1) This may look like a violation of the long standing blog rule "if you can't blog anything nice, get a less weird hobby, you extremely strange person who types too fast".
2) I literally may have no idea what I'm doing. I'm just an aging ape in cool old shoes who types really fast.
3) I could 100% be doing this wrong
4) I think XCORR and, SeQuest, in general is kinda dumb.
5) The dataset that I'm currently interested in and using this to test might be suboptimal for comparisons (more below)
Subtitle for this post:
INFERNYS: A node made specifically for making some old guys in proteomics mad? (For real, y'all are gonna get some phone calls.
Oh yeah. INFERNYS is a new node in Proteome Discoverer(TM/R) that came out in the new release. It's the first addition of deep learning to this software package that I probably literally use every day of my life. I rambled about some of the new stuff a few days ago here.
Let's start with the great stuff first!!!
1) I've ran several comparisons of the exact same workflow with and without INFERNYS. We're currently working on deepening or understanding of the human liver (it's super complex and surprisingly under studied) so that's my focus right now.
2) In EVERY comparison when I've added INFERNYS so far, I've gotten more of everything. I've gotten more Peptide Spectral Matches (PSMs) and that has translated to more peptide groups, and to a higher percentage coverage of the proteins in the liver. This has translated to, but much more modest, increase in the unique protein and protein group identifications. More PSMS is good!
The stuff I think will make some people mad.
In my hands (again, I could be legit dumb, yo) the PSMs have had terrible XCORRs.
What's an XCORR? It is a historically important metric for spectral match quality. Dr. Will Fondrie is a smart guy who does proteomic informatics stuff, and he did a remarkable job of capturing the idea on his blog here.