Thursday, September 25, 2014

MsAmanda for the searching of coeluting peptides!

Okay, so do you see a theme developing?  Everybody is working on co-eluting peptides right now.  Or...maybe I'm paying a lot of attention to it for secret reasons all my own.

I am very excited about the potential of MixGF and the DeMix algorithms I discussed earlier.  Realistically, however, I get about 2-3 hours/week, if I'm lucky, to work on my own research these days.  This typically amounts to 1 or 2 phone calls with collaborators where we divvy up the "to-do" list, I load up a bunch of runs on my new Proteome Destroyer and I remotely send spreadsheets from whatever hotel I'm staying in that week.  (Surprisingly, this is somehow productive.  This is looking like it might be the most prolific year of my career...though that really isn't saying much....) Realistically, there really isn't much time for me to learn new workflows right now.

That is why this is so exciting for me.  I already have MSAmanda.  I already know how to run MSAmanda.  I've done tons and tons of benchmarking with MSAmanda and I know that I can trust the data that comes out of it (no offense to the other new algorithms!  both workflows published well and come from groups I respect a lot, but I have hard data from this one that i generated myself)

Viktoria presented this poster this week at APRS and the results look great.  It is still in its early stages, but there may be a nice, easy solution for chimeric spectra just around the corner for those of us that are addicted to a certain commercial proteomics package.

And the results look pretty great.  This is an extraction of 0.1ug of HeLa digest from QE data using a 3Da isolation window.

Even with a relatively small window, the second search leads to a big boost in PSMs.

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