Tuesday, November 10, 2015

PRIDE Inspector -- Meta-analyze all the things!

Apparently, I've downloaded several versions of the PRIDE inspector, because I have many .ZIP files in my Downloads folder. For some reason, though, I don't guess I've ever Unblocked the Zip file, unzipped it, and then ran it...or I forgot that I did...

A brand new paper in MCP reminded me of it, and I'm assuming that this means that the newest version I just downloaded is the best one anyway (available here!)

Part of the title of the new paper, btw, is:...moving toward a universal visualization tool for proteomics data standard formats...cool, right?

Some people save their data for archiving in some format or the other like: mzml, mxml, mzxml and xzmlzxmllxmzmlllllllzzMxxmz (just to name a few). These have all been very valiant attempts (except that last one. that guy was just being a jerk) to keep our data in a format that would standardize things, so we have all the important data in one place and we can compare instrument -to - instrument.

Problem is, there have been several of these. And it can be daunting. Say, I'm dosing these cells with a super cool drug and I want to do proteomics on it and I see that another lab previously dosed mice with that drug it might not be easy at all to compare that data.

See where I'm heading?

The PRIDE Inspector reads basically all of these data formats (except that last one. the inventor has been shunned by the field this morning). You get a nice graphical output of the spectra and if the data is processed you can check the results at every level.  Perhaps even as nice, if the study is saved in the PRIDE database you can link directly to the dataset.  Just want to rapidly meta-analyze everything in the PRIDE repository? This might be your window!

Now, notice the fact that the title includes "moving toward a universal". I'm sure that means there is more to be done here. But it looks like a albert heck of a nice start.

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