Non Canonical N-linked Glycosylation Motifs

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite

http://fragpipe.nesvilab.org

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Non Canonical N-linked Glycosylation Motifs #1588

Open ABB-808 opened 4 months ago

ABB-808 commented 4 months ago

Greetings,

I am not sure if this is currently possible, but it would be great to allow MSFragger-Glyco (N-linked workflows) to assign glycans to peptides with a motif that is not N-X-S/T. It would be great to also search non-canonical sites such as N-X-C and N-X-V, etc. Is there a way to do this with the current build?

Thanks!

dpolasky commented 4 months ago

Hi, There is not a way to search a multi-amino acid motif other than N-X-S/T currently, but you can search any single amino acid using the labile mode (e.g., any N). Customized motifs is something I'd like to support though - I will plan to add it sometime soon (though probably not in time for our upcoming release) and can share a version with you when it's ready.

Best, Dan