Crosslink user controlled protein N-terminal as a modification site

[lonelu]

So far, protein Nter is included as a modification site. In theory, it should be, as Nter ammonium group (NH3+) is a good reactive spot.
The function related is here:
MetaMorpheus/EngineLayer/CrosslinkSearch
/CrosslinkSpectralMatch.cs. -> GetPossibleCrosslinkerModSites

[ACE-Manager]

Hi Lei(?)...
thanks for taking care of my issue. Just to make clear what my problem is ... In other CL programs like MeroX you have to specifically add the N-term as a site. This is done when you setup the cross linker. You have to add a wavy bracket ({= N-term; }= Cterm). In MM I do not know how to set this up. I do not know what the respective symbol is. Or is the N-term search done automatically, anyway?

With regard to the path your answer (MetaMorpheus/EngineLayer/CrosslinkSearch
/CrosslinkSpectralMatch.cs. -> GetPossibleCrosslinkerModSites) ... where do I find this? My MM installation does not have this path ... I am using MM 1.0.3.

Thanks for your help.
Sincerely yours
Farnusch

[atroel01]

Just bumping this to ask if this has been addressed?
I have a DSSO crosslink that is almost certainly N-term to N-term (seen with XlinkX and MSAnnika) but not picked up by MM, just curious if N-term can be added as a Xlink site (as well as c-term)