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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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PTM-Shephard outputs #1728

Open lbeer272 opened 2 months ago

lbeer272 commented 2 months ago

Hi,

Is there an updated table column guide for ptm shephard outputs. I found the guides for global.profile.tsv and global.diagmine.tsv, but I am looking for more information about the diagnosticProfile.txt and diagnosticIons.tsv tables. I am wondering the best way to use these files to calculate enrichment of Oxonium ion-containing MS2 spectra vs total MS2 spectra for glyco searches. Thank you.

dpolasky commented 2 months ago

Hi @lbeer272,

There is not a guide currently for the other diagnostic tables - I'll add one soon. Calculating the proportion of oxonium ion-containing PSMs reported can be done easily in the diagnosticIons.tsv table, by counting (or filtering) the number of rows with oxonium ion(s) above a given intensity threshold. You can also filter based on the delta mass column to look at only glyco or non-glycopeptides as well. However, these calculations won't include spectra that were not matched to a peptide, only the final PSMs. The proportion of oxonium ions in all spectra (including unmatched spectra) is not directly accessible from our output tables.

Best, Dan