Saturday, December 12, 2015

proBAMsuite! Great new proteogenomics tools!

Man, I love a software package with a catchy title. And I love a free software package that has a ton of promise!  proBAMsuite has all of these things!

Is a set of R tools that are meant to help you integrate the data from your next gen sequencing files with your LC-MS/MS spectra. This is an overview of the steps involved.

Of course, the process isn't trivial. The RNAseq data needs to be lined up and QC'ed and so do the MS/MS spectra and the PSMs and the Peptide matches. When we're looking at millions of measurements the number of false discoveries has to go up, just mathematically, nevermind the fact that not every MS/MS spectra or next gen read is as good as the others.

In order to control the false discoveries, the capabilities are in place to control the FDR at the PSM and peptide level. Even cooler, maybe, is this idea:  The decoy matches are kept and allowed to be mapped against the total genomics data, so you can get a good idea of the FDR at the complete, reassembled level!  Total system FDR.

Why would we go to all this trouble?

1) How bout more data about your protein than you'd maybe even want? Check out the suite's sweet output!

And, of course, more explanations for what those weird MS/MS spectra are!

Open access pre-release of paper here!

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