Whoa! I totally stumbled on this.
I still love the Morpheus search engine the Badgers came up with. Simple, faaast, to the point.
Turns out, its still developing out there.
Case in point? This cool new paper from David Gemperline et al., in this they show how they can add spectral counting functions to the software. You can actually get the program here.
I like the font and layout, so here is a screenshot.
Curious, I went back to PubMed to see if I'd missed anything else awesome that you cool people have done: Answer? Of course I have.
S.Zhang et al., developed a paired ion strategy for Morpheus and...wait...this deserves its own line.
Michael R. Shortread et al., wait...seriously?...used Morpheus to search only for curated PTMs, thus vastly reducing the overhead search space and massively improved their FDR. Wow!
Its almost like the ProsightPC flat-file (contains your annotated PTMs) search methodology, but for bottom-up! Why aren't I doing this?
Only a 10% increase in your search space to add every known human post translational modification? This is brilliant! Improve your matches, improve your FDR, speed up your search?
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