Friday, July 20, 2018

EuPA Practical Proteomics DAY 4 (LATE!!) INFORMATICS DAY!!!

For the first time in my career -- I was the Session Chair!! For INFORMATICS!! PERFECT!

Oh. Umm.. Ugh...I REALLY WANT TO TELL YOU ABOUT Sebastian Dorl's talk. I'm not sure I can. It isn't public and it isn't published. Okay -- soon.

Lecture 2: Robert Van Ling -- 2 meter long nanoLC.columns that run 100 bar backpressure. Actually -- let me write this again. 200 centimeter columns -- 100 bar backpressure.

Not joking. A big thing here was that C-18 UHPLC beads in long columns, while functional, is kind of 1990s technology. The real separation scientists have moved on.  PharmaFluidics uses pillars on chips rather than beads in capillary tubes and can achieve separations that make what I'm doing seem very...

...they're not the cheapest things in the world, but maybe if you see the data for what monolithic columns can do in nanoflow (he showed 1,000 injections with no peak shifts) you might not mind.

Lecture 3: Boris Macek

I might have went all fanboy on this one. Dr. Macek IS the first author on LOCKMASS injection and the first paper I know of using topdown MS3 -- and is responsible for most of what I studied in school regarding phospho signaling in B. subtilis (yeah -- we knew other stuff before those papers, but the model organism for gram+ bacteria -- he was in Mann's lab when they characterized that stuff.)   His lab has done a ton of work recently on elucidating other model organisms that we thought we knew -- and there is something huge in press right now (Science Signaling, I think). Boris gave a VERY clear and very good lecture on studying PTMs with mass spectrometry. There was some high level cutting edge stuff here -- and not every student here had been doing this for years. GREAT TALK.


MSAmanda 2.0 and CharmeRT and Elutator and all the other free nodes that you can use in PD without paying anything. These are all feature prominently here. She also talked about the EuBiC winter school. I'll post details when I have them.

Worth noting -- I'm using CharmeRT A LOT. I think they underestimate what you get from second search. I'm commonly getting 2x PSMs when I turn it on. Yeah -- it could be faster. It's hard to search every MS1 peak in your isolation window -- especially when you've got Fusion #14 and you can't isolate less than 2.5 Th (don't ask me -- apparently it can't be fixed)

Lecture 5 and Workshop: Sebastian Virreia Winter -- Sebastian talked about EASI-TAG (the paper is out now) and did an awesome hands on workshop with MaxQuant and showed us some of what is coming in MaxQuant live -- amazing new instrument methods for the Q Exactive HF-X!   While he was here we made him show us some BoxCar methods and data and answer some tough questions from the audience on MaxQuant data processing.

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