Morpheus: A good, fast, and free search engine.

Wow!  What a busy couple of weeks.  I've completely fallen behind, but you'll soon see that there were some really good reasons for it (I hope...)
I'm somewhat back now with something really cool.  I didn't discover this on my own.  I've been working at the AMAZING proteomics core facility at the University of Wisconsin School of Pharmacy this week and they brought this engine to my attention.  Side note, if you are looking to work or study with a premier collection of just about every top end mass spectrometer, consider moving to beautiful (and cold!!!) Madison, WI.  You name it and they have it here.  If I told you what they had, almost everyone would be jealous.

Back on track:  The little icon above is more than just a way to flirt with a lawsuit from Fox Studios.  It is also a very nice and rapid no-frills search engine that you can get for nothing at all.  My gun toting friend here was described in last month's JPR paper from Wenger and Coon.

It is downloadable, in about 6 seconds on a hotel wireless network.  It installs almost as quickly, and it runs through your massive proteomics files in only slightly more time.  Adding a checkmark in the right place gives you "FDR on the fly" with no real measurable increase in your processing time.

I need to do some more digging.  Mostly because I am skeptical of anything that is free, and I am extremely skeptical of things that are free and seem great, but this is a quick look at the protein level of a single run of a nuclear extract processed against the Uniprot Human database with Morpheus and Sequest HT in PD.

Not too shabby for a piece of standalone software, right?  Want more good news?  It ran this sample at least as fast as Sequest HT.  I do want to mention that in order to save time and to keep everything as even as possible, we ran Sequest with the target decoy search.  The 30% ID boost I'm getting used to seeing with Percolator these days would have shifted this Venn, but it also would have added considerably to the processing time.