Sunday, August 17, 2014

Proteome Discoverer 2.0 teaser!

Look what I got this morning!  It is looking really really good too.  I got it to do some PC benchmarking today while hanging out with a sick dog.

I'll show the benchmarking stuff later.  I need to sort out some variables.  While I was doing it, I noticed a file was taking a whole lot longer than it did on PD 1.4 (or on earlier PD 2.0 alpha copies).

Check out what our friends in Bremen got working!!!  That one file did take longer than normal, but it was because PD was doing a bunch of other things:

If you've spent any time on the job queue on any version of Proteome Discoverer, chances are I just blew your mind a little.  PD is running multiple files at once!!!!  Now, it remains to be determined if those two matching 81% are because PD detected that I was reprocessing the same Fusion files just with different names, but the fact that it is intelligently allocating time is bound to make more than just me happy. I need to do some digging around.  I don't have all that many Fusion files and I'm running them cause they are the hardest to work with.  If we can do them fast, I'm not worried about the QE or Elite files.  Easy.  This RAW file has 16k unique peptides in it!

I'm running on a crazy fast PC (more details on that later, too!) but it knocked out 4 Fusion runs in an hour and 17 minutes.  I was experimenting with different peptide and protein FDRs and it just tore right through them.  By comparison, I just saw a big fancy dual CPU Xeon choke on HeLa files in PD 1.4 for hours.  Better hardware.  Better software.  And all the sudden these huge datasets everyone is generating don't seem all that scary!

BTW, wait till you see how PD 2.0 handles complex experiments! Thermo is about to release the best proteomics software we've ever seen.


  1. where it is possible to download the alpha/beta version for testing it?

  2. Do you know when the final version will be released?

  3. Who have the guide of PD2.0 ? Could you kindly send to me? My email is Thx ahead!

  4. PD 2.0 is now out.

    1. Yup! And you can watch my tutorial videos on how to use it by clicking the link over there --->