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

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

In the case of labelled linkers we do not have a mapping of one peptide chain to one spectrum, both the light and heavy spectrum are used to identify both peptides and contain fragments from both peptides.

Using light-alpha, light-beta, heavy-alpha, heavy-beta SIItems would store the information, but is very redundant and each SIItem now means something different for each experimental setup (normal identification / labelled CLs / cleavable CLs). Since that is the case anyway, we could actually reduce redundancy by only writing half of the combinations, e.g. light-alpha and heavy-beta. It would look exactly like a case of cleavable cross-linkers and all the information would be there, a reader would just have to know what class of cross-linker was used to interpret the data correctly.
But I guess we can live with the redundancy anyway.

Still for both CL cases, cleavable and labelled, the precise mapping of each spectrumID in the list to the corresponding expMassToCharge and charge values of the SIItems is lost. This mapping was obvious before CLs were introduced as far as I can tell (since all SIItems under one SIResult referenced the same one spectrum) and I think it would be good to keep it obvious somehow.
Now an unordered list of IDs has to be mapped to an unordered list of expMassToCharge values.

I guess this could be solved by specifying a certain order in each case, e.g. by ascending expMassToCharge in the ID list and in the order of SIItems (either in the context of one specific "cross-link identification item", or in the context of the whole SIResult block).

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