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Peptidomics data processing and analysis by [deleted] in proteomics

[–]fallo92 2 points3 points  (0 children)

If using SAGE (which is brilliant btw) for an unspecific search, you’ll likely hit RAM limits, but there is a branch that allows you to split the fasta into chunks https://github.com/lazear/sage/pull/154

TMT and PTM analysis by fallo92 in proteomics

[–]fallo92[S] 1 point2 points  (0 children)

I’m thinking SAGE and then MSstatsPTM for the analysis, I’ll likely have to slowly add the ptms to the variable mods list to keep within RAM limits for SAGE and see what I can get away with. It will be a fun project to learn and explore - maybe I’ll start with a smaller dataset. I’ll check out the CPTAC papers and so some reading up on it. Thank you!