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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Crosslink user controlled protein N-terminal as a modification site #2312

Open lonelu opened 1 year ago

lonelu commented 1 year ago

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 commented 1 year ago

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