- 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!
- by UnknownWhoa! This has been a big week or two for plasma proteomics! And this multi-center evaluation goes after the most important part of it – who gives a rat's ass if we can detect a protein? Not me and not you – what we cant to do is accurately quantify it! Let's spike in all sorts of stuff and have everyone you know run it! All sorts of instruments are employed in this study and -HOT DAMN – Did they get 4,000 proteins in neat plasma?????Oh. Okay, When you put E.coli and Yeast into plasma, even at low concentrations on a […]
- by UnknownOkay y'all. I'm going to approach this one with a healthy pile of skepticism, but I need a solution – and probably you do as well. A small label free single cell study for us – like one 384 well plate is generating maybe 500 – 600 GB in RAW (Bruker .d) data. Then to run our data in SpectroNaut we have do first do the absurdly infuriating process of converting it to a special SpectroNaut format. It's called .HTRMS, which is probably Swiss for "Hard drive (T?) Room Makes no Sense". This takes your .d file and makes a […]
- by UnknownHey you! Do you need to do a big multi-batch TMT study? I've got a couple coming up! What if there was a handydandy GUI that would help you designt that study for getting the maximum quantitative accuracy and least effects from impurities and coisolations fudging all your super cool biological findings?CHECK THIS OUT! Don't want to read? I got you, yo! https://marc-antoinegerault.shinyapps.io/TMT_optimization/
- by UnknownIs your awesome new instrument generating so much data that you can't process it fast anymore? My data density has jumped about 5x from my last hardware to my new stuff and the data processing is correspondingly less faster. A huge thank you to the Director of Proteomic Innovation at Cedar Sinai, Dr. Simion Kreimer for texting me about this new thing called InfinDIA (which is in a free [demo?] for academics in DIA-NN 2.3 that you can get and read about here. I stole one page of the important stuff! How much faster are we talking about? One pseudo-bulk run (25 cells) on […]
- by UnknownEdits 10/2/2025: Thanks for the emails and comments! It looks like this is only the first 1,700 files. Still fun to download and take a look at! Also, it looks like the newest O-Link Explort HT can do 300+ samples/instrument setup per day. That's faster than an Astral at 100SPD. My notes were on the previous O-Link Explore 30something which was 82 samples/plate. That's 82 samples prepared per work day/instrument set but I believe that takes 2 days. Even if it's just that is 410 samples/week compared to 700/week on the Astral. And WAY cheaper on the Astral. WOOOOOOO! This paper […]
- by UnknownEven Doctor Who was like "that IS weird, innit?" when asked about the global declining bee populations (it's the pesticides, some of which are now just as abundant in the air as our friends the polysiloxanes)But declining populations aren't all that we need to know about our stinging little friends, and this very thorough review suggests doing true multi-omics to figure it all out.Really cool, but somewhat strange read, because you'll go a few paragraphs and then remember that it is supposed to be about bees, but then they'll mention them again on the next page somewhere.But, for real, take […]
- by UnknownFuck. This new preprint is awesome. For real….this is really really good, and I saw some stuff about it on LinkedIn and assumed it was blown out of proportion. Its not. It's really really cool. What if you found a really good in vivo model that you could control well to try and dissect what and how single cells actually regulate protein abundance. There are amazing resources for protein turnover and mechanisms in bulk digests, but nothing comprehensive in single cells. I mean…we couldn't actually do that…yet…right? In this case they specifically narrowed in on mouse tracheal cells. Then they metabolically pulsed […]
- by UnknownDue to the dispute between Guugle and Virginia Tech that resulted in – finally, I guess – the loss of my email, I also lost a lot of files linked on this blog that were still in that Googl drive. I'm hoping to find them at some point and put them back up. If you do see a link that is down you could try leaving a comments (it's hard to get through spam) or email me at LCMS methods@gmail.com (remove the space).In basically all mass analyzers, we set the mass resolution at a particular point in the m/z range. The […]
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