Not to rub it in if you couldn't attend, but the International Proteome Discoverer User's meeting kicked ass. It was easily the most valuable learning experience that I had personally this year. I'm working on hunting down the talks now and I'll provide links to them as soon as I can obtain them. I want to provide an overview of what happened.
Talk 1) Bernard Delanghe went over basic PD functions, then plowed head on into the power of using multiple search engines, both in parallel and in series for digging into your data. I recently touched on the extreme results the BRIMS has had when using multiple engines in parallel. A big emphasis of Bernard's talk was the enormous value in processing speed and identification rates that occur by using multiple engines in series. I've touched on that a little, but expect a number of experiments from me to follow.
Talk 2) Marshall Bern described Byonic, a software that I've previously beamed about, in particular how Byonic can be used effectively for glycopeptide analysis. He also described the Byonic node that will soon be an purchasable upgrade for PD. Expect an explosion of analyses and announcements and data from me when this launches.
Talk 3) Viktoria Dorfer gave a talk on the power of her creation, MSAmanda, in the scoring of high resolution MS/MS spectra. An interesting note for proteomics software teams out there should be the fact that the creator of this fantastic new tool is still working on her Ph.D. A highlight of her talk, for me was a comparison of the number of peptides that MSAmanda found for ETD spectra when compared to the other search engines. This should be an extremely interesting observation for the Orbitrap Fusion teams out there, as the incredible speed of the Orbitrap (and the ease of obtaining high ETD signal) allows high resolution ETD spectra to be an efficient experimental design. Expect experiments and data from me to follow.
Talk 4) Not to take anything away from the other great speakers, but this was Oliver Serang's day. In an incredibly amusing and informative talk, Oliver walked us through a new way of thinking about assigning protein identity to identified PSMs. These new functions are to be available in PD 2.0. I am currently awaiting library access to the papers that Oliver has written so far on this and other topics. When these arrive, I'll spend some time trying to figure these out. In the meantime, I highly recommend a Google Scholar search on his name.
Talk 5) Automated spectral library generation node for Proteome Discoverer! My good friend Maryann Vogelsang presented a node in development at BRIMS that will take your PD data and automatically generate spectral libraries, which can then be directly imported into Pinpoint!!!!! Remember my entry that spectral libraries are about to blow up? They are, especially with the thousands of terabytes of high resolution/high quality Orbitrap data out there that we can easily convert into high res spectral libraries? Exciting!!!!
Talk 6) David Perlman gave a talk that I regretfully had to miss due to an important meeting. Fortunately, I did get to meet him finally later that evening. In case you aren't familiar, Dr. Perlman is the Director of the Proteomics and mass spectrometry core facility at Princeton University. You can find out more about his facility here.
Talk 7) Proteome Discoverer 2.0! Bernard showed it in action and took audience suggestions. It is currently in alpha testing (and open on this PC I'm typing on, haha!) and it looks great. Tons of new features are coming, but I'll go into them later.
Q/A session: This was a great session. I wrote down a large number of questions and many of them will be the feature of upcoming blog entries.
In sum, it was a great session. I'm eagerly looking forward to next year's. Expect much greater press coverage when the date is set for #4 and seriously think about showing up. It is a valuable experience.
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