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new QC metrics covering DIA-NN output (#333)
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* new metrics covering DIA-NN output

* review changes

* version bump

* Update psi-ms.obo

* Minor rename

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Co-authored-by: Joshua Klein <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>
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@cbielow @mobiusklein @bittremieux
3 people authored Oct 4, 2024
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96 changes: 93 additions & 3 deletions psi-ms.obo
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format-version: 1.2
data-version: 4.1.178
date: 27:09:2024 07:15
saved-by: Eric Deutsch
data-version: 4.1.179
date: 18:08:2024 07:15
saved-by: Chris Bielow
auto-generated-by: OBO-Edit 2.3.1
default-namespace: MS
namespace-id-rule: * MS:$sequence(7,0,9999999)$
Expand Down Expand Up @@ -22794,6 +22794,96 @@ name: environment metric
def: "QC metric related to measurements of the ambient environment, such as the laboratory." [PSI:MS]
is_a: MS:4000001 ! QC metric


[Term]
id: MS:4000025
name: precursor ion current chromatogram
def: "Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time." [PSI:MS]
synonym: "precursor ion chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram
is_a: MS:4000004 ! n-tuple
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_metric_category MS:4000018 ! XIC metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term


[Term]
id: MS:4000026
name: fragment ppm deviation median
def: "The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied." [PSI:MS]
comment: Factors like temperature, airflow, or instrument calibration can cause mass shifts.
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_value_concept MS:1000014 ! accuracy
relationship: has_units UO:0000169 ! parts per million
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000574 ! center value

[Term]
id: MS:4000027
name: fragment ppm deviation mean
def: "The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
comment: Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000178 for the MS1 equivalent.
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_value_concept MS:1000014 ! accuracy
relationship: has_units UO:0000169 ! parts per million
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000401 ! sample mean

[Term]
id: MS:4000028
name: fragment ppm deviation sigma
def: "The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
comment: Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000179 for the MS1 equivalent.
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_value_concept MS:1000830 ! precision
relationship: has_units UO:0000169 ! parts per million
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000237 ! standard deviation

[Term]
id: MS:4000029
name: area under TIC in MS1
def: "The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra." [PSI:MS]
comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides.
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000209 ! area under curve

[Term]
id: MS:4000030
name: area under TIC in MS2
def: "The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra." [PSI:MS]
comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides. Issues such as contamination on the MS front-end and fragmentation efficiency can lead to poor MS signals. Contamination would decrease both MS1 and MS2 S/N, while poor fragmentation efficiency affects MS2 signal but leaves MS1 signal unchanged.
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000209 ! area under curve

[Term]
id: MS:4000031
name: peak area of MS1 vs MS2 signal ratio
def: "The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030)." [PSI:MS]
comment: Poor fragmentation efficiency or precursor fragmentation intensity thresholds affect MS2 signal but leave MS1 signal unchanged.
is_a: MS:4000003 ! single value
is_a: MS:1001848 ! simple ratio of two values
relationship: has_metric_category MS:4000009 ! ID free
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term

[Term]
id: MS:4000050
name: XIC50 fraction
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