It's over!! Ben's ASMS 2016 roundup part 1 -- Software!

Yeah...what a week. Around how excited I am to see old friends and cool new science, I always underestimate what a freaking marathon ASMS is.

For those of you that didn't make it, or just want to read my rambling notes on the conference, here I am rapidly typing in the picturesque San Antonio Airport.

Impression 1:  Software was king!

From the first look at ASMS, this wasn't a big year for hardware. There are some cool things definitely, but there were some major software things!!!

 In no particular order.

1) Fusion software 2.1 unveil.  Whats it do? It adds a ton of new features to the Fusion or Fusion Lumos. Okay. While the QE HF is my current favorite instrument (I'm a biologist, after all), I seriously dig this path that the manufacturers (whatever their name is..) has taken with this instrument. If you invested in the Fusion or Fusion Lumos, every 6 months or so you effectively get an awesome instrument upgrade. With the hardware configuration and the 2 powerful processors onboard the Fusion all sorts of things are possible. Someone just needs to think up an awesome experiment and BOOM!  Its a free new instrument upgrade for everybody.

Fusion 2.1 has some new tweaks, but the highlights are canned methods for crosslinking analysis and standard triggered TMT quan. Doesn't sound super impressive, but hear me out

If you've been doing this proteomics thing for any length of time, I bet you've taken a swing at crosslinking some proteins and then figuring out which ones are partying which other ones.  And chances are you've been seriously frustrated. I've failed at it. Friends WAY smarter than me have failed at it.  So...Thermo created a new crosslinking reagaent, added a really amazingly complex workflow for the Fusion sofware for working with that reagent, and ...

...Proteome Discoverer 2.2 (which I also got to see in action for real!!) automatically processes the data!!!!  P.S. You can also use your crosslinking reagent of choice, but the new one seems pretty bad ass.  Oh, all this work was done with a big collaboration with the Heck lab!

Standard triggered TMT quan (I forget what they're calling it)  You know that Bruno Domon method where they spike in a standard for the peptides you're looking for at high concentrations and the QE starts doing PRMs for the light endogenous peptide when it sees it?  (P.S. There were, of course, more very nice and frustrating posters on this method and it still seems like you have to join some secret fraternity on the solstice in the cellar of the Kirchberg campus -- for added effect I suggest you picture Rachmaninoff playing in the background).

In this method, they are using a TMT0 tag to label the mix of standard peptides. These are spiked into the mixture of your TMT10(!!!) labeled samples(!!!). See where this is going? It gets better. When the Fusion or Lumos sees the TMT0 tagged peptide standard it then starts looking for the TMT10 labeled peptides. In what Dr. Gygi described, they then use a huge ion injection time so they can get ridiculous levels of sensitivity. Its TMT so you don't need a bunch of measurements across the peak. Get that sensitivity!  It does a bunch of other smart things including verifying that the tag really is true with a super fast survey scan or something...

What I care about? The methods are canned. Load this template and get going!  Ridiculous levels of sensitivity on 10 samples at once. The way they're validating it is ridiculous. No offense to the instrument manufacturer, but the three times they described it I was having trouble keeping my eyes open. Then Gygi got on stage and it was like...oh...wait?..what?...WOW!!!  Its like the super secret triggered QE PRM method but multiplexed, better controlled and multiplexed!

2) Proteome Discoverer 2.2 (serious, folks, its real, hopefully beta testing starts soon) -featuring:
a) Peak alignment and label free quan nodes
b) The aforementioned crosslinking nodes
c) Isn't that enough!  Holy cow!  I'd just take label free quan.

3) Prosight 4.0 -Faster better stronger top-down (at lease one non-Kelleher group has it, so betas might be available if the commercial release isn't ready)

4) CrapOme 2.0! (Was shown in poster, didn't appear to be up on the website.

6) New Byonic (on the way, I guess, no real time to stop by the booth...)

5) [Told you. No particular order]. Nuts. I've got 5 cool open source software things in my notebook, but none of them have papers up or their web interfaces active. Okay. Cool stuff on the way for --
protein network analysis, visualization, full core lab unsupervised QC systems

9) DIA Probe - Quality control for those of you who are legally allowed to run and process data independent acquisition experiments!  Its an add-on for the world's most popular targeted quantification program

For now, that ends the software stuff. There's definitely more I forgot, but the WiFi on this plane is super slow so I'm gonna make a Part 2 (and probably edit this a bunch later!)