Y'all are always coming up with so much cool stuff! Peptide Shaker isn't exactly new, but its mostly new to me. Heard of it, but I never went out of my way to check it out. It is real cool. Not only do you get a nice (and interesting themed) GUI, but there is a big reason that you might want to check it out now if you haven't before.
Peptide Shaker supports MS-GF+ now. What's that? It is a program written a few years ago that took a good hard swing at something people ask about a lot. Advanced peptide statistics. Namely, using p values to accurately gauge the efficiency of peptide identifications. In the introduction paper for MS-GF+, the authors showed that on virtually every MS and fragmentation mode, their algorithm produced more and better IDs than Mascot running Percolator. Now, thats interesting all on its own, but I've never seen a link to download this magic code before. Now, its supported by this nice GUI so now these claims can be scrutinized by me (when I finish the next previous 10 things on my list) or by you!
You can get Peptide Shaker here. And read more about MS-GF+ here.
Thanks @compomics for the link to this!
PS, ignore the "Low memory warning" above. My poor personal desktop is about to burst into flames. Replacement is eminent....
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