- by UnknownMan, sometimes y'all send me papers and totally ruin what was otherwise a really focused run or something. This paper is certainly the case, because it is a fix for something I had no idea was an issue. We've had ICP-MS of single cells for at least a decade. Maybe much longer? I don't know. There is even a commercial FACs coupled ICP-MS thing that I'd love to have. So when this paper popped up in my inbox with the suggestion that it is a big deal I thought I was just being sabotaged. Did you know that when we do ICP-MS […]
- by UnknownThe preprint of this paper is on the blog here somewhere I think, but this paper has progressed quite a bit since the initial posting. I'm pretty sure the preprint used just standard "Whisper" 40 and 80SPD. It's been a while, but that's my recollection. Those methods are somewhere in the 100nL/min elution range, though if you watch the EvoSep monitor closely it sort of goes to 50nL/min but maybe just for equilibration purposes. This appears to feature the new EvoSep WhisperZoom methods which are 200nL/min, or what you might consider …the default method on your instrument for nanoflow liquid chromatography… The […]
- by UnknownHoly shit. I'm way too busy today to spend the time on it that it deserves, but I'll set some files to download until I do…Up front – I'm biased. IMP is one of my favorite places in the world and this study features both friends and a personal hero or two, but this is a sick paper.I do very much appreciate how clear the authors are here about cell size, etc., they don't average 5,300 proteins per A549 cell, but they do get that on the largest ones with the highest relative protein content. There is a lot to unpack […]
- by Unknown600,000 freaking samples? FOR PROTEOMICS! The goal is a depth of 5,400 proteins/sample. Quick reminder that when you're using this platform you are PROBING for 5,400 samples. That doesn't mean you detect them all. Obviously they might just not be there. Or they might be below your linear dynamic range. But you tried to measure 5,400. I'm unclear from the press release what these samples are. All plasma? In which case – 5,400 is going to change the game entirely. The human blood atlas (thanks Ben, for the link to this updated page) only lists 4,200 proteins detected by mass spectrometry!
- by UnknownI'm behind the ball on this, it's been a busy year, but Adam's write up on it is a great place to start. Some background would probably be helpful – An IVD is an in vitro diagnostic assay LDT is a laboratory developed testSounds the same? Basically is, but how they're regulated has been – until now -very different. I only know about the mass spec part, so here is my incomplete and quite likely inaccurate interpretation of how this works – Hospital clinics generally have MD/PhDs hanging around helping patients, doing surgeries, training people and doing research in-between getting paged to go to another […]
- by UnknownI honestly don't know why I still have GoogleNews on my phone, it's descended to AI written gibberish that has worse grammar and coherence than this awful blog you're visiting. However, these over the top Science business topics do provide me with thinking points.If you aren't familiar with Quantum-SI, it is a little benchtop box that can sequence a couple of proteins really well by degrading them.If you immediately thought…wait…like the Edman Degradation thing we used to use before mass spectrometry replaced it in about 94% of labs? No! It isn't just an expensive Edman sequencer, it is on the front […]
- by UnknownIn case you're new here or my sarcasm doesn't translate well – this study is amazingly fantastic and probably very very very very boring.Quick summary? These nerds did the stuff that everyone hates to do and they came up with a QC standard that they could run at every site. FOR YEARS. Actually FOR FOUR (4, vier, quattro, cuatro, fier, quatro [cause they like t's less in Portugal than in Italy]) YEARS! Why is this super fantastic? I mean, besides the 9,000+ QC files? 1) The mass spec instrument methods are completely harmonized (settings are the same for each piece of hardware […]
- by UnknownUnless you've been living under a rock where you don't hear much about proteomics, you probably know that a bunch of people did plasma proteomics on 53,000 samples with proximity extension assays (O-link panels, not the little 96 target ones, the big ones that require super high end RNA Sequencers). Here is one of the original papers (October 2023). There have been some really positive statements about how the O-link data correlates well in some regards with GWAS level findings. Now this data is basically out there for people who want to explore it. You can find it here, but keep this […]
- by UnknownHappy New Year, y'all! Wow, I'm busy with this move, it's 1/7/25?? Typing fast! Okay, so a while back I did a funny thing where I put up a survey on LinkedIn and also on some other social media platform and got two very different replies from the respective communities. My exaggerated summary is: Industry people seem to ALWAYS normalize the amount of PTM (for example, phospho) versus the total amount of protein present.Responses from academics were more like – If you're in that latter category, here is the thing from my perspective – you never ever see a western blot for the MAPK […]
- by UnknownA big thank you to Aleksandra Nita-Lazar for suggesting this as one of the most impactful papers of 2024 that didn't make my initial list! Again, the less I type here the better on the physiology/interpretation point, but from the introduction it's pretty clear that: 1) microglia phagosomes are super important biologically and in a "plethora of brain pathologies" (stolen from the abstract) and 2) you'd think we'd know a lot about them, and we do not.The part I do understand here is that a LOT of techniques were employed including proteomics on the purified phagosomes. That part was performed using […]
- by UnknownThe less I type about this one the better because it is way too far out of my functional working knowledge. It was the paper suggested for super important 2024 paper that should have been on my best of 2024 list!
- by UnknownIt's been…a…year….for sure. And for proteomics, this is EASILY the biggest year ever. Mine kicked off with the honor of being invited to speak at the amazing EuBiC Winter School! (Mandatory – you should think about integrating ProteoBench in your lab – it's probably time for protein informatics to grow up and this is one major step forward.)SO! Because NO ONE EVER ASKED FOR IT (should be the official moto of this blog and about half the episodes of THE Proteomics Show)Wait. This is important. This year there will be a winner! I'll send out a trophy and everything. I'll be bugging specific […]
- by UnknownI forwarded this new paper around and it was somewhat relieving to see other people as confused as me about it.Of course, I immediately found the contact page on the Pi-Hub and asked if I could contribute somehow to these huge though somewhat vague and overarching mission(s)!
- by UnknownThis might have been useful this time last year, but we worked it out on our own. Could we have done better with some real optimization because chitin is a very unique material? Probably. It's part of this cool new – 2025 release! Tissue proteomics book!
- by UnknownOne of the things on my checklist to discuss with potential new collaborators for LCMS based proteomics is going to come down to how we currently run the instruments based on current informatics challenges.Data Independent Analysis (DIA) is probably going to give you the highest number of peptides and proteins and best quan.Then why do anything else? Cause the other oneData Dependent Analysis (DDA) is way more likely to identify cool PTMs. I'm convinced this has very little to do with the instruments or the instrument methods – we just haven't sorted out the informatics yet. Probably because 1) we don't really […]
- by UnknownI have things to do, so I'm just gonna drop this here and run, but it's super cool! You know those Waters DESI things that sound fantastic but no one you know has one? They're like a MALDI but things multiply charge like an ESI. Now you can get proteins and peptides and fragment things like any other ESI source – you can even use all your normal deconvolution and fragment prediction stuff in a spatial context! It looks like they don't have to matrix it, so they can do their DESI stuff, then capture off the same tissue to do […]
- by UnknownThis is a save the date I saw on LinkedIn. I'll update when I see a link and registration details!
- by UnknownYing Zhu is having a solid month for his CV! While the resolution might not wow people in the MALDI world, the depth sure should make up for it. 3,500 proteins quantified and more than 120 "pixels" analyzed per day (a pixel is a 50um x 50um square, though it looks like they can cut smaller than this. With this little material and an eye on throughput – the fancy tools on the Eclipse for MS3 and Real Time Search didn't improve things.The other interesting thing I highlighted is the batch effect correction. Original reference goes back to here (small world) with these […]
- 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 […]
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