I'm currently processing the 16 files I ran overnight. All human stuff. All pretty well characterized. As always I find myself wondering things like "what the hell are all these MS/MS spectra that don't match anything!?!?!"
Peptide match on the Q Exactive allowed them to fragment, so they clearly have peptide-like isotopic distributions. They have charges from +2 to +7, so I should be able to sequence them effectively. It is a cancer cell line so I could do some tricks like using the XMan database to find the known mutations and that always pops up some new peptides. I can run the file through Byonic and find PTMs and some novel mutations, but I'm still looking at a bunch of spectra that look nice, but don't match anything.
A while back I was blown away when I saw a talk describing the well-known (not to me...) facts of how systematic apoptosis cleavage events can be. Even in cell culture some of these cells are going to be dead or dying or whatever, so could that be some of it?
To make the biology even more complicated, you can drop your proteins of interest into the new MitoFates program. MitoFates will then search your proteins for known cleavage recognition sites and generate you a new FASTA. So if programmed Mitochondial degradation is occurring you'll be able to identify the peptides that are caused by those events.
You can read about MitoFates (in press at MCP) here.
And you can just go ahead and dump your proteins in here!
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