- by UnknownAre you interested in getting into spatial mass spectrometry but all the super expensive commercial technologies aren't doing it for you? Why don't you…..introducing Tappy-mode scanning ESI! What's that? Okay, they didn't invent it for this paper, but they explain it better than I can! Wait a minute. Is it just like this except really fast and with an electrospray plume in the middle? Close enough! Okay, but analogies aside, we can move tissues at incredibly absurdly high resolutions. Think about the stages they use for electron microscopy! Great imaging mass spec today is like 20 micron. Every vendor will sell you a "5 micron […]
- by UnknowniSCMS 2026 was just announced and it's SO cool. One of my favorite 2 day conferences – not just single cell proteomics, but all single cell mass spectrometry. At King's College in London! And if that's not cool enough it's a joint conference. You can stay an extra day for the British Mass Spectrometry Society Meeting! Alejandro Brenes and Felicia Green are the plenaries for the latter! Did you think that you had to be 90 years old to be a plenary speaker? Not here you don't! Psyched for both talks. You can come for BMSS or iSCMS or both and register here. Here are […]
- by Unknown…ummm….how do you make a 2 um inner diameter LC column….? Leaving it here so I can think about it later.Obviously required addition to this post…
- by UnknownOkay, so what if you did proteomics on a sample and you were concerned that you'd homogenized too much tissue. Maybe you had an obvious phenotype and you just can't see anything differential in the proteome? And maybe you don't have a single cell sorter in your lab and a very very clean Astral, Exploris, Excedrin, 8600 or TIMSTOF sitting around. (For real, yo, I don't think we're past the requirements for very clean or almost dedicated instruments for single cells. This is from feedback from friends with Asstrals and 3 separate Ultra2s. Run 2 days of 50ng samples and […]
- by UnknownWow. I'm completely blown away by this one. If you've got VERY GOOD AD BLOCKERS INSTALLED, you can find the popsci article here. Don't click it if you don't. Hot dog, the little counter on the corner of my screen rang up 74 ads and trackers in just a second. And the banner at the top warned me of "consequences" of blocking those 74 ads. The article is sort of about this new PNAS paper! Click this instead. My school doesn't subscribe to PNAS? Weird. Maybe my ad blockers are too good. Okay, but here is the thing. What if you could […]
- by UnknownThis is so clever! And I absolutely want a deck! (In English, probably, but I'd take the French ones for sure!)If there is an opportunity missed in this EXCELLENT paper… (For real, this is such a great read from authors who understand both mass spectrometry and educational concepts. Neurons from my long ago training to be a teacher stood up and tried to do things when I read words like "pedagogy"). …I would have ABSOLUTELY, WITHOUT A DOUBT, cited a paper by Kenneth J. Rodgers first. It's a preprint, there is still time! Maybe this one?
- by LCMSmethodAdminAre you a trainee of some kind in the US? Would you like to go to some US HUPO member lab and LEARN A NEW SKILL?AND Win a fancy award for your CV? Check this shit out. I'm not saying this is what you should do, but here is a scenario. Imagine you wanted to do some single cell proteomics. You could totally come to Pittsburgh and get trained by my amazing team and do some badass single cell proteomics. And US HUPO would help pay for that experience and present you with an award or something.You could obviously go to some […]
- by Unknown
- by UnknownWhoa. Okay, so someone else was wondering how to minimize low concentration sample prep to EvoTip loading. Turns out one of the culprits can be the lyophilization/speed vac'ing step! Worth checking out, for real.
- by UnknownThis weekend while watching too much stuff indoors because it was 40C (>100F) outside I kept seeing ads for using AI to "design your space".We have a single lab bay not counting my office and the awesome open space for the TIMSTOF and EvoSep, but we do have to think hard when students rotate about where to put them. Maybe if I give an AI all the details of the lab and the dimensions it could……….make me think this isn't the dumbest fad in all of human…..history….
- by UnknownI'm not sure when this special issue actually published this year, but I ran into it while editing a review. And I do love this paper in it. It's all about boring old validation of a high resolution LCMS (!!!!) proteomics assay.
- by UnknownProteomics is in such an interesting place right now! There is so much new interest that I hear people talking about proteins in my day-to-day than genes. Maybe that's environment, but it's definitely the first time ever.Now, you've kind of got two groups of people in proteomics. You've got the nitpicky nerds who aren't just satisfied by knowing what proteins are present. These jerks want to know how much of each protein is there. For no reason at all I'm going to call them "Medical doctors and good scientists". Purely, and only, because I randomly referred to them first in this […]
- by UnknownThis isn't proteomics, but damn, I love this book. 2020 joint publication by 3 National Academies. I stumbled on it while working on a paper that I hope is going out the door shortly and it's a goldmine of insights about how the science works and grows. If you dig around even a little I think you can get it free. I went through my library but it led me around to what appears to be a fully free pdf to download.
- by LCMSmethodAdminHave you ever just ran into a funny differential peptide that seems really interested and thought "…..awesome…where do I even start to figure out what that is….?" I sure have! And before you try to figure out if you can export that single spectrum for de novo (eek!) or hand sequencing with a calculator (double eek!) what if you could just have a starting point? Check out this clever little thing! Don't feel like reading? Check out this hosted web instance of it here! You just type in your m/z or mass and give it a mass tolerance window and it pulls up […]
- by UnknownIf you lose the link to this new paper you will not be able to find it again by looking for "Corona Proteomics". You'll find lots of stuff about the made up thing about protein coronas on nanoparticles as well as a lot about a virus that no politician in my country believes in that caused the deaths of millions of people including an old man with the exact same name as my only child because his church told him that the vaccine was evil or something. But this Corona is a whole lot more positive. It lets you design virtual mass […]
- by UnknownI guess this paper isn't new, I just saw it on Linkedin posted by this guy and I'd totally missed it.If you're here for the mass spectrometry comparisons, they summarized them far more succinctly than I could. I have a tendency to type too much. No real surprise there, MS2 TMT isn't quite as good at quan, particularly if you're doing lazy math and just considering fold change ratios rather than real significance cutoffs 😇, but the higher speed of the Asstral gets you a lot more coverage. However, the reason this paper is here is because I have personally looked for off-target […]
- 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, […]
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