Sometimes elegant solutions are in order.
Other times you've got to put on your cowboy hat and check every possible AMINO ACID where a PTM could co-localize in a gigantic peptide matrix to determine where the heck that modification has ended up. And...maybe that's how you have to do it to accurately determine your FDR.
I don't mean to insult the authors of this cool new paper -- at all -- quite the opposite.
I have loads of respect for the fancy pants statistics stuff that I don't fully understand. However -- pSITE cuts most of that out of the way by just checking everything and in their hands it looks superior for global de novo identification of modifications and their localizations than our classic methods like Ascore and phosphoRS.
You'll have to check out the math for yourself if you're interested. One of the big surprises for me in this paper was in the supplemental info. With all the amino acid specific calculation, I'd expected the search space for pSITE to reflect the actual amino acid length -- for example, a 12 amino acid peptide would have a search space ^12 larger than NovoR or Peaks.
I don't know how this is possible, but pSITE somehow (on the same server configuration) isn't slower than these other algorithms. It is somehow faster than some of them....
pSITE is free to download and you can get it here.
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