Check out the above (click to expand) - Yes, that is the bizarre nomenclature used by our friends at SpectroNaut (PG.normal word you'd expect AND the funnest-to-parse [ mf'ing brackets ] AND a space after the second bracket ] at the beginning of each sample name)!
And in the "EG.PrecursorID" which roughly possibly translates to "peptide sequence with the addition of an underscore at the beginning of the peptide sequence"
THERE ARE A BUNCH OF PTMS!!
Wait! What? No one wants to talk about this, but
YOU CAN'T IDENTIFY PTM MODIFIED PEPTIDES WITH LIBRARY FREE SEARCHES! Sure, there are buttons there, but you won't find shit.
Until now?
SpectroNaut 20 has a new pulldown thing called
"PTM Probing!" If this reminds you of an episode of South Park you might be old.
You can find it here and it's pre-populated with a whole bunch of PTMs.
Now...in my first check....I seem to have found only PTMs on keratins, but there are probably a lot of PTMs on keratins. I dunno.
Are they real? I also don't know yet, but it's absolutely a step in the right direction.
Unless none of them are real and it's a pile of silliness, obviously.
So...what we should do is take some cancer cells and dump something on it that causes a crapload of PTMs. Then we should run some files DDA and run them with FragPipe and MetaMorpheus and then run some injections with DIA here and see how much they agree and disagree. And then we should call it something based on a late 1980s early 1990s actor based wrestling thing.
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