Okay....want a reason for a whole lot of those unmatched spectra in your human LC-MS/MS runs?
Check out this paper in Nature Biotechnology from Hagen Tilgner et al.,! In this study they used transcriptomics (in this case, long-read RNA-Seq) and looked at different tissues. Turns out there is splicing everywhere!
Splicing? Well, that's when DNA that should be over here making this protein -->
ends up hanging out
with DNA
that's way over here -->
(who says blogging can't be hi-tech!)
and you end up with a transcript (and therefore a protein!) that, from a purely DNA perspective, TOTALLY SHOULDN'T EXIST AT ALL! (Definitely isn't in Uniprot/Swissprot...!)
Sorry for shouting. I'm excited. This paper focused on mouse brains and found a whole ton of these things. In regards to some of the recent discoveries in brain proteins, maybe this isn't that big of a deal, but tissue-wise, holy cow....should we be using a different FASTA file if we are profiling liver tissue than if we are doing tissue that came from brain samples? Sure looks like it! Heck, if nothing else, its another great argument for PROTEOGENOMICS! (Yeah, I'm shouting again!)
Worth a read. Sorry it isn't open access. And sorry if this is jumbled. Its kind of late and I've been excited about one thing or another for the last couple of days.
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