times (MS:1000927) for MS1, the mean" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.105. QC:4000149 MS1 ion collection time sigma

Table 106. Term [QC:4000149]
id	QC:4000149
name	MS1 ion collection time sigma
def	"From the distribution of ion injection times (MS:1000927) for MS1, the sigma value" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.106. QC:4000150 MS1 ion collection time low outliers (<Q1-1.5*IQR)

Table 107. Term [QC:4000150]
id	QC:4000150
name	MS1 ion collection time low outliers (<Q1-1.5*IQR)
def	"From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.107. QC:4000151 MS1 ion collection time high outliers (>Q3+1.5*IQR)

Table 108. Term [QC:4000151]
id	QC:4000151
name	MS1 ion collection time high outliers (>Q3+1.5*IQR)
def	"From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.108. QC:4000152 MS2 ion collection time Q1, Q2, Q3

Table 109. Term [QC:4000152]
id	QC:4000152
name	MS2 ion collection time Q1, Q2, Q3
def	"From the distribution of ion injection times (MS:1000927) for MS2, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.109. QC:4000153 MS2 ion collection time mean

Table 110. Term [QC:4000153]
id	QC:4000153
name	MS2 ion collection time mean
def	"From the distribution of ion injection times (MS:1000927) for MS2, the mean" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.110. QC:4000154 MS2 ion collection time sigma

Table 111. Term [QC:4000154]
id	QC:4000154
name	MS2 ion collection time sigma
def	"From the distribution of ion injection times (MS:1000927) for MS2, the sigma value" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.111. QC:4000155 MS2 ion collection time low outliers (<Q1-1.5*IQR)

Table 112. Term [QC:4000155]
id	QC:4000155
name	MS2 ion collection time low outliers (<Q1-1.5*IQR)
def	"From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.112. QC:4000156 MS2 ion collection time high outliers (>Q3+1.5*IQR)

Table 113. Term [QC:4000156]
id	QC:4000156
name	MS2 ion collection time high outliers (>Q3+1.5*IQR)
def	"From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.113. QC:4000157 Peak density distribution MS1 Q1, Q2, Q3

Table 114. Term [QC:4000157]
id	QC:4000157
name	Peak density distribution MS1 Q1, Q2, Q3
def	"From the distribution of peak densities in MS1, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.114. QC:4000158 Peak density distribution MS1 mean

Table 115. Term [QC:4000158]
id	QC:4000158
name	Peak density distribution MS1 mean
def	"From the distribution of peak densities in MS1, the mean" [PSI:QC]
comment	The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.115. QC:4000159 Peak density distribution MS1 sigma

Table 116. Term [QC:4000159]
id	QC:4000159
name	Peak density distribution MS1 sigma
def	"From the distribution of peak densities in MS1, the sigma value" [PSI:QC]
comment	The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.116. QC:4000160 Peak density distribution MS1 low outliers (<Q1-1.5*IQR)

Table 117. Term [QC:4000160]
id	QC:4000160
name	Peak density distribution MS1 low outliers (<Q1-1.5*IQR)
def	"From the distribution of peak densities in MS1, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.117. QC:4000161 Peak density distribution MS1 high outliers (>Q3+1.5*IQR)

Table 118. Term [QC:4000161]
id	QC:4000161
name	Peak density distribution MS1 high outliers (>Q3+1.5*IQR)
def	"From the distribution of peak densities in MS1, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.118. QC:4000162 Peak density distribution MS2 Q1, Q2, Q3

Table 119. Term [QC:4000162]
id	QC:4000162
name	Peak density distribution MS2 Q1, Q2, Q3
def	"From the distribution of peak densities in MS2, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The distribution of peak densities in MS2 can provide insight into the instruments ion selction settings.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_type STATO:0000167
property_value	has_type STATO:0000574
property_value	has_type STATO:0000170

2.119. QC:4000163 Peak density distribution MS2 mean

Table 120. Term [QC:4000163]
id	QC:4000163
name	Peak density distribution MS2 mean
def	"From the distribution of peak densities in MS2, the mean" [PSI:QC]
comment	The distribution of peak densities in MS2 can provide insight into the instruments ion selction settings.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.120. QC:4000164 Peak density distribution MS2 sigma

Table 121. Term [QC:4000164]
id	QC:4000164
name	Peak density distribution MS2 sigma
def	"From the distribution of peak densities in MS2, the sigma value" [PSI:QC]
comment	The distribution of peak densities in MS2 can provide insight into the instruments ion selction settings.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.121. QC:4000165 Peak density distribution MS2 low outliers (<Q1-1.5*IQR)

Table 122. Term [QC:4000165]
id	QC:4000165
name	Peak density distribution MS2 low outliers (<Q1-1.5*IQR)
def	"From the distribution of peak densities in MS2, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	The distribution of peak densities in MS2 can provide insight into the instruments ion selction settings.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.122. QC:4000166 Peak density distribution MS2 high outliers (>Q3+1.5*IQR)

Table 123. Term [QC:4000166]
id	QC:4000166
name	Peak density distribution MS2 high outliers (>Q3+1.5*IQR)
def	"From the distribution of peak densities in MS2, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	The distribution of peak densities in MS2 can provide insight into the instruments ion selction settings.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.123. QC:4000167 Precursor intensity distribution Q1, Q2, Q3

Table 124. Term [QC:4000167]
id	QC:4000167
name	Precursor intensity distribution Q1, Q2, Q3
def	"From the distribution of precursor intensities, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The intensity distribution of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.124. QC:4000168 Precursor intensity distribution mean

Table 125. Term [QC:4000168]
id	QC:4000168
name	Precursor intensity distribution mean
def	"From the distribution of precursor intensities, the mean" [PSI:QC]
comment	The intensity distribution of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.125. QC:4000169 Precursor intensity distribution sigma

Table 126. Term [QC:4000169]
id	QC:4000169
name	Precursor intensity distribution sigma
def	"From the distribution of precursor intensities, the sigma value" [PSI:QC]
comment	The intensity distribution of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.126. QC:4000170 Precursor intensity distribution low outliers (<Q1-1.5*IQR)

Table 127. Term [QC:4000170]
id	QC:4000170
name	Precursor intensity distribution low outliers (<Q1-1.5*IQR)
def	"From the distribution of precursor intensities, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	The intensity distribution of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.127. QC:4000171 Precursor intensity distribution high outliers (>Q3+1.5*IQR)

Table 128. Term [QC:4000171]
id	QC:4000171
name	Precursor intensity distribution high outliers (>Q3+1.5*IQR)
def	"From the distribution of precursor intensities, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	The intensity distribution of the precursors informs about the dynamic range of the acquisition.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.128. QC:4000172 MS1 signal jump (10x) count

Table 129. Term [QC:4000172]
id	QC:4000172
name	MS1 signal jump (10x) count
def	"The count of MS1 signal jump (spectra sum) by a factor of ten or more (10x) between two subsequent scans" [PSI:QC]
comment	An unusual high count of signal jumps or falls can indicate ESI stability issues.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-1A" RELATED []

2.129. QC:4000173 MS1 signal fall (10x) count

Table 130. Term [QC:4000173]
id	QC:4000173
name	MS1 signal fall (10x) count
def	"The count of MS1 signal decline (spectra sum) by a factor of ten or more (10x) between two subsequent scans" [PSI:QC]
comment	An unusual high count of signal jumps or falls can indicate ESI stability issues.
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-1B" RELATED []

2.130. QC:4000174 Charged peptides ratio 1+ over 2+

Table 131. Term [QC:4000174]
id	QC:4000174
name	Charged peptides ratio 1+ over 2+
def	"Ratio of 1+ peptide count over 2+ peptide count in identified spectra" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3A" NARROW []

2.131. QC:4000175 Charged peptides ratio 3+ over 2+

Table 132. Term [QC:4000175]
id	QC:4000175
name	Charged peptides ratio 3+ over 2+
def	"Ratio of 3+ peptide count over 2+ peptide count in identified spectra" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3B" NARROW []

2.132. QC:4000176 Charged peptides ratio 4+ over 2+

Table 133. Term [QC:4000176]
id	QC:4000176
name	Charged peptides ratio 4+ over 2+
def	"Ratio of 4+ peptide count over 2+ peptide count in identified spectra" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3C" NARROW []

2.133. QC:4000177 Mean charge in identified spectra

Table 134. Term [QC:4000177]
id	QC:4000177
name	Mean charge in identified spectra
def	"Mean charge in identified spectra" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric

2.134. QC:4000178 Median charge in identified spectra

Table 135. Term [QC:4000178]
id	QC:4000178
name	Median charge in identified spectra
def	"Median charge in identified spectra" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric

2.135. QC:4000179 Charged spectra ratio +1 over +2

Table 136. Term [QC:4000179]
id	QC:4000179
name	Charged spectra ratio +1 over +2
def	"Ratio of 1+ spectra count over 2+ spectra count in all MS2" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3A" RELATED []

2.136. QC:4000180 Charged spectra ratio +3 over +2

Table 137. Term [QC:4000180]
id	QC:4000180
name	Charged spectra ratio +3 over +2
def	"Ratio of 3+ peptide count over 2+ peptide count in all MS2" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3B" RELATED []

2.137. QC:4000181 Charged spectra ratio +4 over +2

Table 138. Term [QC:4000181]
id	QC:4000181
name	Charged spectra ratio +4 over +2
def	"Ratio of 4+ peptide count over 2+ peptide count in all MS2" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
synonym	"IS-3C" RELATED []

2.138. QC:4000182 Mean precursor charge in all MS2

Table 139. Term [QC:4000182]
id	QC:4000182
name	Mean precursor charge in all MS2
def	"Mean precursor charge in all MS2" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric

2.139. QC:4000183 Median precursor charge in all MS2

Table 140. Term [QC:4000183]
id	QC:4000183
name	Median precursor charge in all MS2
def	"Median precursor charge in all MS2" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric

2.140. QC:4000184 Number of different distinct proteins from all PSM

Table 141. Term [QC:4000184]
id	QC:4000184
name	Number of different distinct proteins from all PSM
def	"Number of different distinct protein from all PSM after FDR filtering. (No undistinguishability groups.)" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.141. QC:4000185 Number of identified proteins

Table 142. Term [QC:4000185]
id	QC:4000185
name	Number of identified proteins
def	"Number of identified proteins at given FDR threshold, first number is the number of proteins (considering sequence only), second number is the FDR threshold applied (negative if no threshold applied)" [PSI:QC]
comment	The number of identifications are likely to only make local sense within a confined set of identification parameters (identification algorithm, searchspace, FDR method).
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.142. QC:4000186 Total number of PSM

Table 143. Term [QC:4000186]
id	QC:4000186
name	Total number of PSM
def	"Total number of PSM before FDR filtering." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.143. QC:4000187 Number of identified peptides

Table 144. Term [QC:4000187]
id	QC:4000187
name	Number of identified peptides
def	"Number of identified peptides at given FDR threshold, first number is the number of peptides (considering sequence only), second number is the FDR threshold applied (negative if no threshold applied)" [PSI:QC]
comment	The number of identifications are likely to only make local sense within a confined set of identification parameters (identification algorithm, searchspace, FDR method).
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.144. QC:4000188 Number of identified spectra

Table 145. Term [QC:4000188]
id	QC:4000188
name	Number of identified spectra
def	"Number of identified spectra at given FDR threshold, first number is the number of spectra, second number is the FDR threshold applied (negative if no threshold applied)" [PSI:QC]
comment	The number of identifications are likely to only make local sense within a confined set of identification parameters (identification algorithm, searchspace, FDR method).
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.145. QC:4000189 ID ratio

Table 146. Term [QC:4000189]
id	QC:4000189
name	ID ratio
def	"The ratio of identified and recorded MS2 spectra after FDR filtering." [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000300

2.146. QC:4000190 Precursor errors (Da) Q1, Q2, Q3

Table 147. Term [QC:4000190]
id	QC:4000190
name	Precursor errors (Da) Q1, Q2, Q3
def	"From the distribution of Precursor errors (mass deviation of precursor to identified peptide in Da), the quartiles Q1, Q2, Q3 value" [PSI:QC]
comment	The absolute precursor error distribution can aid the interpretation of overall identification success.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.147. QC:4000191 Precursor errors (Da) mean

Table 148. Term [QC:4000191]
id	QC:4000191
name	Precursor errors (Da) mean
comment	The absolute precursor error distribution can aid the interpretation of overall identification success.
def	"From the distribution of Precursor errors (mass deviation of precursor to identified peptide in Da), the mean" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401
synonym	"MS1-5B" NARROW []

2.148. QC:4000192 Precursor errors (Da) sigma

Table 149. Term [QC:4000192]
id	QC:4000192
name	Precursor errors (Da) sigma
def	"From the distribution of Precursor errors (mass deviation of precursor to identified peptide in Da), the sigma value" [PSI:QC]
comment	The absolute precursor error distribution can aid the interpretation of overall identification success.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.149. QC:4000193 Precursor errors (Da) outliers (<Q1-1.5*IQR)

Table 150. Term [QC:4000193]
id	QC:4000193
name	Precursor errors (Da) outliers (<Q1-1.5*IQR)
def	"From the distribution of Precursor errors (mass deviation of precursor to identified peptide in Da), the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The absolute precursor error distribution can aid the interpretation of overall identification success.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column QC:4000117

2.150. QC:4000194 Precursor errors (Da) outliers (>Q3+1.5*IQR)

Table 151. Term [QC:4000194]
id	QC:4000194
name	Precursor errors (Da) outliers (>Q3+1.5*IQR)
def	"From the distribution of Precursor errors (mass deviation of precursor to identified peptide in Da), the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The absolute precursor error distribution can aid the interpretation of overall identification success.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column QC:4000118

2.151. QC:4000195 Precursor errors (ppm) Q1, Q2, Q3

Table 152. Term [QC:4000195]
id	QC:4000195
name	Precursor errors (ppm) Q1, Q2, Q3
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
def	"From the distribution of Precursor errors (ppm), the quartiles Q1, Q2, Q3 value" [PSI:QC]
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.152. QC:4000196 Precursor errors (ppm) mean

Table 153. Term [QC:4000196]
id	QC:4000196
name	Precursor errors (ppm) mean
def	"From the distribution of Precursor errors (ppm), the mean " [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000401

2.153. QC:4000197 Precursor errors (ppm) sigma

Table 154. Term [QC:4000197]
id	QC:4000197
name	Precursor errors (ppm) sigma
def	"From the distribution of Precursor errors (ppm), the sigma value" [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000237

2.154. QC:4000198 Precursor errors (ppm) low outliers (<Q1-1.5*IQR)

Table 155. Term [QC:4000198]
id	QC:4000198
name	Precursor errors (ppm) low outliers (<Q1-1.5*IQR)
def	"From the distribution of Precursor errors (ppm), the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.155. QC:4000199 Precursor errors (ppm) outliers (>Q3+1.5*IQR)

Table 156. Term [QC:4000199]
id	QC:4000199
name	Precursor errors (ppm) outliers (>Q3+1.5*IQR)
def	"From the distribution of Precursor errors (ppm), the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.156. QC:4000200 Precursor errors (Da) median

Table 157. Term [QC:4000200]
id	QC:4000200
name	Precursor errors (Da) median
def	"From the distribution of Precursor errors (Da), the median" [PSI:QC]
comment	The precursor error distribution can aid the interpretation of overall identification success.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401
synonym	"MS1-5A" NARROW []

2.157. QC:4000201 Precursor errors (ppm) median

Table 158. Term [QC:4000201]
id	QC:4000201
name	Precursor errors (ppm) median
def	"From the distribution of Precursor errors (ppm), the median" [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401
synonym	"MS1-5C" NARROW []

2.158. QC:4000202 Precursor errors (ppm) IQR

Table 159. Term [QC:4000202]
id	QC:4000202
name	Precursor errors (ppm) IQR
def	"From the distribution of Precursor errors (ppm), the IQR" [PSI:QC]
comment	The precursor error in ppm distribution can aid the interpretation of overall identification success.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401
synonym	"MS1-5D" NARROW []

2.159. QC:4000203 Identification score - Q1, Q2, Q3

Table 160. Term [QC:4000203]
id	QC:4000203
name	Identification score - Q1, Q2, Q3
def	"From the distribution of Identification score, the Q1, Q2, Q3 value" [PSI:QC]
comment	The identification score distribution can help improve scoring function tuning, aid the interpretation of overall identification success, and integration with downstream processing such as percolator. Comparisons will likely only make local sense where the same method of identification is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.160. QC:4000204 Identification score - mean

Table 161. Term [QC:4000204]
id	QC:4000204
name	Identification score - mean
def	"From the distribution of Identification score, the mean value" [PSI:QC]
comment	The identification score distribution can help improve scoring function tuning, aid the interpretation of overall identification success, and integration with downstream processing such as percolator. Comparisons will likely only make local sense where the same method of identification is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000401

2.161. QC:4000205 Identification score - sigma

Table 162. Term [QC:4000205]
id	QC:4000205
name	Identification score - sigma
def	"From the distribution of Identification score, the sigma value" [PSI:QC]
comment	The identification score distribution can help improve scoring function tuning, aid the interpretation of overall identification success, and integration with downstream processing such as percolator. Comparisons will likely only make local sense where the same method of identification is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.162. QC:4000206 Identification score - low outliers (<Q1-1.5*IQR)

Table 163. Term [QC:4000206]
id	QC:4000206
name	Identification score - low outliers (<Q1-1.5*IQR)
def	"From the distribution of Identification score, the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The identification score distribution can help improve scoring function tuning, aid the interpretation of overall identification success, and integration with downstream processing such as percolator. Comparisons will likely only make local sense where the same method of identification is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.163. QC:4000207 Identification score - high outliers (>Q3+1.5*IQR)

Table 164. Term [QC:4000207]
id	QC:4000207
name	Identification score - high outliers (>Q3+1.5*IQR)
def	"From the distribution of Identification score, the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The identification score distribution can help improve scoring function tuning, aid the interpretation of overall identification success, and integration with downstream processing such as percolator. Comparisons will likely only make local sense where the same method of identification is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.164. QC:4000208 Missed cleavages - Q1, Q2, Q3

Table 165. Term [QC:4000208]
id	QC:4000208
name	Missed cleavages - Q1, Q2, Q3
def	"From the distribution of missed cleavages in identified peptides the quartiles Q1, Q2, Q3 value" [PSI:QC]
comment	The missed cleavage distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.165. QC:4000209 Missed cleavages - mean

Table 166. Term [QC:4000209]
id	QC:4000209
name	Missed cleavages - mean
def	"From the distribution of missed cleavages in identified peptides the mean" [PSI:QC]
comment	The missed cleavage distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000401
synonym	"MS1-5B" NARROW []

2.166. QC:4000210 Missed cleavages - sigma

Table 167. Term [QC:4000210]
id	QC:4000210
name	Missed cleavages - sigma
def	"From the distribution of missed cleavages in identified peptides the sigma value" [PSI:QC]
comment	The missed cleavage distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000237

2.167. QC:4000211 Missed cleavages - low outliers (<Q1-1.5*IQR)

Table 168. Term [QC:4000211]
id	QC:4000211
name	Missed cleavages - low outliers (<Q1-1.5*IQR)
def	"From the distribution of missed cleavages in identified peptides, the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The missed cleavage distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.168. QC:4000212 Missed cleavages - high outliers (>Q3+1.5*IQR)

Table 169. Term [QC:4000212]
id	QC:4000212
name	Missed cleavages - high outliers (>Q3+1.5*IQR)
def	"From the distribution of missed cleavages in identified peptides, the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The missed cleavage distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.169. QC:4000213 Identified peptide lengths - Q1, Q2, Q3

Table 170. Term [QC:4000213]
id	QC:4000213
name	Identified peptide lengths - Q1, Q2, Q3
def	"From the distribution of identified peptide lengths the quartiles Q1, Q2, Q3 value" [PSI:QC]
comment	The identified peptide lengths distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.170. QC:4000214 Identified peptide lengths - mean

Table 171. Term [QC:4000214]
id	QC:4000214
name	Identified peptide lengths - mean
def	"From the distribution of identified peptide lengths the mean" [PSI:QC]
comment	The identified peptide lengths distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000401
synonym	"MS1-5B" NARROW []

2.171. QC:4000215 Identified peptide lengths - sigma

Table 172. Term [QC:4000215]
id	QC:4000215
name	Identified peptide lengths - sigma
def	"From the distribution of identified peptide lengths the sigma value" [PSI:QC]
comment	The identified peptide lengths distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000237

2.172. QC:4000216 Identified peptide lengths - low outliers (<Q1-1.5*IQR)

Table 173. Term [QC:4000216]
id	QC:4000216
name	Identified peptide lengths - low outliers (<Q1-1.5*IQR)
def	"From the distribution of identified peptide lengths, the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The identified peptide lengths distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.173. QC:4000217 Identified peptide lengths - high outliers (>Q3+1.5*IQR)

Table 174. Term [QC:4000217]
id	QC:4000217
name	Identified peptide lengths - high outliers (>Q3+1.5*IQR)
def	"From the distribution of identified peptide lengths, the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The identified peptide lengths distribution can aid the interpretation of digestion efficacy.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.174. QC:4000218 Signal-to-noise ratio in MS1 - Q1, Q2, Q3

Table 175. Term [QC:4000218]
id	QC:4000218
name	Signal-to-noise ratio in MS1 - Q1, Q2, Q3
def	"From the distribution of signal-to-noise ratio in MS1, the quartiles Q1, Q2, Q3 value" [PSI:QC]
comment	The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors.
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.175. QC:4000219 Signal-to-noise ratio in MS1 - mean

Table 176. Term [QC:4000219]
id	QC:4000219
name	Signal-to-noise ratio in MS1 - mean
comment	The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
def	"From the distribution of signal-to-noise ratio in MS1, the mean" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.176. QC:4000220 Signal-to-noise ratio in MS1 - sigma

Table 177. Term [QC:4000220]
id	QC:4000220
name	Signal-to-noise ratio in MS1 - sigma
def	"From the distribution of signal-to-noise ratio in MS1, the sigma value" [PSI:QC]
comment	The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.177. QC:4000221 Signal-to-noise ratio in MS1 - low outliers (<Q1-1.5*IQR)

Table 178. Term [QC:4000221]
id	QC:4000221
name	Signal-to-noise ratio in MS1 - low outliers (<Q1-1.5*IQR)
def	"From the distribution of signal-to-noise ratio in MS1, the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.178. QC:4000222 Signal-to-noise ratio in MS1 - high outliers (>Q3+1.5*IQR)

Table 179. Term [QC:4000222]
id	QC:4000222
name	Signal-to-noise ratio in MS1 - high outliers (>Q3+1.5*IQR)
def	"From the distribution of signal-to-noise ratio in MS1, the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.179. QC:4000223 Signal-to-noise ratio in MS2 - Q1, Q2, Q3

Table 180. Term [QC:4000223]
id	QC:4000223
name	Signal-to-noise ratio in MS2 - Q1, Q2, Q3
def	"From the distribution of signal-to-noise ratio in MS2, the quartiles Q1, Q2, Q3 value" [PSI:QC]
comment	A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.180. QC:4000224 Signal-to-noise ratio in MS2 - mean

Table 181. Term [QC:4000224]
id	QC:4000224
name	Signal-to-noise ratio in MS2 - mean
def	"From the distribution of signal-to-noise ratio in MS2, the mean" [PSI:QC]
comment	A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.181. QC:4000225 Signal-to-noise ratio in MS2 - sigma

Table 182. Term [QC:4000225]
id	QC:4000225
name	Signal-to-noise ratio in MS2 - sigma
def	"From the distribution of signal-to-noise ratio in MS2, the sigma value" [PSI:QC]
comment	A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.182. QC:4000226 Signal-to-noise ratio in MS2 - low outliers (<Q1-1.5*IQR)

Table 183. Term [QC:4000226]
id	QC:4000226
name	Signal-to-noise ratio in MS2 - low outliers (<Q1-1.5*IQR)
def	"From the distribution of signal-to-noise ratio in MS2, the list of outliers below Q1-1.5IQR" [PSI:QC]
comment	A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.183. QC:4000227 Signal-to-noise ratio in MS2 - high outliers (>Q3+1.5*IQR)

Table 184. Term [QC:4000227]
id	QC:4000227
name	Signal-to-noise ratio in MS2 - high outliers (>Q3+1.5*IQR)
def	"From the distribution of signal-to-noise ratio in MS2, the list of outliers above Q3+1.5IQR" [PSI:QC]
comment	A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.184. QC:4000228 Identified precursor intensity distribution Q1, Q2, Q3

Table 185. Term [QC:4000228]
id	QC:4000228
name	Identified precursor intensity distribution Q1, Q2, Q3
def	"From the distribution of identified precursor intensities, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.185. QC:4000229 Identified precursor intensity distribution - mean

Table 186. Term [QC:4000229]
id	QC:4000229
name	Identified precursor intensity distribution - mean
def	"From the distribution of identified precursor intensities, the mean" [PSI:QC]
comment	The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000401

2.186. QC:4000230 Identified precursor intensity distribution - sigma

Table 187. Term [QC:4000230]
id	QC:4000230
name	Identified precursor intensity distribution - sigma
def	"From the distribution of identified precursor intensities, the sigma value" [PSI:QC]
comment	The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units STATO:0000237

2.187. QC:4000231 Identified precursor intensity distribution - low outliers (<Q1-1.5*IQR)

Table 188. Term [QC:4000231]
id	QC:4000231
name	Identified precursor intensity distribution - low outliers (<Q1-1.5*IQR)
def	"From the distribution of identified precursor intensities, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.188. QC:4000232 Identified precursor intensity distribution - high outliers (>Q3+1.5*IQR)

Table 189. Term [QC:4000232]
id	QC:4000232
name	Identified precursor intensity distribution - high outliers (>Q3+1.5*IQR)
def	"From the distribution of identified precursor intensities, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.189. QC:4000233 Unidentified precursor intensity distribution - Q1, Q2, Q3

Table 190. Term [QC:4000233]
id	QC:4000233
name	Unidentified precursor intensity distribution - Q1, Q2, Q3
def	"From the distribution of unidentified precursor intensities, the quartiles Q1, Q2, Q3" [PSI:QC]
comment	The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_units STATO:0000167
property_value	has_units STATO:0000574
property_value	has_units STATO:0000170

2.190. QC:4000234 Unidentified precursor intensity distribution - mean

Table 191. Term [QC:4000234]
id	QC:4000234
name	Unidentified precursor intensity distribution - mean
def	"From the distribution of unidentified precursor intensities, the mean" [PSI:QC]
comment	The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000003 single value ! single value
property_value	has_units STATO:0000401

2.191. QC:4000235 Unidentified precursor intensity distribution - sigma

Table 192. Term [QC:4000235]
id	QC:4000235
name	Unidentified precursor intensity distribution - sigma
def	"From the distribution of unidentified precursor intensities, the sigma value" [PSI:QC]
comment	The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000003 single value ! single value
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
property_value	has_units STATO:0000237

2.192. QC:4000236 Unidentified precursor intensity distribution - low outliers (<Q1-1.5*IQR)

Table 193. Term [QC:4000236]
id	QC:4000236
name	Unidentified precursor intensity distribution - low outliers (<Q1-1.5*IQR)
def	"From the distribution of unidentified precursor intensities, the list of outliers below Q1-1.5*IQR" [PSI:QC]
comment	The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000117

2.193. QC:4000237 Unidentified precursor intensity distribution - high outliers (>Q3+1.5*IQR)

Table 194. Term [QC:4000237]
id	QC:4000237
name	Unidentified precursor intensity distribution - high outliers (>Q3+1.5*IQR)
def	"From the distribution of unidentified precursor intensities, the list of outliers above Q3+1.5*IQR" [PSI:QC]
comment	The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000004 n-tuple ! n-tuple
property_value	has_column QC:4000118

2.194. QC:4000238 Charge state

Table 195. Term [QC:4000238]
id	QC:4000238
name	Charge state
def	"The column contains charge states." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units MS:1000041

2.195. QC:4000239 Fraction

Table 196. Term [QC:4000239]
id	QC:4000239
name	Fraction
def	"The column contains fraction values as decimals." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000191

2.196. QC:4000240 Humidity

Table 197. Term [QC:4000240]
id	QC:4000240
name	Humidity
def	"The column contains relative humidity values in percent." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000187

2.197. QC:4000241 Observed MS1 feature areas

Table 198. Term [QC:4000241]
id	QC:4000241
name	Observed MS1 feature areas
def	"Observed MS1 feature areas." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type MS:1001844

2.198. QC:4000242 QC2 sample MS1 feature areas

Table 199. Term [QC:4000242]
id	QC:4000242
name	QC2 sample MS1 feature areas
def	"Observed MS1 feature area from selected peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Selected peptides in the first column to be expected: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'" [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column: QC:4000116 ! Peptide sequence
property_value	has_column: QC:4000241 ! Observed MS1 feature areas

2.199. QC:4000243 Observed mass accuracies

Table 200. Term [QC:4000243]
id	QC:4000243
name	Observed mass accuracies
def	"Observed mass accuracy calculated by 1E6 x (observed mz - theoretical mz)/theoretical mz of selected peptides." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type MS:1000014
property_value	has_units UO:0000169

2.200. QC:4000244 QC2 sample mass accuracies

Table 201. Term [QC:4000244]
id	QC:4000244
name	QC2 sample mass accuracies
def	"Observed mass accuracy from selected peptides of a QC2 sample measurement. Selected peptides in the first column to be expected: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'" [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000006 table ! table
property_value	has_column: QC:4000116 ! Peptide sequence
property_value	has_column: QC:4000243 ! Observed mass accuracies

2.201. QC:4000245 Number of different undistinguishable proteins groups from all PSM

Table 202. Term [QC:4000245]
id	QC:4000245
name	Number of different undistinguishable proteins groups from all PSM
def	"Number of different undistinguishable proteins groups from all PSM after FDR filtering. (Only undistinguishability groups.)" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000009 ID based ! ID based
is_a	QC:4000001 QC metric ! QC metric
property_value	has_units UO:0000189

2.202. QC:4000246 Run name

Table 203. Term [QC:4000246]
id	QC:4000246
name	Run name
def	"The column contains run names as defined by runQuality inputFile name." [PSI:QC]
is_a	QC:4000107 Column type ! Column type

2.203. QC:4000247 PCA Dimension 1

Table 204. Term [QC:4000247]
id	QC:4000247
name	PCA Dimension 1
def	"The column contains Principal Component Analysis scores from the first eigenvalue dimension." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type STATO:0000587

2.204. QC:4000248 PCA Dimension 2

Table 205. Term [QC:4000248]
id	QC:4000248
name	PCA Dimension 2
def	"The column contains Principal Component Analysis scores from the second eigenvalue dimension." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type STATO:0000587

2.205. QC:4000249 PCA Dimension 3

Table 206. Term [QC:4000249]
id	QC:4000249
name	PCA Dimension 3
def	"The column contains Principal Component Analysis scores from the third eigenvalue dimension." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type STATO:0000587

2.206. QC:4000250 PCA Dimension 4

Table 207. Term [QC:4000250]
id	QC:4000250
name	PCA Dimension 4
def	"The column contains Principal Component Analysis scores from the fourth eigenvalue dimension." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type STATO:0000587

2.207. QC:4000251 PCA Dimension 5

Table 208. Term [QC:4000251]
id	QC:4000251
name	PCA Dimension 5
def	"The column contains Principal Component Analysis scores from the fifth eigenvalue dimension." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_type STATO:0000587

2.208. QC:4000252 Batch label

Table 209. Term [QC:4000252]
id	QC:4000252
name	Batch label
def	"The column contains batch label names" [PSI:QC]
is_a	QC:4000107 Column type ! Column type

2.209. QC:4000253 Injection sequence number

Table 210. Term [QC:4000253]
id	QC:4000253
name	Injection sequence number
def	"The column contains the order in which the runs were acquired. Numbers may be missing due to unrelated samples being run." [PSI:QC]
is_a	QC:4000107 Column type ! Column type

2.210. QC:4000254 Peak area feature PCA result

Table 211. Term [QC:4000254]
id	QC:4000254
name	Peak area feature PCA result
def	"PCA score result from multiple runs with (log transformed) peak area input features before batch correction." [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000006 table ! table
property_value	has_column: QC:4000246 ! Run name
property_value	has_column: QC:4000247 ! PCA Dimension 1
property_value	has_column: QC:4000248 ! PCA Dimension 2
property_value	has_optional_column: QC:4000249 ! PCA Dimension 3
property_value	has_optional_column: QC:4000250 ! PCA Dimension 4
property_value	has_optional_column: QC:4000251 ! PCA Dimension 5
property_value	has_optional_column: QC:4000252 ! Batch label
property_value	has_optional_column: QC:4000253 ! Injection sequence number

2.211. QC:4000255 Batch corrected peak area feature PCA result

Table 212. Term [QC:4000255]
id	QC:4000255
name	Batch corrected peak area feature PCA result
def	"PCA score result from multiple runs with (log transformed) peak area input features after batch correction." [PSI:QC]
is_a	QC:4000001 QC metric ! QC metric
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000006 table ! table
property_value	has_column: QC:4000246 ! Run name
property_value	has_column: QC:4000247 ! PCA Dimension 1
property_value	has_column: QC:4000248 ! PCA Dimension 2
property_value	has_optional_column: QC:4000249 ! PCA Dimension 3
property_value	has_optional_column: QC:4000250 ! PCA Dimension 4
property_value	has_optional_column: QC:4000251 ! PCA Dimension 5
property_value	has_optional_column: QC:4000252 ! Batch label
property_value	has_optional_column: QC:4000253 ! Injection sequence number

2.212. QC:4000256 Metabolomics metric

Table 213. Term [QC:4000256]
id	QC:4000256
name	Metabolomics metric
def	"Metrics for metabolomics experiments." [PSI:QC]
is_a	QC:4000008 QC metric basis ! QC metric basis

2.213. QC:4000257 "Detected Compounds"

Table 214. Term [QC:4000257]
id	QC:4000257
name	"Detected Compounds"
def	"Number of detected compounds from a given library of target compounds in a specific run." [PSI:QC]
is_a	QC:4000256 Metabolomics metric ! Metabolomics metric
is_a	QC:4000003 single value ! single value
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
property_value	has_units UO:0000189

2.214. QC:4000258 Maximal MS1 frequency

Table 215. Term [QC:4000258]
id	QC:4000258
name	Maximal MS1 frequency
def	"The fastest frequency for MS collection in any minute over the complete run" [PSI:QC]
is_a	QC:4000003 single value ! single value
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000023 MS1 metric ! MS1 metric
relationship	has_relation [MS:1000029] ! sampling frequency
relationship	has_relation [MS:1000580] ! MSn spectrum
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
property_value	has_units UO:0000106
synonym	"MS1-Freq-Max" EXACT []

2.215. QC:4000259 MS1 density per quantile

Table 216. Term [QC:4000259]
id	QC:4000259
name	MS1 density per quantile
def	"The first to n-th quantile of MS2 scan peak counts." [PSI:QC]
is_a	QC:4000004 n-tuple ! n-tuple
is_a	QC:4000010 ID free ! ID free
is_a	QC:4000023 MS1 metric ! MS2 metric
relationship	has_relation [MS:1000035] ! peak picking
relationship	has_relation QC:4000013 QC metric relation: single run ! QC metric relation: one run
synonym	MS1-Density-Q1" RELATED []
synonym	MS1-Density-Q2" RELATED []
synonym	MS1-Density-Q3" RELATED []

2.216. QC:4000260 Percent

Table 217. Term [QC:4000260]
id	QC:4000260
name	Percent
def	"The column contains percentages of one type." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000187

2.217. QC:4000261 Pressure

Table 218. Term [QC:4000261]
id	QC:4000261
name	Pressure
def	"The column contains measurments of pressure in pascal." [PSI:QC]
is_a	QC:4000107 Column type ! Column type
property_value	has_units UO:0000110