- by UnknownUmmmmm……okay so….these specs are amazing….How do you increase mass resolution? Generally just increase the flight path, right? But you can only go so far before there isn't enough electricity on earth to generate the appropriate vacuum. Reflectrons double the path and the W-TOFs from Pegasus that a big vendor acquired recently can really push those numbers up by multiple reflectrons.The Y-TOF takes that concept to 11. It's one thing to say "I can make my instrument do 1 million resolution". Give me 45 minutes with your Q-Exactive and I can make it do 1 million resolution. Each scan will take […]
- by UnknownWe all know other great protein informatics teams are working on the holy grail for DIA proteomics – deep learning and prediction of modified peptides.Am I extra excited because the team that gave us Prosit is working on it? Yes. Yes, I unfairly am, when I should be evaluating this preprint purely on it's own merits and not the historic success of one of our field's most historically reliable teams. And not just because of their informatics skills. What makes me excited the most is their long history of making tools that anyone can use. Check out this preprint here!
- by UnknownThanks to all the journals allowing Open Peer Review and allowing me to sign about half of the 30 or so papers I've reviewed recently, it's pretty clear to people how unproductive I think things like this title are. Even if, as in here, I really do like the paper. I think I'm just old, for real, but I do think that if you've got cool biology in your paper but you've got the instrument front and center you're doing yourself a disservice. 10 years from now that instrument is going to be $100k from second party vendors or $50k on […]
- by UnknownY'all aren't going to believe this one. For real. Everyone out there complaining about the number of proteins you can identify in plasma proteomics and no one has ever tried fractionating it??? What is wrong with us? Whoops. Not everyone got that this is a joke. Okay…so…literally for all of time everyone has fractionated plasma in some way to get higher coverage. That makes the title funny. 15 years ago I was running SDS-PAGE gels and cutting fractions and running them separately on an LCMS. 13 years ago I was using something called an OFF-GEL to first fractionate the proteins at the […]
- by UnknownDid you know there are other tags out there for multiplexing proteomics? Younger people probably don't and I can't tell you where they to get them because I actually truly can't. Let's change the subject entirely.Did you know lawyers are seriously expensive? Like, for real expensive. If you're struggling with science salaries maybe you should check it out. Okay, let's go back to this paper.If hypothetical multiplex tags did exist in some places where I couldn't tell you about could those ficitious tags be used for single cell proteomics? Are you thinking….ummm…yes…? why wouldn't they be? These people found a […]
- by UnknownIf you've ever tried to look for a glycopeptide in any type of MS/MS spectra you know how very very rare it is that you get all of the information that you're looking for.If you want to get full sequence coverage of everything it's probably going to take ETD and 2 different energies of collision dissociation of some kind. The clever combinations of energies certainly help get you more fragments, but they also increase the background complexity. "Is that 8ppm away from the b5 ion or could that actually be the NeuNaC is the third sugar in which case that's […]
- by UnknownSneaky HUGE PAPER ALERT! Direct PNAS link here. This is so so so cool. Here is the thing, PFEMP1 is this molecule that covers the surface of malaria parasites and it does something very similar to what our antibodies do. It switches domains around to that it is incredibly variable. For a while it was thought that because it's so huge (I forget but I think it's 600kDa or more) it might be able to switch around more than our antibodies.Back in the 1990s or something the amazing Michal Fried was getting malaria samples from women in Africa who had gotten malaria […]
- by UnknownThere have been some bioinformatics initiatives where the goal has been "any dumbass can do this, even you!" and it has turned out that (pronounced doom basses, the latter word sounds like the instruments) Is KOINA really something we could all use, regardless of what languages we do/don't know and how very long ago we had any formal training in informatics? I'm not sure, but the authors seems to have tried really really hard to make it so. The first problem a lot of people run into when integrating tools into other tools is what language is supported? Machine learning is almost always […]
- by UnknownNo time to check this, but I want to come back to it later, and this is the easiest place for me to find it again!
- by UnknownThis was a fantastic read this weekend. Both the technology and the fact it is a cool story overall! I should, however, start with – no, you can't buy one yet. This is some advanced prototype of what was a student project a few years ago. You can read and watch a video about the Isolatrix here. If it was for sale right this second, I wouldn't jump in line to buy it. The reason it is so amazingly super fast is that it makes a decent number of mistakes, but it's smart enough to identify those wells with zero cells or more […]
- by UnknownThe whole point of the EvoSep HPLC is reproducibility, I'm pretty sure. That's what it says on all their things. The tips come with handy little visual instruction cards that tell you exactly how to load them. My team actually made stickers for the boxes where you check off each step you've completed because we can only spin 2 boxes at a time in our centrifuge and we often prep far more tips at a time. And…I swear about half of the papers I read (particularly from one group I'm going to point out right now) seem to just load the […]
- by UnknownI really did read the full body of the text for the published manuscript on AlphaDIA. I kept looking for the "why is this different than the DIA tools that I currently use" and I never had that "OH! That's why this is different!" moment. For real, WTF is a learning transfer? I'm either a poor reader or it is never fully explained in the text anywhere. However it 1) Processes Orbitrap data2) Processes TIMSTOF data3) Processes SCIEX ZenoTOF data4) Processes Astral TOF dataAnd it is fully open source! YEAH! Which doesn't matter a lot to academics cause 2 of the main […]
- by UnknownI won't lie, I'm not even going to go past the first page on this one. I was at Johns Hopkins off and on for like 20 years. I have some cat sized cockroach related psychological trauma I've submerged that I'm not about to bring to the surface because someone decided to put an actual picture of how they get the neuropeptides out of the cockroach. However, every couple of years someone does peptidomics on cockroaches and I do not know why. I probably won't ever know. Hopefully it's some important model or something. I looked and it doesn't appear to […]
- by UnknownListen up gamer nerds. You can keep playing whatever dumb thing you are currently playing – or – hear me out – you can get a free demo for Pathogenic where you play as a pathogen trying to infect a host!! Demo goes live on halloween! More info here.
- by UnknownFor all of you excited to leave a decent pile of what you might consider your human rights behind for a few days of fun in the Middle West you better get on it! Abstract deadlines are TOMORROW! Get 'em submitted so you can go to Missouri!!
- by UnknownAs everyone in proteomics already knows there is absolutely no downside whatsoever to using MaxQuant for every proteomics experiment. It's super fast, visually stunning and modern, incredibly stable and gives you all sorts of insight into your experiments when they succeed and those exceptionally rare times when it just stops running 18 days into analyzing those 4 files.How could you make our field's very favorite toolkit even better? No way, right? Oh. Do I have one for you. What if you could also get your metadata out in the soon-to-be-mandatory (those are single dashes, no generative AI here – every […]
- by UnknownOkay, this one slipped by me. I had a weird 2024…and 2025 isn't going to set any records for normalcy.It all seems brand new to me. There is some smart immunopeptidomics using TOMAHAQ derived methods as well as the clearest description of the ThunderPASEF technique I've seen. The lead in for why you'd want to do immunopeptidomics in the first place might be the star, though. Totally worth checking out!
- by UnknownOver the last few years I think I've seen 5 different company presentations that have been in some sort of an arms race – purely with one another – to deep dive in human plasma. This one now says they can get 3k proteins in human plasma, so the other one says 3,500 and the next one has to say 4,000, and then 5,000. I've visited a couple of them personally and the scientists running the samples seem to spending most of their time trying to find new jobs because their executives and their sales teams seem incapable of shutting […]
- by UnknownI don't know if this is the answer to some of my most pressing current problems, but it does seem silly dumping all the data at once into something that can't handle it.Maybe if we treat the data as a stream(?) we can allow it to be progressively processed(?)In their models they get up at a 3-order(!!!) of magnitude(!!!) increase in speed when processing large (and largely simulated) datasets up of tens to hundreds of thousands of proteomics samples.Worth at least thinking about, IMHO.
- by UnknownSince no one asked for it (and ASMS ignored me)! THE Proteomics Show will record live at International HUPO on Monday, November 10th. Main poster/exhibit hall at 2pm (I think!) It'll be me for sure and one super secret special host – and audience participation! Woooo! Toronto!
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