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

[Lutz F. <not...@gi...>]

Ok first point - terminal cross-links: One reason I did not want to put Protein-C/N-term in is that basically for all non-natural cross-linkers that distinction depends on when you add the cross-linker - e.g. before or after digest. So it's not an inherent feature of the cross-linker. Admittedly there are probably not many experiments that would do cross-linking after a digest...

But I guess we could change to Protein N-Term to keep in line with uniprot. Does anybody else here have an opinion on it?

So we could define a cross-linker that links Protein-N-terminal methionine or KSTY anywhere else  to anything as : 
(N-Term M,K,S,T,Y)&(*)
or
(Protein N-Term M,K,S,T,Y)&(*)
For the uniprot-version.
What ever cross-linker that would be...

Point two : Yes the ampersand means that the cross-linker can link anything from the left side with anything  on the right side but not within the left or the right. E.g. for EDC:
(K,S,T,Y,n-term)&(E,D,c-term)
means 
it links K or S or T or Y or the n-terminal to either E or D or the C-terminal but not K to S or E to D.
Compared to BS3:
(K,S,T,Y,N-term)&(K,S,T,Y,N-term)
- can link any K,S,T,Y or N-Term to any K,S,T,Y or N-Term
e.g K to K, K to S, K to T, K to Y, K to N-term, S to K, S to S ... 

I am not sure if I understand your example right but would that not have been already covered?
Linking K to Y only:
(K)&(Y)
Linking K to K or Y
(K)&(K,Y)
Linking K to K
(K)&(K)



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