- by Unknown1) Today I just discovered the ACS Journal of Chemistry Education (or maybe re-remembered it was a thing?) And it's a treasure trove of interesting stuff. Example? Check out this cool story from the pandemic where students remotely analyzed DIA generated MS2 spectra. This is how it went (stolen brazenly from the paper)!
- by UnknownI can't possibly spend the time on this new study that it deserves, but I really am going to think about it on my commute today. Or listen to the Halo Effect album I didn't know about until yesterday because that's how busy my 2025 has been. And maybe also think about this paper.When Anna Barker was on THE Proteomics Show podcast she stressed how absolutely critical the sample handling was to the setup of CPTAC (that was pretty much her idea, btw). I asked her what she thought about all the people who are just pulling from repositories and […]
- by UnknownI'd have went with the MCP abstract graphic but it's all smooshed up on my screen.Related, we just had Mike MacCoss on The Proteomics Show (dude won the Don Hunt award for distinguished contribution in proteomics!). I try to always ask guests what they're most excited about in the present/future of proteomics and he cited clinical and translational assays that have happened or are happening. FINALLY! (I added that bit, 'cause it's about time!) Having trouble coming up with a list of them? Here's one to add! Check out this sick new one I just stumbled onto while not at all […]
- by UnknownI realize more all the time that I'm in the AI Skeptic camp. Every time I try to get an AI to do a simple task for me and I end up doing it myself I move further into that camp. I've got a whole list of failures in the accounts I or my employer pay for me. Confident python corrections that are definitely not correct, 14 attempts to have my publications on my CV reordered to meet the opposite requirements of my previous and current employer, and artwork that is hilariously awful. I fully expect everything "generated" from an […]
- by UnknownWe kicked this around really hard back when there was a Proteomics Old Time Radio Hour. Not this paper, but the base concept of mixed proteome digests for quantitative studies. I'm still uncomfortable with it as a concept, but let's talk about the paper first.The main part of the study is simulating single cell digests with proteomics people's favorite toolkits. They took a cancer digest and spiked in an E.coli digest at one concentration and Yeast digest at another.Then they used a really cool robot that doesn't appear commercially available that they have designed themselves over the last 16 years […]
- by UnknownDisclaimer: I'm going to ramble about a new commercial product that was totally my idea and if you buy it I'll probably get money back for a whole lot of enzymes I personally bought. This was actually a tough post to write that I deleted and re-typed several times because it seems antithetical (which might be a thing) to this whole blog thing. Meh.Ramble: I had a few months between my academic appointments which ended up being a top notch sabbatical, and that's what I'm going to call it from now on. I consulted for some really cool companies, found time […]
- by UnknownI saw this one 3 times, loved the logo, but questioned whether it was anything useful to me and finally just read most of it. I moved to the Github halfway and started trying to install it. Paper link. Is it the easiest thing I've tried to do today? No, but I also had a 4 year old pumped full of hot chocolate in a Sporting Goods store when dude decided football cleats WERE MISSION CRITICAL and we ended up leaving with nothing at all. But….could you….hypothetically have Dance Partner dig through PubMed and find you a list of proteins, transcripts, lipids and […]
- by UnknownI ran across this looking for something else…. Honestly, I really like the Ultra2 source, but if I still had one of the older ones I'd look into this, for real.
- by UnknownThere is another optTMT, but that one doesn't have a dash and it's for designing smart multi-batch mutiplexed experiments. You can read about that one here. This new one is about how a lot of TMT labs are labeling 400 pounds of peptide (181 kg) and then injecting 200 micrograms per injection on their Orbitraps and 1000 micrograms on their Astrals. If you wanted to just label 10x more peptide than you'd possibly use instead of 10 million times more peptide, how would you do it? That's what the dash is for! While this might seem just a little silly since there are […]
- by UnknownFirst off — CHECK WITH YOUR HPLC MANUAL OR MANUFACTURER!!Is the resolution of GIFs getting worse all the time? If so, it's the only change I've personally seen from this whole "AI revolution", except people saying "I asked ChatGPT" when they would have said "I did a Google search" back before Google reorganized and put their search algorithm teams under the control of their marketing teams. True story, that's why Google really doesn't work well anymore and AskJeeves is back, but now it needs more electricity than all of Spain will sue this year to look up stuff on Wikipedia for […]
- by UnknownUmmm…..so…Imma just leave this here and not talk about it any more, maybe. Wait. Maybe just this – if your technology is producing results that can be validated 30% of the time then you could save a lot of time and just pick a gene or protein and flip a coin and go read up on other technologies….
- by UnknownThis is obviously interesting – and surprisingly easy to pull off. The data is processed in FragPipe and one of the output sheets is put into these python tools to identify the complementary fragment ions. I like the figure above because they use 2 very similar peptides labeled with TMT and demonstrate that they can clearly find clean complementary fragment ion pairs. Oh yeah, here is the paper. They really really don't want to do any spectral deconvolution so they only used 3 of the TMTProC tags that give them clusters of complementary ions 4 Da apart. The open suggestion is here […]
- 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 […]
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