QC metric terms to gauge the ionisation efficiency of a run

[mwalzer]

What is the QC term's name?

Charged spectra ratio +(n|0<n,n!=2) over +2

Briefly describe the QC term.

Obvious from the term name above, this is more than one metric. The metrics actually come all the way from MSQC (IS-3A,B,C).
The metric values look at the fractions of charged spectra either singly, triply, or quadruply charged over doubly charged counts. The original IS-3 metrics used peptide identifications, which is changed here to spectra, accordingly the synonym tags is RELATED and not EXACT.

[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: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_value_type xsd\:float ! The allowed value-type for this CV term
relationship: has_value_concept UO:0000191 ! fraction
synonym: "IS-3A"  RELATED []

[Term]
id: QC:4000180
name: Charged spectra ratio +3 over +2
def: "Ratio of 3+ spectra count over 2+ spectra count in all MS2" [PSI:QC]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_value_type xsd\:float ! The allowed value-type for this CV term
relationship: has_value_concept UO:0000191 ! fraction
synonym: "IS-3B"  RELATED []

[Term]
id: QC:4000181
name: Charged spectra ratio +4 over +2
def: "Ratio of 4+ spectra count over 2+ spectra count in all MS2" [PSI:QC]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_value_type xsd\:float ! The allowed value-type for this CV term
relationship: has_value_concept UO:0000191 ! fraction
synonym: "IS-3C"  RELATED []

What is the QC term's unit?

count fractions

Value type

MS:4000003 ! single value

Describe any additional information.

No response

[mwalzer]

@bittremieux @cbielow @dtabb73 @julianu:

• do we need an additional id-based version?
• do we want to squash the three values into a tuple?

[bittremieux]

All of these can be easily derived from MS:4000063 (MS2 known precursor charges fractions), so do we really need these separate terms?

MS:4000063 is also much more general because it's a table, and thus can be trivially extended with different charge states (for example, top-down data with much higher charge states). Whereas having terms that explicit define the charges, or even as an n-tuple, is much more constrained.

[mwalzer]

@bittremieux raised the right issues which I all agree with. What I would love to do though is to keep old (and published) metrics in context. Unfortunately, we didn't consider those when defining MS:4000063 (only some extensions we developed in an excel sheet way back in 2018). So should we amend the latter's term entry? How would that look?

[mwalzer]

First I think the QuaMeter terms should be NARROW synonyms (not EXACT as the metric contains not only one old metric but multiple). Although these are not listed in the QuaMeter manuscript or supplementary material, only in the manual pdf which comes with the software I guess, I think a stable reference from PMID is preferable as dbxref.
For the metrics legacy, we could add an explanation in a comment.

[Term]
id: MS: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]
synonym: "MS2-PrecZ-1" NARROW [PMID:22697456]
synonym: "MS2-PrecZ-2" NARROW [PMID:22697456]
synonym: "MS2-PrecZ-3" NARROW [PMID:22697456]
synonym: "MS2-PrecZ-4" NARROW [PMID:22697456]
synonym: "MS2-PrecZ-5" NARROW [PMID:22697456]
synonym: "MS2-PrecZ-more" NARROW [PMID:22697456]
synonym: "IS-3A"  RELATED [PMID:19837981]
synonym: "IS-3B"  RELATED [PMID:19837981]
synonym: "IS-3C"  RELATED [PMID:19837981]
comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2.
is_a: MS:4000005 ! table
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000020 ! ion source metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_column: MS:1000041 ! charge state
relationship: has_column: UO:0000191 ! fraction

[mwalzer]

At any rate, this fits well into the argument that I think we should make:
Softwares may come and go,

but open formats make the results of such software much longer lived.
And even if mzQC is no primary data format, to have a legacy layer that allows you to
i. interpret 'old' QC analyses (or convert them to 'new' for integration purposes, say for meta-analyses)
ii. compare with new QC analyses (benchmarking new methods etc.)
are IMO big arguments for mzQC

[bittremieux]

Yes, I think linking the NIST metrics to this term is a better solution. The MS2-PrecZ-X metrics are defined in the QuaMeter ID-free publication (metric definitions are in the supplementary information), so I suggest using PMID:24494671 as dbxref there instead. The RELATED synonyms for the NIST metrics is perfect.