Thursday, September 8, 2016

OpenMS 2.0!!!

Does OpenMS officially have everything now?

Ben, what are your rambling about now?  Oh...just the evolution of OpenMS into something that can do everything, as described in this brand new paper!

OpenMS can already do:
-Peptide ID
-Peptide Quan
-Integration into Proteome Discoverer via the OpenMS PD Community nodes
-Add DNA/RNA binding (to protein) detection capabilities to both OpenMS and to PD
-Allow people to add their own source code and then use the OpenMS downstream workflows (like FDR) to link to whatever upstream source search engines you are using; I think this is how these guys controlled this awesome inference study.
and now?

-INTEGRATION WITH COMPOUND DISCOVERER?  I love HRAM metabolomics and it consumes most of my increasingly rare instrument time these days. As much as I may rant about how easy metabolomics is with an Orbitrap after a beer or two, it is a field that still has its own innate challenges -- challenges that we honestly may not fully understand yet. Flexible software platforms that can address these are going to be critical if metabolomics is every really going to blow up the way we keep thinking its going to. I'm not surprised that the OpenMS team has the capability to add software to Compound Discoverer....considering the cool stuff they've developed for Proteome Discoverer, but...

...I had no idea they'd stated making nodes....and I don't know what the MetaboProfiler is or what it does, but it painlessly installed into my copy of CD 2.0 can't wait to give it a try!!!!

-PROTEOGENOMICS!?!? This study points out a case study where it does, as well as...

-Degradomics!  Have you tried realistically quantifying the degradation of proteins at a global level? No? Well...It. is. not. fun. The tools have to get better before we can track more than a small group in and someone is using OpenMS for that.

-Integration into KNIME and R for collaboration and downstream processing, respectively

-And a bunch of other stuff like Galaxy integration(?!?!), but this list is long enough now.

Does this sound like a sales pitch for OpenMS? It probably does, but this team of talented people are quietly making amazing tools for our community and going to great pains to make these tools as accessible as possible. And I don't mind being loud about it. (There are bunch of new tutorial videos for getting started now!)

You can easily find OpenMS and their spiffy new website with a Google search or directly link here.

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