- by UnknownFor an old post on what a Lab Developed Test (LDT) is vs an In Vitro Diagnostic (IVD) you can go here. And…in what was an altogether extremely bad day for the FDA with thousands of people finding out when they tried to use their badges and they simply didn't work – they also lost a federal appeal in this recent ruling.The American Clinical Lab Association sued to overturn FDA's new rules for moving all new (?) or all (?) diagnostics to IVD designation. So….for those of us who put Aim 4 of our grants things like "and then we'll move […]
- by UnknownYeah! Proteomics is bigtime! Check out this 1) Instanovo is finally out and 2) 2 people I know were interviewed about it and they seem to think it's smart! Instanovo final paper here.
- by UnknownYou know – I was really pumped when my kid's puppy was like "HEY HEY HEY GUY I HATE, WAKE UP OR I'M ABSOLUTELY GOING TO TAKE A DUMP IN YOUR APARTMENT!!" So we walked in the pouring rain without either of our coats until she found the absolute perfect place to poop about 3 blocks from our apartment at 4am. And then my Inbox was like – "HEY HEY HEY GUESS WHAT! YOU'RE GOING TO HAVE TO TOTALLY INSTALL R STUDIO ON YOUR PERFECTLY OKAY NEW LAPTOP!" And here is why I have to stop putting it off….I don't have an accessible […]
- by UnknownForwarding this one in just a second for sure! Most of what I know about the HLA/MHC immunopeptidomics / neoantigen presentation system comes from this amazing old paper in Cell Immunity. The mechanisms for processing and presentation are largely inferred from the large number of high confidence peptides they identify – but again – this is inference.If we really wanted to understand how this system worked could you just knock out each protein along the way and do proteomics and immunopeptidomics? I mean, that's what a lot of people would tell you to do and that's what this cool new MCP paper […]
- by UnknownI was freaking out just a little late last night in lab. You ever get those 100GB warnings from MASSIVE and then the time limit goes by and you're like "false alarm, nothing changed?" If you're over your FairUse limits with Thermo RAW files those files will disappear.With Bruker .d file format you have embedded folders. Those folders stay, they just get emptied out. For real – it'll look like you still uploaded like 800 .d files and they're still there – but they…aren't….As I was trying to figure out what I still had backups of -and what I didn't – […]
- by UnknownWould you believe you could sample single cells directly off a plate and lyse/digest and transfer that cell with virtually no losses? No? Sounds sort of unbelievable and there is some "extraordinary claims require some amazing evidence" or something. Would you believe over 3,000 proteins per single cell with a TIMSTOF Pro 1 system running a 21 minute active gradient on those same cells? No? Would that immediatley make you think -wow – that should have ultra super fucking amazingly extraordinary goddamned evidence cause I don't think I've ever gotten more than 500 proteins on a very similar system regardless of how long […]
- by UnknownWHOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAAAA!!!!!Dataset for reanalysis alert!! EDIT – EEEEEEEEEEEEEEEEEEEEEEEEEEEEKKKKKK! I can't find the data files. Contacting authors now. I have some 100SPD files from Matt Foster's Astral and I think they're like 8GB? So….8GB x 36,000? Is that 288 TB? It might just be uploading and they wanted to preprint something this year? Mann lab optimized perchlorate based enrichment to get a super cheap sample prep method giving them about 2,000 proteins per sample in human plasma. Then did 36,000 of them?!?! No nanoparticles? Off the shelf stuff? I need to read this, but – whoa.
- by UnknownArtificial intelligence stuff has come so far in such a short time. Just last year, a sick 3 year old and I could not get either of the ones I pay for to generate an image of a turtle swimming in ketchup. And – today? Check that out! Totally did it! The future is now! Okay – so in what might possibly be slightly more useful – what about a killer session at ABRF 2025 on AI in proteomics? This featured two young scientists who actually know what they're talking about. Sebastian Paez from Talus bio – who went through where and […]
- by UnknownOkay – so this is really cool as a user – even if I feel like I'd only ever use it to look at someone else's data because I don't think I meet the minimum requirements to share my data. Getting an account and digging through the example data is really intuitive. I'm all about more transparency and so it goes here. Maybe I'm sleepy and moving fast but when we get to a bunch of prompts to install my docker my brain sort of checked out. It seems like every time a software has a docker requirement that means I […]
- by UnknownBen: (Amanda is a postdoc at Dana Farber and some Harvard place and is the Chair of the US HUPO Early Career Researchers (ECR) Committee. Many of us picked up extra stuff, but Amanda pulled triple duty at US HUPO 2025 filling in for government reasearchers who weren't allowed to present to the public…cause… you know…). Amanda: The first time I went to US HUPO we were in the beautiful city of Charleston, SC. We had everything you could want in a conference – innovative science, inspiring atmosphere, great weather, a t-shirt cannon, and a Waffle House within walking distance. However, what […]
- by UnknownAs a lot of people know I've been trying to find the funds and opportunity to launch a formal degree program in proteomics for…a while… I'm cautiously optimistic that I might have found an interested audience with the money and the authority to make it happen. We'll see, though! Honestly – it can almost feel like escapism to put your head down and prep a couple hundred samples for an instrument right now – or submit a crappy grant – but there is only so much protesting and complaining that we can do. (That's what I'm telling myself, anyway!) As I'm […]
- by UnknownTitle first because – by page 2 I was thinking – 1) Can I get another espresso without waking my kid or his puppy up? and 2) What a weird and crappy experimental design! I do need that espresso because I'm clearly misreading Table 1. 24 solid tumors were analyzed? Across both sexes and a wide age range? They are all tumors? Like no healthy matched controls? Wait – are those tumors from different organs? Weird, right? The reason I'm continuing to type isn't (solely) because I'm procrastinating on 10 things I need to be doing. I'm continuing to type because it fucking worked! The question […]
- by UnknownHey! Are you going to ABRF2025? It starts in 4 days! I should pick a seat for my flight! (Strangely you do that on SouthWest now??? Weird. I was asked to amplify some of the mass spec stuff that can sometimes get lost among the FACS and microscopy and inferior technologies like genomics/transcriptomics. Honestly, I have 6 different scSeq things circled on my calendar, as well as some microscopy stuff. There is still mass spec there! Self-serving, the session I designed is the first one that pops up (there will clearly be lightning talks and posters) but the first proteomics session got the super […]
- by UnknownTaluBio is this funky spinout company that has stolen some of the best and brightest young people in our field and is out doing crazy cool proteomics drug discovery work on rare diseases.You probably knew that, but did you know that they're up for some big award against all sorts of funky startups? It's a funny list to go down, like one company makes autonomous tractors. Hopefully…. by… developing their own algorithms and not using these… no one wants what happened to Jeremy Renner (he got better). You can go to GeekyWire and check it out (and vote for TalusBio) here!
- by UnknownI can't wait to try this and compare it to DIA-Analyst!
- by UnknownIf you're ever feeling really good about your skills as a proteomic mass spectrometrist and need knocked down a peg, I strongly recommend going into the amazing field of ADP-Ribosylation. This amazing modification can be one ADPr or long chains of repeated ADPr. Sounds fun, right? Glycoproteomics is great because there are like 1-4 sugars for each mass and they can go on like 5 amino acids? I forget, and each sugar chain can break in like 2 or 3 places. ADPr cranks up the fun by each monomer fragmenting in 7 possible places, the mod can exist on 11 different amino […]
- by UnknownIf you're rapidly drafting some figures – Biorender can be super cool. But what if you don't have a license? NIH BioArt is adding stuff all the time! https://bioart.niaid.nih.gov/Proof? There is no way that it had a Q Exactive when it first made my blog last year! I would have found it, but now it has it and more free/open art to use to really drive that dumb point home that you're trying to make! While you're there check out how much cool new stuff has been put on NIH 3D! https://3d.nih.gov/Mandatory reminder that these government resources are probably at risk right now. […]
- by UnknownWhere was this when I was stinking up the NIH submission system with my crappy grant applications? You want a 110 pt font axis? You get a 100 pt font axis! Introducing EasyPubPlot! And I'm not messing around guys. This isn't easy for someone who knows off the top of their head what version of R is on their computer. I'm not talking easy for someone who knows the difference between a .txt and a .tsv and a .csv that only opens right in Notepad++, not NotePad+ or NotePad-I want to take the vomit inducing plots from SpectroNaut and make a plot that […]
- by UnknownJust like everyone else, I'm absolutely fucking thrilled to see Artificial Intelligence showing up all over the place. A lot of commercial websites now have slow new AI functions that are essentially "ctrl+f" in your web browser – the kind of improvement is assume Elon Musk and his fans are most excited about. (Another amazing new success from Mr. Musk this week. Add that with the fact that they're now leasing office space for HHS bioinformaticians to log into AWS to do their work…cause that's a cost savings over them logging into AWS from spaces that cost the HHS $0! …. Though […]
- by UnknownI was really torn on using the above .gif because I come from a long line of people who have died either in coal mines or thanks to what they inhaled down there. Unfortunately, all of my cousins that are under the ground somewhere in WV bathe in the political disinformation kool-aid to the point that I can't even talk to them, so we're going to have some fun with this important new study! If you think being a coal miner in West Virginia is dangerous just because the governor of the state made his billions of dollars running the least […]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
