Highlights from the Proteome Discoverer User's meeting

What a blast.  I'm so glad I cut my vacation a little short and came by this meeting.  As you can imagine, all we talked about was PD 2.0.  One of the coolest things about PD 2.0 in my mind is that it is much friendlier to developers than previous versions.  Only a few people had the ability to both write new algorithms AND get them to work in PD 1.4.  PD 2.0 changes things around.

My favorite quote from the meeting came from Oliver Kohlbacher's talk about label free proteomics:  "If you have crappy chromatography, you shouldn't try to fix it with bioinformatics."

Here is a more organized breakdown.

Talk 1:  ptmRS and MsAmanda in PD 2.0.  I've mentioned ptmRS and how awesome it is a few times in this blog since Karl let me have it quite a while ago.  I'm a big fan and I'm excited to see everyone using it!  It works even better in PD 2.0.  The highlight of this talk was Viktoria Dorfer describing her implementation of "second search" in MSAmanda.  Chimeric spectra identification in PD?  Its not ready yet due to integration issues, but it works and the results look extremely promising.

Talk 2:  Oliver Kohlbacher describing how great OpenMS is at label free quan AND showing the nodes he is developing for PD.  They won't come in the PD 2.0 install pack, but will be downloadable and installable from the OpenMS website.  Advanced label free quan in PD?!?  Sign me up!

Talk 3: Christopher LoBner (my keyboard doesn't seem to have the funny letter that looks like a super B) from Proteome Sciences described my favorite reagent, the TMT 10plex and its history, development and processing

Talk 4: Jeroen de Keijzer showed his research and the application of PD to solving biological problems in pathogenic bacteria.  I love the bioinformatics, but this was a great reminder that, in the end, we want to use all this cool new stuff to solve a biological problem.

The afternoon was the PD 2.0 team, Michaela and Kai walking us through PD 2.0.  Release is currently slated for January and we're going to work hard to make sure resources are available to help you get going with it out of the box.  Best news of the day?  If you still have PD maintenance (PD full licenses come with 3 years of this), then the upgrade from PD 1.4 to PD 2.0 is free!  If your maintenance has expired you will need to purchase a maintenance deal from your sales rep to upgrade (PD 1.4 and PD 2.0 will exist on the same PC.)

(Day 2) Talk 5:  Lennart Martens took us through a new FDR calculator.  It won't be in the initial PD 2.0 release.  It uses a lot of data reduction steps and is close to as good as percolator, but fast!  Excited to see that one in action.

Talk 6: Richard LeDuc from Northwestern showed us the awesome capabilities of the Prosight nodes for PD 2.0.  Top down in proteome discoverer?  Yup!  And it works.  Release of these nodes should shortly follow the PD 2.0 release.  I just got them myself so I'll be able to check them out and let you guys know how its going soon.

The rest of the time was spent talking about how to do specific experiments in PD 2.0, mostly advanced questions and troubleshooting.

Great meeting with over 65 top-notch scientists in attendance.  My only regret is that I didn't get to meet everyone!  I'm already looking forward to number 5!