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

[sulezinha <not...@gi...>]

In that case, for example, is XLMOD-specificity for DSS going to be _(K,S,T,Y,Protein N-term M)&(K,S,T,Y,Protein N-term M)_?

Because, I received one data set from a group and this group also provided me their FASTA file. 
I ran pLink and Kojak to identify spectra for DSS linking. 

Their fasta file has one protein sequence that starts with G. 
Both algorithm gave identification with considering Protein N-term G as linkable, for the validated list.

That fasta file has another protein sequence that starts with M. 
These two algorithms identified both M and also the second residue after M for this protein as linkable, as well.

So, if the specificity checks for DSS considers _Protein N-term M _but _Protein N-term_, such identifications will fail and mzIdentML is not going to consider this identification then, is it? 
Is it right what I understood? What do you mean exactly by saying "So we could define a cross-linker that links Protein-N-terminal methionine or KSTY anywhere else to anything as"?



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