Making the possible impossible: Small window DIA TMTPro!

Why does this look like I took the screenshot with a potato? Meh? 

Okay, so this has been attempted before, but this is probably the first time it's really worked. 

Here is the question: Why wouldn't you just do isobaric tagging (TMT) with little tiny DIA windows? We know from things like TomaHaq that you can do targeted TMT quan and it can work well. So why wouldn't little DIA windows be better than data dependent acquisition for TMT? The biggest problem with TMT stuff (aside from coisolation interference) is stochastic sampling. If you miss fragmenting peptide A in run number 2 you don't just lose that peptide in one sample - you can lose that peptide in 18 samples! 

If you did little DIA windows across the whole mass range? Problem solved. 

New problem?

It's super duper slow. Man, I'm on a roll. I don't think that's even moving? Meh. 

But with these new fast TOFs could you do it? 

It doesn't look bad at all. Loads of optimization stuff here. Because if you fill for longer then you get more signal but you get more coisolated peptides. Totally worth checking out! 

CasanovaGUI - next generation de novo sequencing for the rest of us!

 

Hey you! Do you want to denovo sequence some files? Yeah! 

Do you want to put a docky on your graphics card and run a bunch of programs by typing long things into something called a commandy promptier. Yeah. Me niether. 

And now you can! CasanovaGUI runs on Mac, Linux and Woondoows.

Great new book alert! Bioinformatics for Mass Spectrometry!

No way I'll get time to go through all of this soon, but highlights include 2 very good chapters I have spent time on that focus on PTM site occupancy and normalization.

rRoma looks like a very nice tool with a clean and organized Github and the other one is about strategies. Not a bad start! And there is a chapter on boring and important metadata stuff! 

Faster mass spectrometry = better metaproteomics differentiation power!

 This great new paper in JASMS shows what this generation of mass spectrometers can do for the most complex of samples! 

Bonus! Did you know that Asstral actually stands for something? This is where I learned it. 

Mix a bunch of different microbe communities together and what do you get? With hundreds of scans/second you get a lot more of those little peptides that can really differentiate bacteria A from bacteria B. This is important because when you're looking at HSPs or ribosomes that are super evolutionarly conserved the peptides that are the same among all the organisms are multiplicative in each sample. And also not useful for telling them apart! Great argument for TOFs in metaproteomics applications for sure. 

fracSLIM - the next step toward the inevitable death of nanoflow in proteomics?

 

If you've ever been here before 1) I'm sorry and 2) you probably have seen me make fun of aptamers a lot and you know I despise nanoflow chromatography. Is it a necessary evil? It is in single cell proteomics for at least a bit longer. Otherwise there are other options, like microflow or even analytical flow. 

What about high flow fractionation and then direct infusion SLIM (high resolution ion mobility) + Orbitrap (high resolution mass spectrometry)? Could that work? Maybe it's worth taking a look at this new paper! 

...and in next week's lab, we'll build a mass spectrometer to use the rest of the semester....

11.1% of students said that BUILDING THE MASS SPECTROMETER DIDN'T HELP THEM UNDERSTAND MASS SPECTROMETRY! 

I WANT TO TAKE THIS CLASS! 

Where do proteomics people come from (and why aren't there enough of us)?

 

Wow, this thing has gotten all sorts of positive comments (thank you! reviewers and readers!) and I guess I forgot to post it here. 

Background: Right after the pandemic there was SO much proteomics excitement. (Reminder we had a huge Forbes article with a picture of something from a museum on the cover. WTF is that thing even?)

And there seemed to be a pile of new money for a while right after that. A lot of it ended up used up by confident people who had no idea what they were doing (not a surprise, that's how all science business stuff seems to work) and decided it was time to enter the proteomics space.  I know of multiple situations where people with no proteomics experience - and with none on their teams - successfully scored investors, bought instruments and.....are having slow starts...because they either had to learn how to do proteomics in a startup pressure cooker (fun) or had trouble finding experienced operators, because there aren't lots of us. 

But here is the question, though. Why ARE there so few of us? And that's the reason behind my most recent paper.  I figured if we knew where people were coming from (even from a small sample size like the people who will respond to social media surveys [thank you!!]) we could start working on strategies to fix the problem. 

This is the year the Gairdner Awards committee discovered proteomics!

WHOA! 

The Gairdner Awards are a big deal. A whole lot of people who get this also get Nobel Prizes later. 

And - in the year 2026 - they discovered Proteomics exists! 

Among this year's winners are this guy I talked to yesterday (and maybe last week as well)! 

and this guy I have talked to (and have proof! he drove our podcast listener numbers averages way up) 

and this guy I've somehow still never met. At this point, it's weird. How many proteomics people are out there that I haven't annoyed in person? As an aside, he sure publishes a lot for a dude who supposedly retired a couple years ago. Not complaining. I cite him all the time. Just noting a fact. (Author of one of my very favorite papers ever.) 

Congratulations to all the winners! I'll pay attention to this one now. I only knew about it because Bonnie Bassler got it a few years ago and she's so nice you'd never guess she was ultra famous. 

More proof you can do proteomics on anything - let's tackle kidney disease in cats!

 

I swear, it wasn't that long ago when you could do mediocre proteomics in humans, mice, poplar trees, E.coli and everything else seemed completely impossible. You could argue that even the .fasta databases in rats even a few years ago were rough and made it hard to do anything.

How is the cat genome? I'm guessing it hasn't gotten 1% of the effort the model organisms have. And here is high depth proteomics of cat urine. There is a word in the methods section which will make you wonder "how do they get cat pee?" Don't look it up! But otherwise this is a great proof of concept of how wide the applications of proteomics can be today! 

US HUPO 2027 Albuquerquely! Registration is open!

Is the above the very first thing you think of when you hear Albuminquerking? 

Congratulations for being old! Need something else to associate with Albuquerkley? What about US HUPO 2027?!? You can register here! 

Are you bummed you can't associate this great conference with being EXTREMELY COLD? Sorry, we can't have it in Chicago in February every year (though Chicago was legit). With the climate collapsing around us, who knows what it's going to be like anywhere, but traditionally it looks like Albuqwurkey is warmer than the last few US HUPO locations in the first week of March. 

In case you were living under a rock (or not yet alive) around the year 2000, Alvuquorkee is the home of someone who's name is completely impossible to ever forget how to spell. There is an entire song where he practices it so many times you learn how to spell it backwards before the end of the song. 

Is this song is now stuck in your head as well 22 years after the last time you ever possibly heard it on the radio? Congratulations, again, for being old!  I'm not linking the video, it might be awful, who can remember?