format-version: 1.2
data-version: 0.1.2
date: 14:04:2021 12:39
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://raw.githubusercontent.com/obi-ontology/obi/master/obi.owl
import: https://raw.githubusercontent.com/ISA-tools/stato/dev/releases/1.4/stato.obo
ontology: qc

[Typedef]
id: has_relation
name: has_relation

[Typedef]
id: has_type
name: has_type

[Typedef]
id: has_column
name: has_column

[Typedef]
id: has_optional_column
name: has_optional_column

[Typedef]
id: has_tuple
name: has_tuple

[Typedef]
id: has_units
name: has_units


[Term]
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

[Term]
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

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

[Term]
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]

[Term]
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]

[Term]
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

[Term]
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

[Term]
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

[Term]
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

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

[Term]
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

[Term]
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

[Term]
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

[Term]
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]

[Term]
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

[Term]
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

[Term]
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

[Term]
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

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

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

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

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

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

[Term]
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

[Term]
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

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

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

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! XIC metric
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! XIC metric
relationship: has_relation MS:1000086 ! full width at half-maximum
relationship: has_relation QC:4000013 ! QC metric relation: single run
synonym: "XIC-FWHM-Q1" RELATED []
synonym: "XIC-FWHM-Q2" RELATED []
synonym: "XIC-FWHM-Q3" RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! 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
synonym: "XIC-Height-Q2" RELATED []
synonym: "XIC-Height-Q3" RELATED []
synonym: "XIC-Height-Q4" RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
relationship: has_relation MS:1000016 ! scan start time
relationship: has_relation QC:4000013 ! QC metric relation: single run
synonym: "RT-Duration" EXACT []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000235 ! total ion current chromatogram
relationship: has_relation QC:4000013 ! 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

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000023 ! 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
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

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000024 ! 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
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 []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000023 ! 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
synonym: "MS1-TIC-Change-Q2" RELATED []
synonym: "MS1-TIC-Change-Q3" RELATED []
synonym: "MS1-TIC-Change-Q4" RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000023 ! 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
synonym: "MS1-TIC-Q2" RELATED []
synonym: "MS1-TIC-Q3" RELATED []
synonym: "MS1-TIC-Q4" RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000023 ! 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
property_value: has_units UO:0000189
synonym: "MS1-Count" EXACT []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! 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
property_value: has_units UO:0000189
synonym: "MS2-Count" EXACT []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! 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
property_value: has_units UO:0000106
synonym: "MS2-Freq-Max" EXACT []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
relationship: has_relation MS:1000035 ! peak picking
relationship: has_relation QC:4000013 ! QC metric relation: single run
synonym: "MS2-Density-Q1" RELATED []
synonym: "MS2-Density-Q2" RELATED []
synonym: "MS2-Density-Q3" RELATED []

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
is_a: QC:4000025 ! ion source metric
relationship: has_relation MS:1000041 ! charge state
relationship: has_relation QC:4000013 ! 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 []

[Term]
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
is_a: QC:4000024 ! MS2 metric
is_a: QC:4000025 ! ion source metric
is_a: QC:4000006 ! table 
relationship: has_relation MS:1000041 ! charge state
relationship: has_relation QC:4000013 ! 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 []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000023 ! MS1 metric
is_a: QC:4000025 ! ion source metric
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000023 ! MS1 metric
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000235 ! total ion current chromatogram
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000109 ! Relative intensity

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000026 ! environment metric
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000260 ! Percent

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: single run
relationship: has_relation QC:4000067 ! Total ion current chromatogram
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000109 ! Relative intensity

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: single run
relationship: has_relation QC:4000067 ! Total ion current chromatogram
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000109 ! Relative intensity

[Term]
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 
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000239 ! Fraction

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000013 ! QC metric relation: single run
relationship: has_relation QC:4000072 ! Interquartile RT period for peptide identifications

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000086 ! full width at half-maximum
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000086 ! full width at half-maximum
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000086 ! full width at half-maximum
relationship: has_relation QC:4000013 ! QC metric relation: single run

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

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1000235 ! total ion current chromatogram
relationship: has_relation QC:4000013 ! QC metric relation: single run

[Term]
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 
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation MS:1003019 ! pressure chromatogram
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_column: QC:4000108 ! Retention time
property_value: has_column: QC:4000261 ! Pressure

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000014 ! QC metric relation: multiple runs

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000014 ! QC metric relation: multiple runs

[Term]
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

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

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

[Term]
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
property_value: has_units UO:0000187
property_value: has_type NCIT:C68811

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

[Term]
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
property_value: has_units UO:0000189

[Term]
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
property_value: has_types NCIT:C45253

[Term]
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
property_value: has_units PATO:0000161

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

[Term]
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
property_value: has_types NCIT:C45253

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

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

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000006 ! 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

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000006 ! table
property_value: has_column QC:4000114
property_value: has_column QC:4000115
property_value: has_optional_column QC:4000116

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "MS2-4A" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "MS2-4B" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "MS2-4C" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "MS2-4D" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000300
synonym: "MS1-3A" NARROW []

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units MS:1003085

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000300
synonym: "MS1-2A" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "MS1-2B" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000574

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units MS:1000040

[Term]
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
property_value: has_units UO:0000010

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000106

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000106

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000106

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000106

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units MS:1003085

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units UO:0000106

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units UO:0000106

[Term]
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
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_type STATO:0000167
property_value: has_type STATO:0000574
property_value: has_type STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
synonym: "IS-1A"  RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
synonym: "IS-1B"  RELATED []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "IS-3A" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "IS-3B" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
synonym: "IS-3C" NARROW []

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

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

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
synonym: "IS-3A"  RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
synonym: "IS-3B"  RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
synonym: "IS-3C"  RELATED []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

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

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000300

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401
synonym: "MS1-5B" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000006 ! table
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000006 ! table
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401
synonym: "MS1-5A" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401
synonym: "MS1-5C" NARROW []

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401
synonym: "MS1-5D" NARROW []

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000401
synonym: "MS1-5B" NARROW []

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000401
synonym: "MS1-5B" NARROW []

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_units STATO:0000167
property_value: has_units STATO:0000574
property_value: has_units STATO:0000170

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000003 ! single value
property_value: has_units STATO:0000401

[Term]
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
is_a: QC:4000001 ! QC metric
is_a: QC:4000009 ! ID based
property_value: has_units STATO:0000237

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000117

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000004 ! n-tuple
property_value: has_column QC:4000118

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

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

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

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

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000006 ! table
property_value: has_column: QC:4000116 ! Peptide sequence
property_value: has_column: QC:4000241 ! Observed MS1 feature areas

[Term]
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
property_value: has_type MS:1000014
property_value: has_units UO:0000169 

[Term] 
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 
is_a: QC:4000009 ! ID based 
is_a: QC:4000006 ! table 
property_value: has_column: QC:4000116 ! Peptide sequence
property_value: has_column: QC:4000243 ! Observed mass accuracies

[Term]
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
is_a: QC:4000009 ! ID based
is_a: QC:4000001 ! QC metric
property_value: has_units UO:0000189

[Term]
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

[Term]
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
property_value: has_type STATO:0000587

[Term]
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
property_value: has_type STATO:0000587

[Term]
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
property_value: has_type STATO:0000587

[Term]
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
property_value: has_type STATO:0000587

[Term]
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
property_value: has_type STATO:0000587

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

[Term]
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

[Term] 
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 
is_a: QC:4000010 ! ID free 
is_a: QC:4000006 ! 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

[Term] 
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 
is_a: QC:4000010 ! ID free 
is_a: QC:4000006 ! 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

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

[Term] 
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
is_a: QC:4000003 ! single value
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_units UO:0000189

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000023 ! 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
property_value: has_units UO:0000106
synonym: "MS1-Freq-Max" EXACT []

[Term]
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
is_a: QC:4000010 ! ID free
is_a: QC:4000023 ! MS2 metric
relationship: has_relation MS:1000035 ! peak picking
relationship: has_relation QC:4000013 ! QC metric relation: single run
synonym: "MS1-Density-Q1" RELATED []
synonym: "MS1-Density-Q2" RELATED []
synonym: "MS1-Density-Q3" RELATED []

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

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

[Term]
id: QC:4000262
name: Retention time mean shift
def: "Based on reference retention times of detected features the mean shift of all features is calculated in seconds." [PSI:QC]
comment: Low deviation in retention time indicates consistency and reproducibility in chromatographic separation.
is_a: QC:4000003 ! single value
is_a: QC:4000009 ! ID based
relationship: has_relation QC:4000013 ! QC metric relation: single run
property_value: has_units UO:0000010 ! second

[Term]
id: QC:4000263
name: Pump pressure mean
def: "The mean pump pressure in bar for the whole run." [PSI:QC]
comment: Detecting inconsistencies in pump pressure between runs early helps troubleshooting and prevents instrument damage.
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
relationship: has_relation QC:4000013 ! QC metric relation: single run
relationship: has_relation MS:1003019 ! pressure chromatogram
relationship: has_relation QC:4000079 ! Pump pressure chromatogram
