[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Consensus Spectra (labelled and unlabelled cross-linkers) (#19)

[Eugen N. <not...@gi...>]

Current state:
As it is specified now, the two spectra are referenced as an unordered list of spectrum IDs in the SpectrumIdentificationResult.
For some use cases it could be useful to know which of these is the light and which is the heavy spectrum, since they are not necessarily treated equally.
Also the experimentalMassToCharge and chargeState from only one spectrum are written in SpectrumIdentificationItem and it is not specified from which, while it would actually be useful to have both.
For cleavable cross-linkers it was agreed to use different values here for the two SpectrumIdentificationItems corresponding to the MS3 spectra each containing one peptide.
Although the information is there, it is still unclear here, which spectrum ID in the list belongs to which SpectrumIdentificationItem, MassToCharge and chargeState, since one only has the IDs and the other only the other values.
But I think MassToCharge and chargeState values for each spectrum ID should be in the file and somehow linked to their corresponding IDs.

Proposals:
Could we add CV terms to make that more clear?
One easy thing to do would be to specify, that in the case of labelled cross-linkers there is a fixed order for the spectrumIDs, e.g. the first ID must be the unlabelled or light spectrum, or more generally the IDs should be in ascending order of label weight or MassToCharge.
That would already add a crucial bit of information.
Or we could add lists of MassToCharge and chargeState values, that must have the same order as the list of IDs.
I would like to avoid specific CV terms for light and heavy spectra and come up with something general enough to cover labelled and cleavable cross-linkers. 

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https://github.com/HUPO-PSI/mzIdentML/issues/19