Friday, June 30, 2023

Where are spatial proteomics technologies today? Check out this great new breakdown!


Right? And it is super tough to keep up with what technology can do what and when.

A big thank you to these authors for this timely modern review (focused on breast cancer, but applicable to everything). 

While the illustrations are very nice and informative -- like this one -- 


Table 1 is AMAZING! 

What is the realistic resolution of staining with immunofluorescent antibodies? How many proteins could you examine at once? What about MALDI-MS? Where are the current limitations for laser capture microdissection? Yeah. That's table 1. 

Based on recent publications and talks I've seen I bet a lot of these things are moving goal posts as everything aims for higher spatial resolution, but what an amazing resource for whatever year it is now! 

Thursday, June 29, 2023

Who has throughput issues? Time for 1,000 proteomic samples/day!


Nerf machine guns are okay....I think....for method which the authors call MachineGun proteomics...

It's a preprint, they have time to change their minds....but they really only go as low as 720SPD in the study! (They also have time to add their JPOST and ProteomeXchange accessions so I can get these files. Imma ping them).  

How'd they dothe study? 

Monolithic silica columns at 7uL or 10uL/min using a Shimadzu pump with a 6 port valve setup. Load, switch valve, elute, load switch valve. Seems pretty darned simple. Right into a TIMSTOF Pro for dda or diaPASEF. They did make a custom emitter setup for handling this flowrate. I suspect this is through the ESI source. 

They do reference the dual trap method just about everyone is frantically setting up in their labs right now (Kreimer 2022), but this is faster. 

Wednesday, June 28, 2023

TMTc (complementary) ions leveraged in Alzheimer's insoluble proteome analysis!


TMTc comes up once in a while, but relatively few groups have leveraged the complementary high mass fragment ions that are generating during fragmentation of TMT labeled peptides.

There are reasons for this, like a limitation on the number of tags you can use (because they either can not be resolved or because you can't resolve them, which is a different thing, but effectively the same).

But when you consider the likelihood of fragmenting 2 or more things that will produce a 126.012 and a 127.013 fragment ion vs two things that will produce a (for example) 1386.042 and 1387.043 it is pretty clear that you'd have loads less interference in the latter. (Everything you tagged with TMT will make those first 2 things, including lipids and small molecules with amine tags, but relatively few things will elute at exactly your same retention time and will produce the same high mass ions). 

More on TMTc here and here and - this new paper! 

What this group dissected was detergent-insoluble proteins. If you take a "normal" human brain and you solubilize the proteins in detergent and centrifuge it you'll get a little pellet. If you do the same thing with a Huntingin's disease brain or Alzheimer's (or more controversial -- a brain from someone with schizophrenia) you'll get a BIG PELLET. The question in a lot of these disease proteomics studies is WTF is in this pellet!

And the problem with doing it with TMT is that you're probably talking about some really big ratios. Presence/absence sort of things. And TMT ratio compression, plus the fact it has a somewhat limited dynamic range seriously confounds things. 

TMTc to the rescue! In this study they thoroughly optimize with TMTPro reagents using human/E.coli ratios to dial in their quan and use a multistep fractionation scheme to simplify the insoluble brain fractions from post-mortem human brains with Alzheimer's disease.

They use an HF or HF-X (I can't tell if I scribbled an X or if the picture I drew while trying to figure out how they combined their offline fractions just makes it look like and X and I'm not looking for the PDF again). The actual samples were fractionated by gel slice, but the libraries were made from a pool using offline HpH fractionation.

All the data was processed using JUMP, and I'm excited to see something outside of the top secret Harvard server that no one else can use can process these data and I will be exploing -- but I'd just use the free version of Proteome Discoverer with the IMP-Hyperplex nodes which could do this since it is Orbi/Orbi data. ( 

I don't understand what they found here. Something about "proteins with low complexity domains" but they seem excited about it, and with the prevalance of these awful diseases (and just terrible "diagnostics" for them), I bet they aren't the only ones. 

Tuesday, June 27, 2023

N-Glycoproteomic alterations in Amish population with cardioprotective mutation!


Just north of Baltimore there is a surprisingly large population of Amish people. You can tell when they're around up here because people will tailgate the buggies and blast their car horns at them. It is likely because people are in a hurry, but I bet some percentage is just tired of all the animal abuse stories that are directly linked to a 40,000 person Pennsylvania population.

What is interesting from a scientific perspective is that this population really hasn't moved about much over the last century or so and there is a lot of genetic data out there on them thanks to things like Geissinger (sp?) which has kept this information. 

What can you do with that information? Maybe you could explore functionally enriched genetic variants and then figure out what those gene products do with proteomics? 

Sure you could. But why would you want to? Well...what if this population also had a phenotype that a lot of other people would like to have? Like really low levels of the bad cholestorol (LDL)?

In today's world with every biologist rushing to unproven technologies like O-link and SomaScan, you'd think that's where they'd go.

And they'd strike out.

Because, while there are protein level alterations in this population (which these authors have previously explored and got one word "Science" for their efforts -- they summarize protein level changes in the MCP paper we're actually talking about) this isn't the most interesting aspects -- or the ones easiest to link to the observed phenotype in question. 

Because (I heard you can't start sentences with because so I'm going to do it multiple times just to prove you can) what appeares to be happening is that the product of this missense mutation is altering the glycan profiles on what the authors describe as "critical targets".

Check out the middle panel in this stolen screenshot: 

That looks pretty striking, right? 

So you've got this missense mutation enriched in a small population that can improve human health. Ain't a genetics tool on the planet or a protein microarray panel or aptamer or other global panel out there that can tell you how this is functioning, but you can find it through the flexibility of a mass spectrometer and some people who know how to make it do tricks.

This was TMT labeled plasma proteomics analyzed on a QE HF-X. The identifications were made by Byonic from Protein Metrics. Cool story, right? 

Monday, June 26, 2023

Improve your DIA-NN quan and annoy the physics people with QuantUMs!


We can all detect thousands and thousands of proteins in really short periods of time! What do we need next? Quan that is way better than O-link and SomaScan? Well, we already have that. But we should really make sure that we don't have some low abundance stuff getting quan that is at the same level as those technologies.

AND if we can get on the nerves of people in other fields -- that's just a bonus, right? 

Introducing QuantUMs! New smart stuff from the DIA-NN people that you can't yet download, but they're working on it. EDIT: Apparently I can't read, you can download a functional copy following a link in the preprint. Not sure how where I got mixed up. 

What's it do?  Wait. I can just cut the cool part and that will definitely reduce the typos in this post! 

Makes sense, right? 

There is some extra gold in this study as well! There are some pull-down options in DIA-NN over here 

And, no, I didn't know what the quan strategy stuff did until this preprint and now I might! 


Sunday, June 25, 2023

High end TOF comparison - Astral vs Ultra vs Zeno!

Please note: Errors/corrections to image above that I'll fix when I'm back in the right office. 

Corrections to original post include:
1) FAIMS Pro is available for the Asstral
2) There is only one "s" in Asstral.
3) The thing on the far right is a ZenoTOF (originally copy/pasta error said TIMSTOF) 
4) Resolution on the Ultra is incorrect -- the specification sheet says 60,000. Which would almost double my throughput because I should be able to use all TMTPro reagents -- and I could use the whole CellenOne ProteoChips AND the full nPOP workflow. HUGE.  Dying to see data. I might need to fly to Boston.

Now that every vendor has embraced Time Of Flight technology fully, it's time to do a completely inaccurate roundup of where, I believe, they stack up right now.

Disclaimers over there somewhere, 100% apply here. ---> Also, I'm running off of basically rumors here. Please consider this post completely unsubstantiated (actually, probably all of the posts on this blog!).

What a fun time it must be to be doing instrument demos to send that amazing old Orbi Velos out to the desert! 

In no particular order, let's list off some things that you might want your next proteomics instrument to have or do.

1) Is blue and grey your thing? Do I ever have news for you? Any of these instruments will fit in with Yale or UCLA themed walls (I don't know if those are actually those school colors). Winner? Tie!  

2) Have you been turned off by TOFs in the past because of the lack of ion accumulation? Me too! But that's the whole point. All 3 of these next generation TOF instruments have cool ways of accumulating ion signal prior to TOF, which circumvents most of the reason that TOFs basically died out for proteomics in the first place. Worth noting, the ZenoTOF (for reasons I do not fully understand) only ion accumulates for MS/MS, but PRM and DIA are just fine. I think we don't have enough information yet for the sensitivity game, but both the Ultra and OrbiTOF are getting huge numbers of proteins in single human cells. With the IonOpticks team taking building a nanospray source for the ZenoTOF into their own capable hands, I suspect we'll hear some ridiculous numbers from that combination soon as well

For now, no score! 

Let's start with the obvious: 

Are you obsessed (for valid reasons or not) with mass resolution? The OrbiTOF really stands on its own out there with a high field Orbi stuffed in one side of it and a surprisingly high resolution TOF on it's butt. 1 point to the OrbiTOF! 

Are you more obsessed (for valid reasons or not) with ion mobility separation? If so, you do have FAIMS as an option for the OrbiTOF, but I don't think it was used in the preprints I've read so far. Even with FAIMS pro, it is basically a +1 filter, which is super valuable. The TIMS has way more resolution. 1 point for the Ultra!

Do you need MSn? Well, you're out of luck here. These are all MS2 devices. Don't let them haul off that Orbi Velos yet! 1 point for the Orbi Velos! Or LTQ or Fusion system. 

However, if you want multiple collision energy types, the ZenoTOF is in the fight. I suspect some big time EAD papers in the near future because it is efficient and very very fast. 1 point to the ZenoTOF

Speed? This is crazy because last year around this time the ZenoTOF was the fastest name in the game and now it appears to be third? Wow, right? I'd like to some more data out of all of them, but from marketing it looks like the Ultra is the fastest right now (300 Hz? WTaF?) but at slightly less (see edit above) than the OrbiTOF. I can not wait to see this preprint. Heck, I'll help you write it if you need help. Trip to Boston time? 1 point for the Ultra!  

Software compatibility? It depends on that application, I guess, but I do think that Thermo really does have a lead here. The majority of the software in the world can read a Thermo.RAW file. If you're doing DIA, these are all SpectroNaut and DIA-NN compatible. Skyline can process the data. I think the ZenoTOF might have some limitation with FragPipe for DDA that I'm not sure if it has been resolved yet. I think this point would go to the OrbiTOF for this big reason: 

The real achilles heel of the TIMSTOFs in general is that it is very hard to dig into the data to look for specific targets. For example, if you wonder if your peptide is there and it didn't get identified, it is really hard to look through the TT data to find a mass spectrum to look at. When someone fixes that, they'll get 10k citations in about 5 years and I'd have to neutralize this one out. If you've been looking at SCIEX data in the past, you know how to deal with those data. I'm going to narrowly give this point to the OrbiTOF

HPLC compatibility? This one is easy -- unless you've got a Vanquish Neo. I don't know why, but even Thermo's HPLCs are more compatible and work easier with the TIMSTOF software. Open the driver, checkmark the HPLC, hit apply, done. Agilent, Dionex, Proxeon (I don't know about Waters, we don't have that combination on campus), EvoSep. Point to the Ultra. (Neo doesn't play with Bruker, you can always contact closure, but you can do that with anything)

Top down/intact protein capability? There is a Biopharma option for the Astral, so $$$ and the ZenoTOF can do native protein work (m/z goes to 60,000 or something) but that might have $$ attached, I don't know. Surprisingly the new TIMSTOF control software has default workflows for mAB characterization, which I did not think was possible. Strangely, I guess this is a tie somehow

Footprint? These are all TOFs and sorta big, but none are huge. All are smaller than your Orbi Velos. The ZenoTOF is the smallest. Point to ZenoTOF

Autocalibration for proteomics? The TIMSTOF is pretty close to autocalibrating, but I don't think it can do it yet. The air filters are really handy for being able to quickly check if your mass and TIMS are behaving, but the ZenoTOF and OrbiTof both get a point. 

Did that tie it up? I figured ending it that way would get me fewer phone calls about this post, PLUS it is now all application specific and personal preference. Are you unwilling to learn a new vendor solution? Great time to be you! Everyone hasa powerful new things. 

I also didn't think I knew enough about the other vendors to throw them in here. 

The instrument vendors are the only ones that benefit by our somewhat unique obsession, as a field, about hardware. People are so diehard that sometimes you've got to move your study to a different journal if you land on the wrong reviewer and you use the wrong instrument. My wife made a lot of fun of Thermo DNA/RNA sequencers for some reason when she was in a lab in grad school that had everything. Something about voltage differentials. So maybe it is all the -omics people and not just us. 

In the end these are measurement devices and we don't get all riled up about which scales we are using to weigh reagents. (Unless you are getting an ISO audit! My gosh. We bought a new scale that came with an ISO-6001 calibration, not an ISO-17025 calibration and if we hadn't found a guy who would jump in his car immediately for and recalibrate it in returns for roughly what the scale cost, we wouldn't have been allowed to run samples. So that's a bad example? 

You'll note I didn't give a point for price. I don't know what those numbers really are, I've just heard rumors and I bet vendors are feeling people out right now on what they would be willing to pay. I expect those to be pretty unstable for a while. 

These are really cool, very sensitive, very fast, very capable measuring devices and it is great time to upgrade your performance by just swapping in a different box and changing nothing at all. However, the coverage coming in from every direction from every instrument (thanks in almost just as big part by better sample prep and fancy new informatics) is crazy right now. We right up and went all exponential growth phase a while back after kind of leveling out for a few years. 

I (and our reviewers, I think) would still much rather see a super smart biological study with a well-thought out experimental design on a Q Exactive or Synapt or 6490 or TIMSTOF Pro or 6600 than read a "we mixed HeLa with yeast and Arabidopsis and got 24,000 proteins quantified" or something. But with the unproven tools like O-link and SomaScan out there bashing us and eating our lunch money without solid quantitative assessment of the values they return, this shiny new stuff and the press noise they're generating is coming at a good time.

NOW we just need to get some super high n biological cohorts out and more proof that proteomics by mass spectrometry is a valid and valuable tool to help people! 

Friday, June 23, 2023

Mass spectrometrists write unbiased study on why nanopores will never work for proteomics!


I do not know how I missed that this was out. I totally knew it was coming

It is easy to think sometimes that every scientist has their own preferences for what methods are the best and that this might, in some tiny way, shape their opinions on alternative technologies. 

That's just you being skeptical and negative, in my humble opinion.

And this study absolutely proves this point. Here, 5 experts in mass spectrometry totally got a nanopore guy to help them write a paper on why nanopores will never ever be a useful technology for proteomics. 

I imagine the writing meetings were like this --

With that out of the way, this is a seriously cool paper that digs deep into some of the fundamental aspects of protein expression dynamics in a really approachable way.

Edit here, because I felt like this comes off as too much sarcasm. I will reference this paper all the time. Breaking cells down to the per molecule level, as they've done here, is extremely valuable. It has gone in to the folder on my desktop for papers that I'll probably read over and over. 

At a pure molecular level, what would you guess costs more? An Illumina short read sequencing analysis? Or a 2 hour proteomics run? LCMS is the winner! might question the metrics used for comparison...because it was something like "which one would be the cheapest to measure 1 BILLION molecules"? Which really shines when you're like "how much would it cost to measure 1 molecule with this technology?" 

Therefore, if you had to choose a technology for measuring one single molecule, you'd obviously choose mass spectrometry, right? But you could see how an approach from another direction might come to different conclusions by shining a light on other limitations.

It isn't all nanopore bashing and vendor worship in this study at all. There is really great, valuable and insightful measurements throughout this paper. There is also some questioning of the role that mass spectrometry vendors have played in (limiting) protein measurement technologies. I mean...they have their motivations as well. I've had a really long month and being snarky is helping me kick off the last few minutes while the last grant application of the month goes out. The guy who learned grammar in Tallmansville, WV doesn't do the last round of proof reading. I get a few minutes. 

The study thinks about what lessons could be learned from each technology (mostly what mass spec can teach nanopore) and ways to circumvent the perceived challenges of where nanopores are today. 

Again, totally worth a read, and I'm not joking it is a really inciteful analysis. 

Temporal epitranscriptome profiling -- by targeted proteomics (PRM)?!?!?

This short little study is reeeeeaaaally cool, especially if you were just at an epigenetics meeting and 2 people stopped by your poster. And one was to compliment your tie (which was still appreciated!)

They have their technology for studying the epigenome and epitranscriptome. It's evolving and amazingly cool. Who cares about proteins? 

Well -- this group knows what 150+ proteins do in regulating epitranscriptomic markers. So they targeted them during stem cell differentiation. And -- guess what -- the abundance of these proteins that make those modifications on nucleotides can tell you what those post-transcriptional control mechanisms are doing -- just as accurately as measuring the modified sequences themselves.

Add it together and you get an even better picture of what the cells are doing -- or what they'll be doing down the road after you stop monitoring -- which is the whole point of these epi- things! Predicting what cells and organisms will pass down to later generations outside of DNA sequence alterations. 

Super cool. Short read. Good targeted quan. 

Thursday, June 22, 2023

midia-PASEF webinar on July 11th!


Out of all of these smart new ways to leverage pasef and DIA in tandem, a consensus is rapidly building that midia-PASEF might be one to emerge victorious.

If you're like me, you might also find it the one that is the most difficult to grasp. 

TechNology NetWorks to the ReScue! 

I want to be at this thing so much that I'm fitting it in-between 2 PhD committee meetings, making me be in front of my computer for 6-7 straight hours without a break. I'll still be there. 

Wednesday, June 21, 2023

GlycoPASER -- Figure out your glycopeptides with real time logic!


Gotta run, but I will lose this link cause 400 tabs are open for this final grant application for June! 

Check this out! 

So you know how TIMSTOFs can look at low mass fragments and high mass fragments simultaneously due to the time of flight out of the collision cell? 

What if you used that to your advantage in the case of where looking closely at low mass fragments and high mass ones give you different information? 

That's what GlycoPASER does. It uses the extra processing power of that big GPU thing sitting by your PC that you might only use for QC/QA runs and triggers from oxonium ions to tell it when it should do more work.

Then in data analysis the low mass fragments are used to rule out different glycan chains (since all sugars have basically the same mass, but make different fragments sometimes) 

The .d files are available here and they're pretty weird to look at because the mass ranges don't typically change in TIMMY files, but these look different from scan to scan. 

I can't find the actual tools themselves so I think this is part of an upcoming official release. 

Tuesday, June 13, 2023

If you get a weird "US HUPO" email asking for money ignore it!

Some scammer is pulling email addresses of proteomics people offline and pretending to be US HUPO.

If it doesn't come from the email (with no silly aliases) it probably ain't real.

Monday, June 12, 2023

THE Proteomics Show Season 2 (Faces of US HUPO) is on, sorta!


For today's 60 seconds of "wait...I still have a blog? I should write something in the orange box..." 

We tricked US HUPO into giving us more money to ramble with smart successful proteomics people! 

AND our sponsor made us artwork and put up a cool landing page on their website. You can check it out here.

The first 2 are live with Birgit Schilling (and some guy in California....Yotes..? Jack? Jerry? ....John? yeah..? yeah...!) John Yates! A guy so interesting to talk to you can get through a 2 hour conversation you really didn't get to papers that your read over and over at the beginning of your proteomics career? For me, it is these two malaria papers: and

Due to some mass spec meetings messing with everyone's schedules, we won't have another podcast for a while, but we're lining up guests for the summer right now. 

Sunday, June 11, 2023

Potential PTM depth in Astral data might be absurd...

 Like a lot of people I know, I've been downloading any Orbitrap Asstral file that has become available and been digging through it.

The MacCoss lab data is up on Panorama here

The files will open in QualBrowser (so...probably FreeStyle) so you can dig through them. The first thing that is extremely obvious is how unbelievably dense the data is. Sure, the TIMSTOF and ZenoTOF are absurdly fast but there is just something striking after looking at Orbi-Orbi data and then moving into Astral data in the same interface.

As I was just leisurely browsing through one file, I kept seeing a couple of my old friends like 204.086 and the smaller mass oxonium ion glycan fragments. 

I set an MS2 filter in XCalibur for 5ppm on 204.086 and -- holy cow....(example shown above is one of the gas phase chromatogram libraries.) The filter in QualBrowser for MS2 fragments has always been a pain to make and I didn't feel like making a screenshot of another file. 

I dug up Conor Jenkin's original DIDAR script that pulls out MS2 spectra that contain diagnostic fragment ions (....can't find the github link, I'll ask and put it up later -- actually, here is the script, you just need to change the text in the diagnostic ion file, I finished a GUI for it, but that paper is a bit down the pipeline) it pulled out crazy numbers of potential PTMs based on diagnostic fragment ions --

The file I ran it on (didn't scan MS2 down low enough to pick up the lys+acetyl or citrulline or lys-GG fragment ions), but these numbers are amazingly high.

It pulled out 205,000 potential oxonium ions +/- 0.002 Da of this list of fragments out of a file with like 100,000 MS2 spectra? 

Since I'm lazy and it took a long time, I didn't set it to count each one individually, so an MS2 with a very typical HCD of a single GlcNaC would produce the top 3 ions in this list and it would count that as 3. 

Still -- I run this the lazy way on files all the time to see if it is worth going in and running a PTM search and I've never pulled out 205,000 ions out of a single file. 

I know Dionex and Friends dropped like 18 preprints during ASMS and I can't read those until after I get this last June grant application out, so probably someone has looked at PTMs in Asstral data, but if not -- it looks like an absolute goldmine for unenriched PTM searches. 

Friday, June 9, 2023

Overdue SCP2023 post! (Single Cell Proteomics, Boston, 6/1/2023)


Wooo..what a month so far! This will need to be brief, but I FINALLY got to attend the single cell proteomics conference at NorthEastern, and I even got to ramble about why I'm doing SCP. 

For a full list of the speakers and topics, check out the main meeting website here. Many of the full talks will go live I'm sure as soon as people get caught up from their packed June schedules. 

Don't be deceived by this picture, this meeting was paaacked and big numbers of people were tuned in remotely whenever we saw the zoom screen between talks. 

I've got to move sort of fast, but here were some main highlights for me.

Meni Wanunu (who might have the best name to try and say 3 times fast) really broke down where other technologies are tody for getting to single cell or single protein sequencing. My interpretation -- we don't have much to fear from them in the forseeable future.

Two versions of nanopore are working, one in which the regular old nanopore is adapted for proteins. At this point in time no one has successfully pulled off more than a small tryptic peptide. The second type actually binds the protein to an oligonucleotide string and the protein gets "ratcheted" through the pore as the oligo gets through. This seems super promising until you think about the detector....which is current now you've got the current shift from the nucleotide coming out of the pore (which has an error bar on it AND you've got the current shift from the amino acid coming through (which has  an error bar AND a 20 different possibilities). The best anyone has been able to show is that they can pretty much get every amino acid that comes through to 1 of 3 possibilities. I bet after 30 get through you could say #1 is A,E or N and #2 is E,T or D and #3 is L(I),I(L), or P and so on and eventually figure out exactly what that sequence probably is. Which is probably better in some ways than where things were when Don Hunt was doing stuff in the 1980s with mass specs....?

The ending estimate was that current technology with 1 million nanopores could completely read about 1 billion amino acids (one cell worth, give or take an order of magnitude) in about 24 hours. So...I bet that's enough to raise an easy 10 billion dollars on a technology that probably won't catch up before I retire. 

Erwin Schoof and Ryan Kelly were excellent of course, and they dropped some very small hints about an Orbi TOF (or Orbi - HOOET, or whatever) that was about to come out at ASMS. 

Neil Kelleher showed a DESI based single cell profiling technology FOR TOP DOWN SINGLE CELL at thousands of cells per day. Link here. Crazy.

The biologists sort of stole the show, though. Sabrina Spencer at UC Boulder demonstrated live cell imaging and how her team has been working out how cell cycle really works (at the protein level) and Kristin Burnum-Johnson (PNNL, and you could argue also big time mass spectrometrist) demonstrated spatial profiling to study super complex multi-organism systems to find important metabolic enzymes for biofuel production. Super innovative stuff I'd never ever seen before. I don't think what she described has been published yet, but I'll be on the lookout for it. 

Gotta move to the next project, but again super glad I got to finally attend this great meeting and see some of what is going on in this amazingly innovative space. 

Wednesday, June 7, 2023

TimsTof Ultra full marketing specs are now live as well!

 I kept looking for this to be up, and it now is. Check out the full marketing dump on the TIMSTOF Ultra!

(Obvious marketing disclaimers, but...I've been told by someone I really truly trust that she/he is obtaining these numbers...)

5500 proteins from 125pg of material... 2k from 15 pg...????

If you haven't been to this awful blog or haven't been able to weather any of my recent tirades in full length, my estimate has been that the amount of peptide I actually get from a cell with 250 picogram of protein is...around 100-150 picograms... 3k proteins is unreal. 5,500 is....

Preprint from Olsen lab -- Astral analyzer details!

Want more details on how the weird new Astral analyzer works? Check out this new preprint! 


Monday, June 5, 2023

SCIEX ASMS Release -- icIEF-MS-coupled to a ZenoTOF!


I suspected SCIEX was working on something badass and totally secret. It was all too quiet. I figured it was EchoTOF time or something else...but...even the release has been subtle....unless you're doing antibody characterization (maybe other proteins as well, I don't know).

Our friends at SCIEX have a uniquely weird capillary electrophoresis system or kit that allows them to separate charge variants by their electrophoretic mobility! It's super cool because it is coupled to a UV readout so you can rapidly (a couple of minutes) realize that there is more complexity in your mAB you produced. 

Now....what if you very carefully separated your charge variants....and they eluted right into a 7600 for intact/top down analysis? The drop in complexity in your sample input is going to be so so so helpful. BTW, the 7600 has a huge upper m/z limit. I forget, but it is 40k or 60k or something. Throw in the ability to do EAD/CAD and combinations of the two and you've got a ridiculously poweful solution for antibody characterization. 

I can't find the picture online that I saw, but it is all sort of streamlined together. The box looks a lot more elegant than the's something like icIEF-MS. 

I'm willing to look past the name and think hard about how I'd use this sort of data, and so should you weird biopharma/top down people. 

Waters -- Imaging QQQ!! (Triple Quad) Xevo TQ Absolute!


I told everyone not to sleep on the other vendors. This is the biggest ASMS for new hardware advances since I've been doing this stuff.

What are the biggest weaknesses in mass spec imaging? Dynamic range? Limited targeting abilities? 

What if there was an imaging triple quad? 

Check out the Waters Xevo Absolute with DESI! 

Sunday, June 4, 2023

What I think we know about the new TIMSTOF Ultra so far!


Well... so...if you take the TIMSTOF SCP, and put the TIMSTOF HT digitizer and higher dynamic range TIMS and 


Did that lady just say 300 HZ????  300 HZ?? I probably misheard her....

For some context, I really have to make my library files for single cell on my TIMSTOF Flex I can't put more than 20 nanograms on the SCP, and 20ng doesn't give you the kind of depth that you get with 400ng on a Flex. But my Flex can't see hardly anything in an unlabeled single cell, so the SCP has to be here.

The Ultra has the sensitivity of the SCP, the dynamic range of a more normal TIMSTOF and it looks way way faster? AND they looked at the worst nanospray source ever designed and tried to do something about it? 

Orbitrap Asstral preprint drop shows how innovative (weird) the new instrument is!


We've been had! Clever patent releases and some misconceptions regarding how very sneaky Dr. Makarov can be let us think we were just looking at an Orbitrap with a TOF where the ion trap should be.

It turns out this thing is a whole lot weirder, but I can't spend another 3 minutes on it.

Check out this preprint!