generating new XML libraries from search results? - feature request

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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generating new XML libraries from search results? - feature request #2007

Open Dmorgen opened 3 years ago

Dmorgen commented 3 years ago

Hi Guys,

is it possible to generate new XML databases from search results? i'd be especially interested in "beefing up" the uniprot XMLs with new modification sites (especially for O-glyco).

Cheers, David.

trishorts commented 3 years ago

Hi David,

In Search/Advanced Options/Post-Search Analysis you want to check the box to write the extra databases. Then you want the "Protein Pruned" which only contains proteins with PTMs observed @ 1% FDR. Still need to be a bit careful as those PTMs might not necessarily be localized. Especially important if you want to submit to UniProt.

Dmorgen commented 3 years ago

Thanks!