- by LCMSmethodAdminI have a very nice scSeq dataset (11,000 cells) that someone else generated that I've been looking at for years. I also have mediocre single cell proteomics (I did myself on much older technology) on the exact cell line and drug conditions, and it's cool when they seem to line up.This new study attempts to resolve these differences with very smart biological models, and it's a lot of fun. I copied Figure 5 above completely because it's my favorite. What if you took a cell line and did something super extreme to it like inducing hypoxia (suffocating it!)? You could pretty much […]
- by UnknownThis new preprint takes an old concept to the next level in hunting down those annoying little HLA/MHC endogenous peptides! The trick with running data through a whole bunch of different engines is generally the pile of peptides where the engines disagree about whether A) there is an identification or (worse) B) that spectrum is matched by different engines to different sequences. It's similar to the workflow I use for TMT single cells that I called "The Trifecta" that I'm sad to say I can't get to work anymore. At some point some update caused MSFragger and PD to never play together […]
- by UnknownOkay, so this is a vendor application note, but it's not written by company scientists. In fact, it appears to be the next edition of this sub-radar preprint from earlier in the year. I've had this preprint open on my desktop for a while in tab 713, because it's the first time we've seen Astral vs Ultra vs 8600 (and 7600+).As it said on our US HUPO poster this year "vendor instrument comparisons are boring" or "…because Ben (Orsburn) said vendor instrument comparisons are boring…" maybe that was it. In the preprint the authors completely and totally avoid any point where […]
- by UnknownThis post is probably not actually about this great new review. I'm just leaving a link about it here because I'm reasonably sure one of the peer reviewers put this team through the wringer. Is that a thing? Why would it be related? I don't know, but it's a great and valuable review! 👮This post is about ALLLLLLLL the ways we can now go way way beyond those top 300-800 most abundant proteins in human circulating blood liquids. Definitely not all, I can't keep up! Edit: Definitely not all. Geez. The last paper cited below mentions 4 other ones! Okay, […]
- by UnknownI wish I had more time to spend on this one, but I've got to get out the door.The best I can tell, no new data was generated for the study. What it did was leverage riboSeq data in public repositories in tandem with well-curated proteomics data. Looks like CPTAC and another study of hepatocarcinoma. What they're looking for is sections of RNA that were protected by the ribosome, and are therefore likely in the process of being translated to protein.Then they take those sequences, make a FASTA database and go back through the proteomics data looking for them. Ultimately, […]
- by LCMSmethodAdminYesterday I really wanted to play basketball and I walked onto a court even though there were high school kids on it. Every ice pack in our home has been in use since, so I was feeling pretty dumb. Wow, do I feel better now. Someone bought IGNITE Proteomics for $150,000,000.00 dollars. If you aren't familiar, Ignite is a reverse protein array. Their only current product that I'm aware of is a 32 protein panel that costs $2,200 per sample. I think that I might limp into work and see if my team can measure those same 32 proteins in human blood […]
- by UnknownYo, these are both SO cool. I'm very very jealous. I've been trying to find collaborators who can differentiate out some cells for me for over a year now. I'm lumping them together now becaus I'm still trying to dig my inbox out. One is cardiomyocytes! And they use the AIP! Apparently these can only be obtained in certain countries, btw. In Austria, they'll sell you the upgrade, but you can't get it installed. And this one is differentiation out to motor neurons! So cool.If you were a total jerk you could point out that this is differentiating big cells out to massive cells […]
- by UnknownWow, there are so many great ASMS week preprints, I can't even read all the ones from Jenny van Eyk's lab. This one, however, needs to jump the queue, just a little.The topic of the paper is well detailed in the title. It's a comparison of Asstral DDA vs DIA. There are some gems in it, including the statement "DDA isn't dead yet". But what is really really super interesting is the relatively low degree in overlap when they run the same samples with DIA, small window DIA and DDA methods. Which leads the authors to type out this really […]
- by UnknownCould the next advance in LCMS sensitivity actually be — — is this the most perfect gif ever for…This new study? Is it the most practical thing ever? I'm going to guess probably not, but the sensitivity gain math is large enough to think about it for at least a minute or two, if you haven't already.
- by UnknownIf you've been on this "science" blog: 1) I apologize and 2) you might know I'm very skeptical of teaching bitcoin miners how to put words together into LLMs (I'm pretty sure this stands for lazy lama math).However, when I saw the above plot on this site for an incredibly absurdly overvalued company and their made up metrics for the performance of their tool, I had to think about it twice. Please note that I did edit the plot above because you can't have an axis without units labeled. As a reviewer and editor, I feel that I applied the correct […]
- by UnknownThis post is a little delayed because I needed to do a check of what I know vs what I'm allowed to talk about. 😇 I'll select a random date to reinsert this. What is Waters doing on a proteomics blog? I guess I mentioned them last 2 years ago when they rolled out the reflectron thing. That thing was doing 100 Hz at 100,000 resolution. Which would be insane at any other point in history but is sort of normal today. But they had talks on DIA proteomics this year! And they had a new box that, according to this weird site…Wait. […]
- by UnknownAnother company at ASMS is also thinking in a new direction. SCIEX rolled out just one piece of hardware, the novus55 QQQ/QTrap system.This cute little box is focused on being space, energy and temperature efficient, while still being screaming fast. There is an example 20 min method where something crazy like 500+ pesticides are measured. It might be 800. I forget, maybe that was transitions. Still, I've never built anything above 130 MRM targets ($1M. I signed up for a demo for whenever they can squeeze in some time for me. Because scientific funding isn't getting better here. And I literally […]
- by UnknownEdit #3 (6/8/2026): This original and then second post generated way too much traffic and too many messages. I've got 2 proposals I'm working on and don't have time for it. So…I took it down and took a little break…Actual Bruker release at ASMS didn't feature new hardware, which I was very excited about. There is a new diaPASEF variant and some improvements to the PASER/BPS thing. They just rolled out the AIP and TIMSOmi last year and this year was focused on applications of these devices. Cool stuff across the board. Hoping this means a focus on supporting the stuff […]
- by LCMSmethodAdminOfficial site link here! Highlights? 75 Hz in a Tribrid? That's rocket fast. Probably rocking the Excedion Pro's lower resolution Orbitrap scan rates? Unclear, but that would be the safe assumption. It looks like there will be 4 versions of ApeX aimed at different markets? There is a long held tradition for this vendor to take a big 'ol dump on the systems that you currently have…..wow, they rolled out a lot of details on these systems…. but there it is…….a giant jump forward from the venerable Assend….If this is the one that is boring enough to release several days before the conference, […]
- by LCMSmethodAdminI find it more helpful these days to simply point out the failure rate of transcript level measurements (because just about every wet bench scientist out there has ran into it), it is relatively cheap and easy to get those transcript measurements. (However, I've still never been offered a $100 genome. Have you? I hear it's a thing, but it still seems like $100s plural). What if it still had some value (besides finding point mutations in variant call files, of course!)? These authors suggest straight out heresy and suggest implying that you could integrate these data to group those peptide IDs […]
- by LCMSmethodAdminJust leaving this here so I can get back to it later in case we have some drug response data with a lot of variables! Super smart and some of the most honest writing. "Yes, in this dataset this other tool actually proves more sensitive"! I love it. The authors use both simulated and real datasets they generated using DIA and TMT and compared them. Refreshing and clever, even if you can't follow the maths.
- by UnknownI do like it when a new group gets on the the single cell proteomics train and starts optimizing/reoptimizing things. Despite the 300 reviews, 50 method optimization papers and 20 biological studies that have been published, each new one brings a new perspectice and observations.While I don't love every aspect of this paper (some insight on what LC gradients were used when seems to be entirely absent from the main manuscript, which makes me question the title which seems to describe a single workflow) there is some gold in here! In my lab we don't reduce and alkylate the single cell […]
- by UnknownIf you've been on this blog much recently, I am sorry.Also, you have probably seen me in some level of outrage about some recent studies where people have gotten anywhere from 1-4 measurements of the peptides they are looking at. Is it better than Illumina ProteinCrap? Absolutely. But is it good for mass spectrometry data? No. Why is it bad? Because some blogging academic says so? This new preprint looks at the problem in depth and finds that for high abundance proteins in blood, the 1-4 measurements per peak is actually not all that bad. Unfortunately….the cancer biomarker you are looking for […]
- by LCMSmethodAdminThere is some replication is flattery quote, right? I forget what it is.You might need a free account to read this, though. And the stuff from the article that I found most interesting was a link to another GenomeWeb article. Not sure what the rules are for taking screenshots from it…. But the point is that the Oxford people have taken a page out of the ProteomeTools project and have 150,000 peptides multiplexed labeled that they're currently running through nanopores! Smart, right?Which seems similar to what this group recently published on here, except they aren't working from synthetic peptides, rather […]
- by LCMSmethodAdminWhen I first saw this I thought – okay, so someone copied the nanosplits paper but they had an Asstral.And it's almost what this is – …but nanosplits requires a technically tough step where you split the droplet containing your mostly lysed single cells. This protocol gets around that step. They still use the same silly robot to isolate the cells, but you absolutely don't need it here (where you basically do need it for nanosplits, it's tough to print that droplet array in a FACs core), and that's a huge win for anyone who doesn't have the slow silly robot.
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