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HUPO-PSI mass spectrometry CV
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QC metrics to track (absolute) delta ppm errors for identification #241

Closed mwalzer closed 5 months ago

mwalzer commented 7 months ago

What is the QC term's name?

absolute dppm sigma and absolute dppm mean

Briefly describe the QC term.

The terms track the mean and sigma of the error distributions of spectra identification. For the proposed definition, please see below.

What is the QC term's unit?

No response

Value type

MS:4000003 ! single value

Describe any additional information.

Here are drafts for the terms' entries

[Term]
id: MS:4000xxx
name: absolute dppm mean
def: "From the distribution of absolute values of observed mass accuracies (MS:4000072) in ppm of identified spectra within the run after user defined acceptance criteria are applied, the mean" [PSI:MS]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_concept STATO:0000401 ! sample mean
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

[Term]
id: MS:4000xxx
name: absolute dppm sigma
def: "From the distribution of absolute values of observed mass accuracies (MS:4000072) in ppm of identified spectra within the run after user defined acceptance criteria are applied, the sigma value" [PSI:MS]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_concept STATO:0000237 ! standard deviation
relationship: has_units UO:0000169 ! parts per million
relationship: has_value_concept MS:1000014 ! accuracy
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
cbielow commented 6 months ago

I would slightly change them to

[Term]
id: MS:4000xxx
name: mean of precursor ppm deviation
def: "The mean of observed precursor mass accuracies (MS:4000072) in ppm of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_concept STATO:0000401 ! sample mean
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

[Term]
id: MS:4000xxx
name: std of precursor ppm deviation
def: "The standard deviation of observed precursor mass accuracies (MS:4000072) in ppm of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000008 ! ID based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_concept STATO:0000237 ! standard deviation
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

i.e. keep the sign (no abs), since this is free but useful information.