Big DIA software advances - peptidomics and PTMs are the clear focus!

 I just upgraded to the fancy new SpectroNaut 20 and was flipping through all the things! 

Here are the release notes (in screenshot form, which is by far, the most convenient way to share text!) 

And I'm having the guys at the HPC upgrade FragPipe Academic to the newest one for me as well (I don't have permission) and there are a lot of concepts that are shared.

In case it needs to be typed, I'm not accusing anyone of sharing notes. These teams are very user centric and we are all probably complaining about the exact same things.

Why can I find more PTMs in my non-enriched DDA data? 

Why is DDA so much better for peptidomics? 

Why isn't this faster? 

And here we are, at a great time to test some cool stuff out! 

Symposium on proteomics in the life sciences at the Broad! Registration open!

 

Wow. Sort of short notice, but this looks like an amazing use of a few days in Boston/Cambridge. This wasn't on my radar for the summer. The program is a little vague, but the organizers are some of the best scientists in proteomics and have picked extremely relevant topics. Definitely something to think about! 

Edit: I found the list of speakers as well. I was just on the wrong page. Geez. Check it out, the week is stacked. Here are the main themes. 

TMT in FragPipe with TMTIntegrator!

 I gotta move fast, but for those of you on the TMT32plex or 35plex or whatever it is, I think you'll really like this screenshot! 

How? What? I don't know! Check it out here! 

Peptides bistability in ion mobility might explain a lot of things!

 

Okay - somewhere on this blog a few years ago is a post that is called something like "what the hell is ion mobility"? And I'm continually learning - or trying to - and might have just given 3 talks doing proteomics with ion mobility devices. I might still only partially know what it is and I certainly couldn't build you one.

However, I'm occasionally surprised by measured versus predicted ion mobilities. And I'm often troubled by how ion mobility clouds are altered by things like isobaric tags. And for the former problem....this new preprint is really really interesting.

Why couldn't a peptide have multiple ways to be pulled through a gas gradient? I mean...it seems like you could probably flip 50% of your peptide population A one direction and 50% the other and they'd have different "shapes" - and it's not like the peptide bond is a crystal lattice. (Lettuce? Now I'm hungry). It seems like a curiosity until you see how much their IMS predictions improve when the model allows the entry of 2 stable IMS readings for each peptide....

ASMS2025! Press report 1 - Proteomics Hardware Advances!

 

Guess who finally got the ASMS PRESS PASS! Now....would....it have been an easier conference to have given 3 separate talks and not had a bunch of press responsibilities? Yes. it would have been. 

Waters saved me a bunch of time by inviting me to their conference but then not letting me in, so I used that to sit in my room for just a few and stare at the wall in the dark to recenter, and I sincerely appreciated that time. I don't think they had anything in proteomics to show off. I just went to be polite.  

On the proteomics side the big 3 had big hardware drops.

SCIEX dropped the 8600 which could possibly maybe put them up there as having the most sensitive high resolution system in the world? Maybe? Those numbers are crazy. Let's see where they go. And the proprietary quad sliding stuff on top of it makes it a really interesting and competitive bit of hardware. This launch was, of course, overshadowed to some degree by a very public disagreement with a popular open software development team. I'm not paying attention, but people being open minded about demo'ing different big proteomics solutions seemed to be paying very close attention to it. GenomeWeb dropping a story on it during the conference couldn't have been the coolest thing for their marketing people to deal with. 

Thermo had the Astral 2 Zoom. Higher sensitivity, 270 Hz max speed (up from 200), capable of doing TMT 32-plex -with some important caveats. Like the TIMSTOFs you have to do 2 scans for TMT. One for the peptide sequencing and one for the low mass fragment ions. In the second scan the fragment ions spend more time in the TOF region so they make more passes and then they get the minimum resolution to separate out the ions. The bonus is you can optimize the high mass and low mass fragment acquisitions - and - of course, Proteome Discoverer first launched when the first Orbitrap XL was out there and it had to do 2 MS/MS for every TMT/iTRAQ, so it can take these data. The Astral is super fast, so even 2 scans/peptide and even when one scan is a little slower, is probably really fast.

Thermo also had the Excedrin? Excedion? Benchtop high resolution with higher scan speeds. You can run your Orbitrap at 3,000 resolution and get 70 scans/second. It also has ETD built in. Who would want 3,000 resolution and ETD? Anyone worried about the collapse of their transient in the Orbitrap! Big intact protein, people, for sure! The signal optimization seemed to allow bottom up where the MS/MS actually looks pretty good at 3,000 resolution - from a signal perspective. Some people have noted the mass accuracy seems a bit wonky. Not something I'd worry about, Makarov probably has that fixed already, but it's not like you can't run a higher resolution on it. 

EvoSep had the EvoSep 2 (Eno). Higher pressure loading pumps, better chromatography and higher signal. Looked very plug in play for anyone with and EvoSep One.

Bruker had a pile of launches as detailed in earlier blog posts. The TIMSOmni seemed to be stealing the show on the proteomic side, but we also saw an improvement on the TIMSTOF Ultra2 in the addition of the Athena Ion Processor. (Box now says TT Ultra2 AIP). From van Eyk lab stuff, it looks like a solid signal boost but it also adds some interesting level of control to the Ultra2 that seems under-explored. Imma send some samples up. The fun thing about the TIMSOmni is that you just turn off the OmniTrap and you've got a TT Ultra2 AIP. 

Man - was there some cool automation stuff - everywhere! Robots for proteomics!! And downstream data analysis. I'm currently demo'ing Mass Dynamics stuff and I'll post how it goes here. 

OH. And this was a big one for me. New vendors for N2 generators!! Parker was there and excited to talk to anyone who was tired of the generator that came with their instruments but Swissgas was a completely new vendor to me and we talked a lot about longterm cost breakdowns. It's one thing for me to whine about my N2 generator. It's nice to have useful information to share with people when they say "okay, what are my other options?" 

Alternative suppliers for some things you use a lot? That probably shouldn't go here, but if you were there, you could see where maybe someone else was like "we're also very good at making stage tips..." or "would you like to try one of these things?" I'm rarely going to turn down free stuff even if it is a stranger offering me something that looks suspiciously like a captivespray emitter. I'm probably not going to try it out, though. 

I was part of the Mobilion BILLIE launch (and, again, I'm a compensated member of advisory board) and that was really fun. Hopefully data will be up on PRIDE super soon so you can look at it. All of the data showed was on Agilent QTOFs that were not designed for proteomics, so it's super impressive to see the instrument doing competitive proteomics. It was super cool to work with that team and to field questions like "what could that front end do to a system that was already a good proteomics system??" And I'd also like to know that answer! It's currently a completely vendor neutral system, so hopefully we'll all know sometime soon.

Now, more than ever, proteomics needs better chromatography! ASMS 2025 edition!

 

As my very first takeaway from ASMS2025, I'd like to start with this paper that is just a little bit older than I thought it was when it came up in my talk on Monday. 

Oh man, did we ever see some awful chromatography this week. Whole proteomics on 5cm columns was often higher resolution LC separations. There are 4cm columns and probably shorter. And often at low pressure. Now, maybe all the hardware advances that have happened on the gas phase should negate the statements in this commentary? But I'm skeptical that is truly the case. And maybe I'm just old and old  fashioned, but proteomics did seem to be the one place where the LC seemed to be left the most behind. I popped in on some food chemistry talks and a couple environmental and - they also have big complex matrices - and they were still leaning on UHPLC - often with very fast gradients and the discrepancy was a little jarring. 

Time will tell, I guess! I just wanted to drop this overall impression while I had a second - not long enough to write anything more involved. 

How much ion mobility would be necessary to replace the quadrupole?

 

Conflict of interest statement on this one - I'm both a compensated member of the Proteomics Advisory Board for Mobilion Systems and the first author of this preprint met weekly with me for 4 or 5 years while getting her PhD. I'm even more impressed by her work than by the quality of her education. ;)

Okay, but here is the real question and I know I've certainly wondered about this..... at what point would ion mobility and quadrupole isolation overlap? Or maybe this? Could you crank up your ion mobility resolution to a point you could widen your quadrupole and get equivalent data? Or if you had 1,000 resolving power ion mobility, would the quad just slow things down? 

Those are the questions tackled here. 

The short answers appear to be - absolutely, yes, and maybe. There is certainly a point where you can get enough ion mobility to get the same isolation you would get with a quadrupole alone. On the SLIM system the coisolation can be limited to about the coisolation of a quad running 5 Th windows. If you want the cleanest data you've ever seen, SLIM + 25 Th windows would get you there. And....yeah... in the world of wide window DIA or wide window DDA and now wide window PRM...these numbers are relevant. 

New Exploris confirmed! And...print cartridge LC columns....?

 

Just stealing Chris's post! 

Bonus, if you see Ian watch what he's eating and model your diet after it. He's at least 114 and he's out there on stage giving talks at 8 in the morning? 

Oh! Website went up on the Astral 2 "Zoomie"

270 Hz and the resolution to do TMT 32-plex (I thought it was 35? Does anyone know?) Big question should be - can it do the 32-plex at the highest acquisition rate? Or do you need to slow it down? 

We're going to see a lot of 300SPD proteomics on it, I guess. Probably with a 4cm column so everyone get excited to do label free quantification at 2 scans/peak! Still better than an aptamer! 

Informed DIA allows transcription factor quan in single cells? Also, new Astral?

 

If you've seen me talk about single cell proteomics, I like to point out the proteins I can see (50,000 copies and up) and I make a joke suggesting you come back in a decade if you're interested in transcription factors.

They turn on transcription at your DNA...you only have a couple copies of each gene. In many, most cases, we only expect a few copies of each of those proteins in each cell - certainly not tens of thousands! 

Yes this preprint demonstrates measuring them in global single cell data! 

How? Well...it's complicated. But basically it looks like we've got MS1 - DIA - and then what appears to be heavy isotope triggered wide window PRMs all in one cycle. I *think* the instrument sees the heavy spiked peptides and then moved a PRM window over to where the light should be. 

For you hardware nerds you may be interested in the fact this preprint seems to feature an Orbitrap Eclipse, and Orbitrap Asstral and something called an Orbitrap Astral Zoom, which might suggest we'll see an Asstral 2 at ASMS tomorrow? I guess we'll see! 

The first author will be presenting it as poster WP724 (Wednesday? Poster 724? I think!) if you're in Baltimore! 

pre-ASMS media drops - two new TIMSTOFs confirmed!

 

Hardware is already leaking to the media? Here is the first one - and a surprisingly well-written article with insight from a bunch of early adopters and/or beta testers. 

Oh crap, and my news feed was like "oh, so you like mass spectrometers? First I've ever heard you mention that... here's another! 

Looks like it's a top-down focused instrument with MSn(?) capabilities and some electron transfer thingamabobs, but I'm excited to see what it can do in the area of PTMs in bottom up as well. There area lot of PTMs that are just no fun at all to do with MS2 alone. 

I wonder if they had to get Disney's permission to use the same name or if it's so far from the meaning that there couldn't be confusion and trademarks wouldn't apply?