[CV] Request for new CV entries

[rolivella]

Dear all,

Julian told me that I can request new CV entries here. Ideally we would like to have all the metrics that we are taking into account in the QCloud (see Table 1 of our paper http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189209). By order of priority, we would like to have the Peak Area, Mass accuracy, Retention Time, Median Injection Time for MS2, Chromatographic Resolution, Peak Capacity and Total Ion Current.

Thank you!

Roger

[bittremieux]

Probably there are a few terms in the MS CV that can be reused?

• MS:1001844: MS1 feature area
• MS:1000014: accuracy (m/z or ppm)
• MS:1000894: retention time
• MS:1000927: ion injection time
• MS:1000285: total ion current

These seem to be pretty direct matches, I'm not sure about the two remaining metrics.

[rolivella]

Do you mean that I should use this MS CVs or are you going to add them into the QC CVs?

Besides, I'm not 100% sure that these MS CVs are exactly the same parameters we are using. For instance, we're using the median IT of identified peptides in MS1 and MS2 (NIST codes MS1-1 and MS2-1). Is "MS:1000927: ion injection time" referring to exactly the same? Also instead of the "MS:1000285: total ion current" we are indeed computing the sum of all TICs instead of the TIC for one particular spectrum...

[julianu]

I will review them and think about, whether it is a good idea to use the entries of the MS CV. For some it might work, but it might also be cleaner to make new terms with a "QC metric of" to the name or something.

[rolivella]

OK thank you Julian. I also want to let you know that we have a forked version of your main qc-cv.obo document with the QC parameters we are working on in the new version of the QCloud. We also created a lc-cv.obo (for Liquid Cromatographers) and nc-cv.obo (for non conformities reasons). We don't want to replace at all your work, for us your documents are the main reference, but we need something more operational to do not stop our work. If you want I can invite you to the Github where we have this files and you can have a look. As you wish, just let me know.

[julianu]

Hej roger, Apologies for the long silence, we are "cleaning" the in-work-CV right now and during this I could add your proposed terms as well. For some of them it is not clear to me, whether the actual values are averages or whether you report the values for each identified spectrum/peptide/feature, though. This is for the terms "Peak Area", "Mass Accuracy" and "Retention Time Drift": should they be tuples or single values? Or (what we also have by now) corresponding lists, where one list e.g. gives feature IDs and the other one the value?

All Other terms seem to be single values, right?

[rolivella]

Hi there! Thanks for your answer. In fact my previous message became old because we are using like a fork of your qcML doc beacause we need it for our QCloud v2 we are implementing. You can see it at:

https://github.com/rolivella/cv/blob/master/qc-cv.obo

I'll give you access to it. Do you think that we can actually create a fork of your doc and eventually merge them in the future?

[mwalzer]

So a branch would always be an option, of course. We have the 'old' CV in one file and the restructured in another (qcML-development/cv/v0_0_11/). I think it would be best if you'd still in parallel open issues for each term you add (so we can follow up). I just created a label for QCloud-CV terms, you should add to the issue to let us know there is no immediate action item to be followed up on because you changed it in the branch already. @julianu what do you think?

[julianu]

I think requesting to add them into the CV is the best option for now, yes. If you already branched it, we can of course merge your additions back into the current version as well.

[mwalzer]

As discussed lc.obo requested to go to PSI-MS CV, let's have a look at the remainder

[mwalzer]

Maybe tackle the nc.obo next?

[rolivella]

As discussed with Mathias, I attach the work we've done with lc (liquid cromatography) and nc (non-conformities) controlled vocabulary:

nc-cv.txt lc-cv.txt

[rolivella]

I copy&paste first the lc-cv:

[Term] id: LC:0000001 name: Proxeon Biosystems instrument model def: "Proxeon Biosystems instrument model." is_a: MS:1000031 ! instrument model

[Term] LC:0000002 name: EASY-nLC™ II LC 110 def: "Proxeon Biosystems Easy-nLC II LC110." is_a: LC:0000001 ! Proxeon Biosystems instrument model

[Term] LC:0000003 name: EASY-nLC™ 1000 LC 120 def: "Proxeon Biosystems Easy-nLC 1000 LC120." is_a: LC:0000001 ! Proxeon Biosystems instrument model

[Term] LC:0000004 name: Eksigent instrument model def: "Eksigent instrument model." is_a: MS:1000031 ! instrument model

[Term] LC:0000005 name: Eksigent autosampler def: "Eksigent autosampler." is_a: LC:0000004 ! Eksigent instrument model

[Term] LC:0000006 name: Eksigent NanoLC AS-2 autosampler def: "Eksigent NanoLC AS-2 autosampler." is_a: is_a: LC:0000005 ! Eksigent autosampler

[Term] LC:0000007 name: Eksigent Nano Ultra LC 1D plus system def: "Eksigent Nano Ultra LC 1D plus system" is_a: LC:0000004 ! Eksigent instrument model

[rolivella]

An then the nc-cv:

[Term] id: NC:0000001 name: Non conformity def: "Instrument indicia that are associated with a performance out of the limits of acceptance." is_a: MS:1000547 ! Object attribute

[Term] id: NC:0000002 name: Non conformity reason def: "Cause that genrates a non conformity." is_a: MS:1000547 ! Object attribute

[Term] id: NC:0000003 name: Decrease of MS1 signal def: "The intensity of the signal in MS1 is lower than expected" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000004 name: Sample carry over def: "Part of the analyte present in a sample appears to be presest in the next or following samples." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal & part_of NC:0000011 The intensity of the signal in MS1 fluctuates & part_of NC 0000019 ! No signal in MS1 & part_of NC 0000020 ! Bad chromatography

[Term] id: NC:0000005 name: Air bubble in QC sample vial def: "Air bubbles are present in the QC sample vial." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal

[Term] id: NC:0000006 name: Bad QC sample def: "QC sample is not correct." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal

[Term] id: NC:0000007 name: Empty solvents def: "Bottles from LC solvents are empty." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal & part_of NC 0000019 ! No signal in MS1

[Term] id: NC:0000008 name: Air in the chromatographic path def: "Air bubbles in the chromatographic path." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal & part of NC:0000020 ! Bad chromatography

[Term] id: NC:0000009 name: Deteriorated column def: "Chromatographic column is deteriorated." is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal & part_of NC 0000014 ! Loss of MS1 signal in the central part of the chromatogram & part_of NC 0000020 ! Bad chromatography

[Term] id: NC:0000010 name: Column overpressure def: "The column pressure is above the set limits" is_a: NC:0000002 ! Non conformity reason part_of NC:0000003 ! Loss of MS1 signal

[Term] id: NC:0000011 name: MS1 signal fluctuation def: "The intensity of the signal in MS1 is sometimes lower than expected and sometimes inside the thresholds of acceptance." is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000012 name: Dirty column emitter def: "The emitter of the column is dirty" is_a: NC:0000002 ! Non conformity reason part_of NC:0000011 The intensity of the signal in MS1 fluctuates & part_of NC 0000019 ! No signal in MS1

[Term] id: NC:0000013 name: Dirty ion transfer tube def: "The ion transfer tube is dirty" is_a: NC:0000002 ! Non conformity reason part_of NC:0000011 The intensity of the signal in MS1 fluctuates and part_of NC 0000019 ! No signal in MS1

[Term] id: NC:0000014 name: Loss of MS1 signal in the central part of the chromatogram def: "The intensity of the signal in MS1 for complex samples is lower than expected only in the central part of the chromatogram" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000015 name: Dirty ion path def: "The ion path is dirty" is_a: NC:0000002 ! Non conformity reason part_of NC:0000014 Loss of MS1 signal in the central part of the chromatogram

[Term] id: NC:0000016 name: Sample injection step does not finish def: "Sample injection process get stacked in the loading sample step" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000017 name: Sample too concentrated def: "The amount of injected sample is too high" is_a: NC:0000002 ! Non conformity reason part_of NC:0000016 Sample injection step does not finish

[Term] id: NC:0000018 name: Dirty sample def: "Sample is contaminated with non peptidic compounds" is_a: NC:0000002 ! Non conformity reason part_of NC:0000016 Sample injection step does not finish

[Term] id: NC:0000019 name: No signal in MS1 def: "There is no signal in MS1" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000020 name: Bad chromatography def: "The shape, intensity or retention times of the chromatographic profile do not correspond with the expected" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000021 name: Leak in the chromatographic system def: "There is a leak of solvent in the chromatographic system" is_a: NC:0000002 ! Non conformity reason part_of NC 0000020 ! Bad chromatography

[Term] id: NC:0000022 name: Uncalibrated masses def: "The mass accuracy of the measured peptides is out of specifications" is_a: NC:0000001 ! Non conformity

[Term] id: NC:0000023 name: Communication error def: "The acquisition computer cannot connect with the instrument" is_a: NC:0000001 ! Non conformity

[rsalek]

Can I make a suggestion to make it more generic, hence fitting metabolomics too? e.g. [Term] id: NC:0000018 name: Dirty sample def: "Sample is contaminated with undesirable compounds" is_a: NC:0000002 ! Non conformity reason part_of NC:0000016 Sample injection step does not finish. <---- Not sure it is related to? Just will creates a poor quality spectrum!

[Term] id: NC:0000022 name: Uncalibrated masses def: "The mass accuracy of the measured molecules is out of specifications" is_a: NC:0000001 ! Non conformity

[mwalzer]

:+1:

[rsalek]

Do we have CV entries for, internal standard -different types-, system suitability and other types of QC present in a run?

[julianu]

I have urgently to go through the CV, but as far as I remember we don't have them yet. But feel free to ask for them (maybe with some small sample), and best in a new issue, which we will tag as CV request.