Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-link site specificity might need refinement (#13)

[Timo S. <not...@gi...>]

Ok thanks for the comment. 

Maybe it's not really relevant at this point but I give some information how it is done in unimod.

If we decide to be consistent with the naming scheme in unimod, we could use:
"Protein N-term" or "Protein C-term" for protein terminal cross-linker
"N-term" or "C-term" for peptide terminal cross-linker (probably less relevant as you pointed out)
(or the empty string for non-terminal ones)
and then add the residue (if it is site specific cross-linker):

What I currently did not understand (sorry I did not make it to the calls) how the pairs are specified. Is it possible to say (and does it make sense?), e.g. the cross-linker can link K and Y, but not K and K or Y and Y? How would this definition differ from a cross-linker that can link e.g. K and K, too?

If we need to express something like this (sorry again if this has already been discussed) is this already possible using the encoding in the column?

I am asking, because as I understand it, the & currently stands for the cross-product of the two sets (=all combinations pairs between the left side and the right side). 

If we want to support the general case this could be easily extended.

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