Friday, May 30, 2014

Proteome Discoverer as a multivendor platform?

It is clear that I'm biased.  I love Proteome Discoverer.  I didn't always.  When PD 1.0 came out, I was like "No thanks! I'll keep using Bioworks."  I evaluated PD 1.1, but it didn't win me over until PD 1.2.  I think 1.4 is on-par with any shotgun proteomics package ever.

But, what if you don't have a Thermo mass spec?  Do you miss out on all the fun?  Not at all!

PD can support virtually any instrument.  It has had this capability almost all along, but I have never had the chance to verify it.  A friend of mine (who will remain nameless right now) recently left the Thermo only lab her worked in for his postdoc and is now running a facility that has Orbitraps AND a bunch of Q-TOFs.

Where to start?  Well, PD can't directly accept RAW files from other vendors, so you need to use distiller or ProteoWizard to convert the data to a compatible file type.  For simplicity, we chose MGF.

You'll also probably need to tell PD what instrument you are using in your method template.

Thats what all these settings in the Spectrum Selector that we never use are for.  Check out the blue box.  TOFMS!  Just go through those settings and match them to your instrument and save the template.  Boom!  Easy, right?

You'll need to set your mass tolerances according to what you normally would when running a search.  But outside from that, PD will process your data just the same as described in all the tutorial videos on the right side of this screen and you can process all of your data from all of your instruments on one (very good!) software package.  One less variable to worry about!


  1. Unfortunately, PD only supports MS2 reporter ion quantification (no MS-level quant) as the event detector node requires raw files...

  2. Thanks for your comment! Hmmm, I'll have to investigate this. The XML converted base files should contain all the original data. We should be able to extract the MS1 data out of that. Can we communicate privately? I'd love to try working with one of your RAW files to see if I could come up with a solution.

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