One ASMS 2020 TakeAway -- GPUs are finally coming!

I'm woefully behind on ASMS stuff. 2020 (the year itself) has been a little tiring.

One takeaway that I've got for this year is that we're finally seeing Graphics Processing Units in Proteomics. I think I've rambled about this here before, but I can't find it. Anyway, in today's computer stuff we basically have 2 kinds of processors

Central Processing Units (CPUs) -- these are the stickers on your computer "i7" "XEON" or, more commonly now "Ryzen" and, if you're really lucky, "Threadripper" (I am not this lucky yet)

CPUs have a small number of cores but each core has access to tons of resources.

Graphics Processing Units (GPUs) have TONS of cores, but each core is capable of doing only very small things, like controlling a few pixels.

A lot of genomics has even gotten to the point where it has advanced even further

to Application Specific Integrated Circuits (ASICs) these things are even dumber than GPUs -- an ASIC is designed to do only one job. And when you focus processors to just one task they can be really really good at it. The first ASICs for genomics were advertising 100x increases in speed over GPU alignments. We'll get there one day! 

Most of us are using CPUs and doing just fine with it. Someone I talked to at ASMS had his PC running for about a month solid on one analysis for his talk....indicating that sometimes we do need more power....but most of the time we're okay. 

Where do you need GPUs in proteomics? 

1) Deep learning (PROSIT, etc.,) 

2) Processing absurdly large files (liket those 40GB per run TIMSTOF files, maybe?) 

Worth noting, John Yates did a talk for Bruker (you can find it in the clunky Horsebrutality suite thing they have set up) and it's one of the best educational talks about the evolution of proteomics data processing I've ever seen. 100% recommended. The Yates lab has been using GPUs for data processing for several years through the commercial program IP2....which... I think my search bar is broken, I know there is stuff here about that....

3) Other programs are out there, like ANN-Solo GPU, and G-MSR. This isn't new, but -- okay -- this is big -- 

4)  You know that Phase Constraint thing that we keep hearing about (and finally saw in a very very limited form on the Exploris 480 and Eclipse instruments last year)? 

You know why it isn't running on everything all the time? It's super computationally difficult. You're pushing your resources on the Exploris hard to even do the phase constraint in the narrow window around your TMT tags (what, 10 Amu?) 

I strongly recommend you check out 

MP 127 High dynamic range proteome analysis with BoxCar DIA and super-resolution Orbitrap mass spectrometry

-- because these jokers set up some GPUs (TITANs!! The crazy expensive server ones) so they could phase constraint across entire mass windows. The speed and resolution increase is so much that they can do BoxCarDIA using EvoSep separations and dig way deeper into the plasma proteome. 

They process the data in SpectroNaut, which I'm going to guess now does something with the BoxCars, cause I swear it did look like it didn't look at the BoxCars MS1s at all, but I bet they fixed that! 

ASMS Statement And Characteristic Rambling

There is some great -- unfreaking believable -- amazing science streaming as the ASMS reboot and ... just when the world seemed like it couldn't get more chaotic ....protests about excessive use of force by the police were met by even more excessive use of force by police.... during a global pandemic ...and it's hard to pay attention to even the best science in the world.

This blog isn't right when it's serious so I'll throw in the true story about the one time that I met Richard Yost. We're all missing our ASMS friends right now. One of mine is about 5 foot tall and hilarious -- and she might be able to lift a small car. One year she'd loaded up on cool vendor swag like cannabis themed light up gear, including a brightly flashing cowboy hat that I think had a pot leaf and Shimadzu logo on it. She was carrying me piggy back style and running really fast. 100% her idea. And I got to say something characteristically intelligent like "Holy shit. You're Richard Yost." And he said something like "It looks like you guys are having a fun conference!" And we were gone. As I said, she was going really fast.

2020 has been a tough year. I can not wait to see everyone in Philly next year!!

And....

....stay strong, y'all.

Want to help? Here is a great article on how.

Needing inspiration on what ASMS Talks to Watch? Here is the FeMS list!

ASMS can be (i.e. IS TOTALLY) overwhelming even the best and easiest years. Even if you've been strategizing all morning on what talks to catch you probably have a hole or two in your schedule. Want to try a different sort of list?

Check out the FeMS list here! It's a live document so I'm sure there will be updates coming!

IT'S ASMS 2020!!!

We're 97 minutes from my favorite holiday! As appalled and furious as I am about what is happening in my country right now, I'm selfishly going to step away from thinking about it and tune in as much as possible to see what the best scientists in the world are doing with earth's most accurate measurement technologies.

My blog is having some glitches, this morning, however.... but that isn't important. What IS important is that I see you at ASMS!  Hit this button to go there! 

....Appropriate music for today....

Logging into ASMS Reboot!

Confused about how you get into ASMS Reboot?

Me too, but Dr. Ashwood has us covered!

Wait. Okay. I think if you click on the Tweet image above it will take you directly there. Wait. I'll make a button!

HIT THE BUTTON BELOW TO GO TO THE ASMS 2020 REBOOT!

Great COVID-19 webinar and Mass Spec diagnostic clinical trials underway in Europe!!

My quick overview

#1 MALDI-TOF with a low(er) resolution bench top instrument -- maybe 90 minutes of sample prep to inactivate the virus and spot gets you to 3 minutes on per spot.

Beyond COVID-19 -- Dr. Iles made it clear that what they're doing with this stupid virus would work really well for other viruses!


#2 -- is the paper that Wiley Proteomics accidentally paywalled and I was a jerk about (they fixed it)

Actual paper link here!

I'm going to mix up what I'm taking from the second talk in the YouTube thing above and from the actual paper, but I'm too excited to try getting it straight.

Which is a really nice study that shows 20min DIA and 8 min LCMS (QQQ) using acetone precipitation and 4 hour tryptic digestion.

Correlation with the gold standard WHO approved qPCR assay? r(squared) = 0.887 !!!

They can get to 180 samples/day and point out that in Ghent alone, they have 20 comparable instruments that could be used to help relieve testing backlogs.

Okay -- THEN -- they bring in 80 people to help! And they optimize, optimize, optimize and spike in QconCAT as internal standards and then even push the data processing with machine learning -- sped up the digest (to 15 minutes?!?!?) and push the accuracy even higher.

That great talk ends with this beautiful and inspirational slide -- maybe -- just maybe -- we should stop making fun of how old and slow PCR is and how stupid antibodies are and work together to get to the number of tests that we need to?

....I'll...try....

COVID-19 MS Coalition -- And tomorrow's London's Proteomics Discussion Group (5/29/2020)

I know I mentioned this cool thing before -- but there is also a paper now!

Hell yes. If anything good has come out of this global pandemic it has been highlighting how underpowered traditional diagnostics -- and clinical medicine truly is. Time to kick some insurance companies and hospital administrators to the side and let accurate instruments like mass specs start filling bench spaces (once we confront some of our remaining demons). What better way to do it than with tons of people working on it?

Also -- tomorrow is 2 more great talks on COVID-19 proteomics from the London Proteomics Discussion Group.

Tomorrow we'll finally see the BioTyper-type MALDI-TOF analysis of SARS-CoV-2 infected materials that we've been hearing about in the media. And we get to see more targeted peptide diagnostics by LC-MRM!

You can register here!  And then get your rest, cause it's ASMS for real!!!

Wiley wins! We knew someone would paywall a COVID-19 paper!

EDIT -- It was just a mistake. I'm an impatient jerk. You can read the paper at the link below and read my interpretation of this great work here. 

Go Wiley Go! Get that money! 

I'm sure this is an honest mistake, and I'm just drawing attention to it so they can fix it and I can read this paper. 

Edit -- 944PM EST -- it's fixed! I'll put a real note about the paper in here when I have time. 

Holy shit. Is it ASMS already?!?!?

Monday is June 1st!  Time to start our favorite impossibly exhausting week of the entire year -- sorta... Things are already starting....LIKE...?

Skyline User Meeting was today (5/27) and tomorrow (5/28)!!

You can see what happened today or see the great talks tomorrow by going here (register for tomorrow -- we'll see MSAmanda in Skyline and other cool stuff).

From today's stuff (which was totally great, except for my 5 minutes of not understanding how Windows 10 works still....how can it be this bad...?..where are my thumbnails....?) -- my recommendation:

If you're a core lab -- definitely check out Roman Sakson's "Skyline in core environment" -- what he does with locked down layouts for sharing data is stuff I've never seen before and I hope other people will start doing all the time.

Lipids and ion mobility and hunting clinical biomarkers round out the first day. If that's your jam, it's there.

Big shoutout to whoever just typed "Go Hokies" -- I saw it before the moderators dismissed it.

User meetings for vendors are in progress or start tomorrow!?!?!

Okay -- so -- I need more time to digest all this -- BUT THERE IS A BUNCH OF NEW HARDWARE!!

There are 2 new Exploris instruments (the 120 and the 240)

Mandatory --

The best I can tell, the 240 is an Exploris 480 with very few limitations (max resolution 240k) and a new paint job.

AND -- ACQUIREX added!   You can check it out here.

The 120 appears to be an Exploris focused on small molecules. I'll read more later, but it's up on this here website.

Something to pay a lot of attention to? The world's 3rd worst acronym -- uHTPPP -- Say it 3 times fast -- and then -- consider what Ultra High Throughput Plasma Proteome Profiling might do for you. And then say it 3 times fast again. Outloud, please.

Other vendors have things as well. I'm really interested in this Acoustic Ejection thing. I think SCIEX talked about it last year, but you couldn't actually buy it yet.  The QTOF still isn't ready, but the Triple Quad is. I've got some budgetary numbers and it's about the same price as a stripped down Orbitrap Eclipse -- but...can your triple quad run 2,000 samples today?  Its out of my price range, obviously, but if the sensitivity specs aren't made up....it's massively impressive. There is an extremely vague video and a clock that is ticking down to something? here!

For less vague information, check out this preprint from January.

Bruker isn't just sitting around, but it's a lot more applications focused this year for them. You can see a lineup of their user meeting talks here.

Talks I will try not to miss?

P.....R.....M.....at 100Hz(!?!?!?!?!?!??!)
ZipChip integration! Okay -- this big dumb thing is fast enough for what I keep trying to use a ZipChip for! Fingers crossed.