This is a piece of software I've been dying to talk about for the last 6 months or so. Legally, however, I've just had to enjoy it myself and keep my mouth shut.
I know, there is a ton of software out there. Why would I want to learn another package? If you are interested in characterizing 1 protein, I've never seen anything that even comes close to PepFinder.
Highlights?
-You don't need an MS/MS spectra to make an ID. MS1 for IDs, MS2 for sequence confirmation
-It can find your PTMs
-PepFinder can do error tolerant searches (find PTMs you didn't know about)
-It can find amino acid substitutions (ranks them in order of likelihood in your organism of interest, internally, and uses that data to score the sequence output.
You'll hear all about it at ASMS and you can read about it at the Thermo Omics Portal.
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