Viewing MM results in Scaffold

[duselis]

I'm trying to view MM results (the individual mzID files) in Scaffold Q+S. The individual_ProteinGroup.tsv MM output has 2k protein groups with q-values of 0. Scaffold reported only 3-4 proteins with different statistics (e.g. the individual_ProteinGroup.tsv reported 24 PSMs for keratin, Scaffold shows a total of 3.)

Its completely likely the problem is Scaffold or something I'm doing within Scaffold. Issue #915 showed MM and Scaffold do work together. Has this been tried since 2018? Are there any tips or hints that you think could help me?

I appreciate any help!

[trishorts]

i don't really have any idea off the top of my head. I'll see what I can find out.