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HUPO-PSI / psi-ms-CV

HUPO-PSI mass spectrometry CV
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Probably duplicate CV Terms for ETciD and EThcD #285

Open caetera opened 2 weeks ago

caetera commented 2 weeks ago

Describe the question or discussion

Using the current PSI-MS CV, ETci(hc)D fragmentation can be represented in two seemingly equivalent ways. For example, for denoting ETciD it is possible to use MS:1003182, or a combination of MS:1000598 (ETD) and MS:1002679 (supplementary CID).

Is there any use case for supplementary CID/HCD outside ETciD/EThcD? Is there any "correct" way to denote ETciD/EThcD and, if so, shouldn't the "wrong" way be marked as obsolete?

For further context, please, see the following discussions: https://github.com/OpenMS/OpenMS/issues/7499 https://github.com/compomics/ThermoRawFileParser/issues/182

edeutsch commented 1 week ago

After some discussion on the PSI-MS call, we decide to move "combined dissociation method" so it is not a child of "dissociation method", which is not the best, but automatically disallows use of these two combined terms in mzML.

mobiusklein commented 1 week ago

To add some more detail here from the discussion:

  1. The combined term names a "thing" that is used in the field and that is therefore something we want to keep in the controlled vocabulary.
  2. The combined term doesn't make it obvious to the reader how to interpret collision energies for the two parts, and implies that dissociation method combinations require explicit terms.

There isn't a way for the mzML validator to express a "may not" rule in the format it uses, in-so-far as I can tell, hence the re-parenting.

caetera commented 5 days ago

Thanks for looking into it. To confirm, two separate terms (for example, ETD + supplementary CID) should be used in mzML, while the combined terms (ETciD) are meant to be used for other applications, for example, SDRF.

mobiusklein commented 5 days ago

Correct.