- by UnknownWOW! Did I ever blow my initial take on this paper. Not a little, but by so much that I'm a little concerned about whether I have some level of impairment in my reading and/or comprehension right now. I'm tempted to write it off as flu like symptoms while moving my family to a new city in the winter, and hoping it isn't a brain tumor, but – if you saw that post it was way off. I'm tempted to leave my original post up here because, if there is a strength I have as a scientist, I think it is […]
- by UnknownToday you can buy a mass spec package and – as long as nothing breaks – and you take really good notes most people can be generating really good proteomics data.When it's not working – well….that's different. Troubleshooting still seems to require an expert or a lot of work and logical exclusion of components one at a time. If your fancy neural network machine intelligence thing that turns those spectra into biology decides to have a headache and not work? Well, sometimes you have to look at the original data. Where do you learn that in 2024? While proteomics is growing at […]
- by UnknownFollow this if you don't want to watch it in my silly blog interface. https://www.youtube.com/watch?v=wzmJDNmsWK8Is the US HUP Ed&Out the coolest committee you can be a part of (used to be VMO)? YES! Huge success that started when Amanda Smythers started pulling together amazing silly rhymes last year at a meeting and Dragana Noe ran with it and made this super clutch finished product. So much work! Who is pumped for the US HUPO video competition this year? Me? You? Really? Submit your videos!
- by UnknownI swear, I thought this was on the blog somewhere and I can't find it. If you're in Europe or other places, I guess, you can just disregard this entirely. Rumor is you have a variable or variation DIA window button. If you're in the US, there is a trademark thing and only one vendor(?) can give you a V on your instrument by default. Huge shoutout here to the Slavov lab for posting RAW files in the plexDIA preprint back in 2021 or something because this way of setting it up is more efficient than how I was setting it up. As […]
- by UnknownOkay – so this is really interesting and I may need to sleep on it, but here is the idea – Ideally we'd be able to see every proteoform MS1 rapidly and have instruments fast/sensitive enough to sequence them. We can use 2D separations to get there pre- or post- digestion, but in no case are these experiments fast.What if we tossed the MS1s? Could we still do good biology? I mean….an intact proteoform mass with 600 amino acids is a lot less likely to occur completely at random than a 10 amino acid peptide…Seems to work, too! The proof of concept […]
- by UnknownY'all, I am SO PSYCHED for US HUPO 2025. As you might know, THE Proteomics Show podcast was renewed for a 6th(Six? 6?) season! And the whole reason US HUPO put up with our antics in the first place was that we were highlighting invited speakers, award winners and the big deal plenary people.Not to brag, but I don't really have any hobbies except reading proteomics papers and maybe finding out that there are a bunch of proteomics people together in some city (or ski resort) and going there whether I'm invited or not. As such, I'm sorta plugged into […]
- by UnknownMy favorite part about this new Nature news feature was that I thought it was an article from 10 years ago.No…but the first citation is that article from 10 years ago…Look – antibodies do work. But is that discount mass produced antibody for $400 what you want to stake 15 years of your career on without validating the hell out of it? Probably not, right? It's a really super ultra complex tool. Like any complex tool it needs QC/QA and we don't see enough of it.
- by UnknownI'm again going to put off blog posts on the 50,000 human proteome cohorts using "next gen" spot-based targeted proteomics.I get it – I love the idea that we can use alternative technologies and get to this kind of population level protein level studies. But -just to remind you – we don't know the answer to this question – What we do know – without any possible doubt, whatsoever, that evolution is super ridiculously stingy when it comes to making new stuff. Sure, there are excessive things that don't negatively impact the overall survival of a population – but those are […]
- by UnknownSTOP. IGNORE THE FLOWCHART ABOVE. These are bioinformatics people, they think this stuff is mandatory. I assume their conferences all have contests where the winner makes the flowchart most likely to make someone in another field throw up.Again – don't look at it – 'cause this is legitimately important. You know how the genomics people have been doing things for years with illustrious sounding titles like "The 1,000 Human Genome Project?" Particularly when a lot of those things kicked off and the technology was more expensive, these things absorbed HUGE amounts of research dollars. The goals were to undestand how human […]
- by UnknownWow. This new study of kinase inhibitor treatment of cancer cells – using top down (intact protein/ no digestion) proteomics is 1) Super legit2) Seems really approachable3) Kind of resets the bar in my head for what we can do right now with today's off-the-shelf technology.And I might have a surprise for you. While Neil Kelleher's name is here because it is part of a special issue in his honor – this isn't a Kelleher lab study! Generally when we see a super impressive top down study I flip through it and then think – cool – maybe I'll be able to […]
- by UnknownI think it is, though I also thought that in 2022….and…maybe I did win the Chicago one…? No, it looks like I tried to print my own shirt and the company thought I was playing a joke on them? Weird. Well, if you think you can beat my entry, go ahead and try! Mwhahahahahahaaaa. You can waste your time submitting one here.
- by UnknownCheck out one of my favorite techniques of the last few years – the NanoSplits paper here! The first preprint of this study is somewhere on the blog, but the work evolved considerably since we initially saw it.If you aren't familiar, what this does is label free preparation of REAL NORMAL SIZED SINGLE ONE (1, uno, um, eins, jeden, yski, en siffra, een, ichi) at a time on glass slides using precision robotics. THEN the lysed cell is split into 2 fractions with most of the protein going one way and more of the little transcripts going the other way. You do […]
- by UnknownWOOOOOOOOOHOOOOOO! Editorial here! Last year it was long read sequencing or something (they forgot to include it in the 2014 issue, I'm pretty sure).Check out this special virtual issue (click on the references!) highlighting a bunch of cool people in our field and their work!
- by UnknownFor an old and probably inaccurate description of match between runs (MBR) you can check out this old post. Also, you probably shouldn't go past Fengchao and Sarah's paper here. Link might be the preprint.Quick breakdown, though -Imagine you run 50 LCMS runs on different patient samples.In 35 of those runs you fragment and successfully identify PEPTIIIIDEK, it's pretty much 100% +2 charged and 634.3608 and comes off at 15.6 minutes In the other 15 runs you see a +2 peptide at 15.6 minutes but you don't fragment it or don't get good enough sequence quality for a positive ID. Match Between Runs (MBR) to […]
- by UnknownWell…that was a run! I was on Twitter for 11(?) years and Tweeted over 10,000 times. Mandatory, obviously. It's done, though. Biorxiv won't link your Tweets and I don't see a tab on Altmetric. That increasingly bizarre drug addict killed what was at one time the best device for rapidly disseminating scientific advances I'd ever seen. BLUESKY is going to be better, I think. The expertise density is legit and some people are starting to figure out some of the cool features that I haven't yet. And! BLUESKY IS TRACKED BY ALTMETRIC, JUST LIKE THIS WEIRD BLOG! Wait. What? Sure is! And has been […]
- by UnknownHere, I fixed it for ya! Even though I can clearly see why I also wouldn't have recommended Ben Orsburn as a reviewer for this one, I do actually really like this new study. I will, however, complain first. Last week I had a great meeting set up with a potential funder for my program and we got to an impasse that was something like the most important person on the call saying"-of course we understand that single cell proteomics is not actually a single cell" And, while that was not at all unexpected because this was not a dumb group of […]
- by UnknownI would like to thank these authors and the prestigious Journal of Proteome Research for something new to have nightmares about – SPONTANEOUS ACHILLES EXPLOSIONS! Proteomics to the rescue! (By the way, there is this whole series of bizarre children's books where there will be some silly problem and it's all COWS TO THE RESCUE or something. It's funny by the 11th page and continues through the 6th book somehow.) Obviously, this group wants to understand why sometimes people's achilles up and explode just for fun, and they are able to get samples from patient who end up getting correction surgeries! Obviously, this […]
- by UnknownIt'll take me a while to update everything on all the internet things but we can finally wear these new hats openly.We'll get used to the colors, though orange and maroon will likely always be my favorite combo.We're moving so I can get started as Assistant Professor in the Department of Pharmacology and Cellular Biology (through the new institute I don't know if I can talk about yet -soon!). I'll also be helping out Stacy Gelhaus as an Associate Director in the phenomenal Health Sciences Mass Spectrometry center. I JUST ORDERED SUPER EXPENSIVE BIG HEAVY THINGS and saw pictures of crates […]
- by UnknownThis new paper is an improvement over a super cool already existing technology that I had NO IDEA EXISTED AT ALL. Did you know that you could dump in something that cells would mistake for normal methionine that you could selectively pull down, so that you knew what proteins were being made at that point in time? I did not. I bet the nerds pulling down ribosomes and cutting the attached DNA with nucleases, then busting up the ribosomes and sequencing what didn't get digested (RiboSeq, definitely not convoluted at all) don't either. Sure, RiboSeq is cool – and programs like ProteoFormer […]
- by UnknownI don't know about you, but I'm waaaaaay dumber than usual when I'm at really high elevations. Not only dumb, but also lazy and tired and 2 glasses of wine and I might just fall right off of a ski lift. I went to a wine convention thing in Colorado at a Ski resort years ago and found out all of these things. This study tried to get to the bottom of this by collecting proteomic and metabolomic samples from people who went to work in high elevations for 6 months. Holy crap. Some of this work was at 4,800 meters in […]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
