Monday, September 26, 2016

GAPP -- Proteogenomics and PTMs for microorganisms! statue is in DC...and I'm pretty sure you aren't allowed to climb on it. But it is my favorite image that popped up when I went for "on the shoulders of giants" cause this is what GAPP reminds me of.  Watch for the park police, kid!

So...what if you looked at the open source toolkit landscape for proteomics (and had programming capabilities!)? Would it make sense to completely build your own tools right now? I totally wouldn't!  There is so much cool stuff out there, I'd just piggyback some existing framework and add what I needed.

And this is EXACTLY what GAPP is doing.

You can read about it (in press and currently open at MCP!) here.

Check out what is inside the Zip file if you get it from SourceForge here!

I was a little alarmed by how long it took Windows Defender to scan through this file (it was clean, but always scan whatever you download!) but it made sense when I opened it.

GAPP fills the gaps all our favorite tools leave in the Microbial proteogenomics workflow. They couldn't find anything that would make their database -- search their proteomics data (extensively! look at all those engines) and process their PTM data, so they made a Java interface that would by using a bunch of tools that are already out there -- awesome and can be networked together.

This is the general scheme:

To validate that the complicated thing all works -- they downloaded a very nice and extensive H.pylori dataset from PRIDE (this one from Muller et al.,) and went to work.

Worth noting:
 There are some pre-requisites necessary to install this. You must have Java 1.6 or later and you must have Perl already installed to use the Java interface. I can't tell for sure, but I'm going to suspect that you are going to need the MSFileReader separately installed as well, as its a pre-requisite for the ProteoWizard.

I really like this study. We don't need to reinvent the wheel every time!  Sometimes we can just tweak the awesome stuff that is already out there!

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