QC sample metrics

[mwalzer]

What is the QC term's name?

QC sample metrics

Briefly describe the QC term.

Hi there :wave: with a mini package of QC metrics and related terms request! I thought it made best sense to open one issue for a small number of term requests that are inextricably linked on a conceptual level: QC by measuring known-content samples aka QC samples. (A concise description you can find in the Methods here )

New term suggestion summary list:

• observed mass accuracy
• QC sample metric
• QC2 sample metric
• QC2 sample mass accuracies
• QC2 sample intensities

Best practice for the QC samples is to run them continuously interspersed to monitor the analytical performance (incl. software analysis) over time. Two main aspects of performance are the detection and 'abundance' measurement of the known contents. For the former, we'd need the observed accuracy of detection, for the latter we already have a number of measures :relieved:

name: observed mass accuracy
def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected peptide spectrum."

I did not find any existing compatible description of delta ppm in the CV, so I hope this can be generally useful.

There are at least two established known-content sample types (see publication link above) and I think it'd be good to introduce them as a category and then also include a bit of detail.

name: QC sample metric
def: A QC metric based on a QC sample of known content.
is_a: MS:4000007 ! QC metric category

and the sample-type 'QC2' which is the commonly used name, unfortunately. I think it would be best to stick to it and explain in definition and the is_a inheritance.

name: QC2 sample metric
def: "A QC metric based on the results of a QC2 sample measurement (see Pichler et al. (pmid:23088386) Chiva et al. (pmid:29324744) for details on QC2 sample design). Expected peptides from sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'" [PSI:QC]
is_a: MS:4000xxx ! QC sample metric

Lastly, the proper metrics would be like this:

name: QC2 sample mass accuracies
def: "Observed mass accuracies for the peptides of a QC2 sample measurement. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:QC]
is_a: MS:4000xxx ! QC2 sample metric
is_a: MS:4000008 ! ID based metric
is_a: MS:4000005 ! table
relationship: has_column: MS:1003169 ! proforma peptidoform sequence
relationship: has_column: MS:4000xxx ! Observed mass accuracy

and

name: QC2 sample intensities
def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:QC]
is_a: MS:4000xxx ! QC2 sample metric
is_a: MS:4000008 ! ID based metric
is_a: MS:4000005 ! table
relationship: has_column: MS:1003169 ! proforma peptidoform sequence
relationship: has_optional_column MS:1001858 ! XIC area
relationship: has_optional_column MS:1001859 ! normalized XIC area
relationship: has_optional_column MS:1001844 ! MS1 feature area
relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity
relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity

What is the QC term's unit?

*

Value type

MS:4000005 ! table

Describe any additional information.

Here the collection of new terms in obo mockup (sans the id accessions):

[Term]
id: MS:4000xxx
name: observed mass accuracy
def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected peptide spectrum." [PSI:MS]
relationship: has_value_concept MS:1000014 ! accuracy
relationship: has_units UO:0000169 ! parts per million

[Term]
id: MS:4000xxx
name: "QC sample metric." [PSI:MS]
def: A QC metric based on a QC sample of known content.
is_a: MS:4000007 ! QC metric category

[Term]
id: MS:4000xxx
name: QC2 sample metric
def: "A QC metric based on the results of a QC2 sample measurement (see Pichler et al. (pmid:23088386) Chiva et al. (pmid:29324744) for details on QC2 sample design). Expected peptides from sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'" [PSI:MS]
is_a: MS:4000xxx ! QC sample metric

[Term]
id: MS:4000xxx
name: QC2 sample mass accuracies
def: "Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS]
is_a: MS:4000xxx ! QC2 sample metric
is_a: MS:4000008 ! ID based metric
is_a: MS:4000005 ! table
relationship: has_column: MS:1003169 ! proforma peptidoform sequence
relationship: has_column: MS:4000xxx ! Observed mass accuracy

[Term]
id: MS:4000xxx
name: QC2 sample intensities
def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS]
is_a: MS:4000xxx ! QC2 sample metric
is_a: MS:4000008 ! ID based metric
is_a: MS:4000005 ! table
relationship: has_column: MS:1003169 ! proforma peptidoform sequence
relationship: has_optional_column MS:1001858 ! XIC area
relationship: has_optional_column MS:1001859 ! normalized XIC area
relationship: has_optional_column MS:1001844 ! MS1 feature area
relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity
relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity

[mwalzer]

And if you want me to open a PR after discussion, that's fine, just let me know.

[mobiusklein]

If you can, please open a PR with appropriate ID numbers filled in for this and #111 then.