Y'all know I'm biased. I love what Proteome Discoverer has become. It was a voyage for me. From unfiltered hatred for version 1.0 to grudgingly using 1.2 to really liking everything after 1.2 a whole lot. With 2.0 I think we've easily got the most powerful commercial platform in the world. Sure, it could use some statistics and better label free algorithms, but I hear lots of work is being done to that effect.
But if you were going to do one thing to make PD better today, what would that be?
Well, the IMP thinks that one way to do it would be to make it FREE!
Wait. What? I know! Confused? Me too! But this is what it says:
PD has always had some nodes that anyone could use. The ability to convert Thermo .RAW files to MGFs, for example. In PD 2.x users get the ability to use many of the Consensus and filtering nodes without a license (or with an expired demo key). But what about the free nodes that groups like IMP, OpenMS and Protein Metrics have made? Apparently they can work in that expired demo environment.
So Karl Mechtler and his group decided to fill in the gaps. They made nodes that will allow you to run full workflows in PD 2.x.
Oh...and they also threw in a node that does quantitative statistics based on the Limma R software package developed that was originally developed for transcriptomics.
As a win for everybody? They also resurrect the MS2 Spectrum processor!!
I'll throw out a healthy disclaimer here. As with any of these nodes that aren't released by the manufacturer, you can't get these and then bug the software manufacturer if you have problems with them. Fortunately, IMP has set up a GoogleGroup and help documents!!
Enough of my ramblings? You just want to run a single .EXE file and get a bunch of cool new nodes and the ability to run a new version of PD on any computer?
Go to this link: http://ms.imp.ac.at/?goto=pdfree