- by UnknownTHIS is the study that I've been waiting for. I don't know how it wasn't blowing up the interwebs when it dropped, but here it is.
- by UnknownDespite the fact that bacteria have little genomes (1,500 protein coding regions for the tiny ones and 6,000 for the big complex ones like Pseudomonas?) not even all of the model bacteria have been explored really in depth by proteomics. This study goes a whole lot of different directions with some great findings pretty much every way the authors point it. The data from bacteria were acquired on a nanoflow Orbitrap Eclipse and a microflow Exploris (50uL/min @90min). There is a helpful table that tells you which experiments were performed on what and when. The authors also do classical 16s rRNA sequencing […]
- by UnknownWhile I am skeptical of the currently accepted machanism for how those magnets induce electron activated dissociation (EAD), it's a super cool new technology. ETD but with basically no reaction time and no scary reagents? Wins all around.In this newest application of the technology these authors apply it to top down proteomicsThey mix up some commercial histone standards and show they can resolve and identify their PTM sites, then they do some bigger proteins (heavy chain might be the biggest protein they try in the paper) and then also resolve some intact glycosylated proteoforms.I thought this was a neat trick […]
- by UnknownUmmmmm…..that's this week! Fortunately, I only have responsibilities on Sunday (Early Career Researcher "Difficult Conversations in Science" – woo!) Monday – co-chairing the most popular and absolute best session – Tuesday….ummm … should probably make a slide or two….And the astrologer they use to provide weather forecasts to my telephone says that we'll only have 15 inches of snow on Thursday. Which, given current accuracy means absolutely no precipitation whatsoever and I probably won't even need a jacket! US HUPO sold out of the conference block of rooms, but you can still totally go. I registered last week! https://www.ushupoconference.org/registrationOh yeah, and these are […]
- by UnknownWow, am I super pumped to see this one out! You know all those minimum handling techniques for single cells generally means that EVERYTHING is injected into the mass spectrometer, right? This is a pretty minor alteration from my favorite paper of 2024 – CellenOne pulls out single cells, but instead of digesting them you drop in lipid standards and methanol and then run the TIMSTOF optimized for larger small molecules (lipids). They have to do optimization in both positive and negative mode, the latter I've never even tried on a TIMSTOF unless I was doing MALDI, and then the entire screen changes. […]
- by UnknownBig shoutout to Anthony for sending this preprint over! We spend a lot of time talking about how much specific antibodies can hurt science. We've been talking about it for as long as I've been able to have somewhat intelligent conversations about science. What hasn't gotten as much attention is how terrible "pan" antibodies are. I see papers all the time where they still do phospho-tyrosine enrichment with the 4G10 antibody- and I first used that thing 15+ years ago it wasn't very good then, and I ask at conferences all the time if it's improved and I don't think it has. You […]
- by UnknownA while back my nanoLC column provider was acquired. There are always growing pains with those things, particularly when production is shifted to a new location or continent. I switched to a nice small company with super friendly people – and some techbro bought that one too! I've been part of a couple of failed startups. I know a techbro when I run into one. I was so enamored that I immediately got a column bomb and dug out 15 year old notes on how to pack columns. As you might be aware, I have a blind spot in my right eye […]
- by UnknownLook at these nerdy Europeans and their multi-institute studies! This one is on the achilles heel of mass spectrometry based proteomics – non-depleted plasma! It looks to me like they prepped plasma and sent it out and everyone could basically run it however they wanted on whatever they wanted – and ….400 proteins is the high water mark…. now, this isn't enough for me to stop running plasma on mass specs, but it is enough for me to go across the hall later and ask how that O-link thingamabob we have here works!
- by UnknownLeaving this link here so I can find it. There is a point sometime when an ASAP JPR paper appears google searchable and may not make the ASAP page tab on the JPR website. Thanks @cportgrrl.bsky.social for helping me find it! This straight up surprised the fuck out of me, btw. I assume when you dump in formaldehyde for any length of time you just stuck all your lysines together and globbed up the nucleotides and left oxidative secondary changes all over the place.This does not appear to be the case! The authors take some HeLa cells and hit them with […]
- by UnknownSince this is a proteomics blog you probably aren't aware that Agilent makes mass spectrometers. While most of my commercial dealings with this company by, unit order, is the 5 qPCR/rtPCR instruments that we piled up on a loading dock during the pandemic that kept showing up functional for somewhere between 0 and 60 days – I have gotten hands on time with both Agilent QQQs and QTOFs in the last couple of years. The ESI sources these instruments arrive with are….unique… and interesting….. and quite honestly make the nanoESI sources of the early 2000s seem both mature and intelligently engineered. […]
- by UnknownI missed this one with the move and never ending sickness 3 (now 4? eeeek!) year olds create when they climb all over each other in "class" and big open gyms. Thankfully it came up during the new US HUPO sponsored podcast mini-series "The Undergrad Expo" which highlighted shockingly capable undergraduates (which you might have gotten from context clues) and their research. If you want an intro, Noah Earls is the guy who brought it up and his podcast is a cool 30 short listen. My understanding is that there are 3 main isoforms of ApoE and one is good, one is […]
- by UnknownThe last time I was part of a study where we needed to understand what a bunch of kinases were doing, we sent samples out to 2 different labs. Some were measured fluorescence activated cell sorting (FACs) while the rest were ran by a group who had validated immunoprecipitation based QQQ assays. Now, in my defense, we couldn't go into the lab for a few months due to a serious flood that led to both mold and asbestos problems because….well… you don't go to Johns Hopkins because of the nice modern clean safe facilities…. But I didn't mind getting out of […]
- by UnknownSo….everything you ever wanted to know about KRAS inhibitors but didn't have the time to do 670,000 DOSE RESPONSE CURVES? Proteins, phospho-peptides (critical, cause these things screw with MAPK/mTOR/etc) and OTHER PTMS? Crazy.
- by UnknownMan, this is so freaking smart and inciteful – and comes with suggestions for how to fix it! Now, the rumor is that the reviewers put them through the ringer on this to make them prove this wasn't something isolated to wherever the heck Heidelberg is. So they extracted data from files in ProteomeXchange from other locations and since the Bruker crazy .sqlite database format keeps information on freaking everything – they could pull weather reports and show the same stuff happens in Boston. Totally worth keeping in mind, because if you're doing something like the last paper on the blog where […]
- by UnknownWOOOOOOOOOO! Man, this paper is a lot of fun to read. I can't spend a ton of time typing here. I've got tons and tons to type elsewhere, but it's just in time to be cited in what I'm writing. Why would you read it? 1) This demonstrates that terminal cell types that we like to categorize as "cardiomyocytes" that don't really divide and more or less hang around the full extent of your life…- have different proteomes! Does that make them a different cell type? Does that make them a "sub-cell-type"? I'm not the person to answer that question, but it […]
- by UnknownI legitimately thought this was going to be one of those silly mass spec things we all do where we tinker with settings and get 5% more IDs at the cost of reproducibility.It is probably the second thing, but the improvement level is worth taking note of. The paper is open access so check it out, but a TIMSTOF Pro going from 5,000 some protein groups to 7,000 protein groups (? hard to see on the bar plot? by using 10 different 1/k0 isolation settings across the gradient vs the default instrument settings? That's a surprising improvement. Worth noting that the gains […]
- by UnknownOkay…so not to distract you guys from doom scrolling the news or the "news" if you're in the US where the filters on what we're seeing are…blatantly obstructive at a level we've maybe never experienced. Need some youthful enthusiasm? Start here. But actually go here. https://map.emsl.pnnl.gov/app/pmart-classic – you will need to register with PNNL. But then check out the short tutorial videos on how to use it. I had them playing in the background while I puzzled through making a plot or two. The narrator of the video seems to be really having a great time walking you through these tools. It carried me over […]
- by UnknownI've been moving and writing and just got internet in our new apartment a couple hours ago and – I'm leaving this link here. I'm going to take some time to permanently block on my browser any "news" site that doesn't have this on the front page. Why do you think that these right wing fanatics think that the US has had a technological lead on most countries for decades? I seriously wonder, because I think it's the fact our government has invested in unbiased research and that every dollar has translated into hundreds of dollars eventually. Scary times. Stay safe and […]
- 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 UnknownI was looking for this and realized I'd put it with a bunch of other new videos I'd found.This is from last summer's Northeastern University /Parallel Triangle Institute hands on single cell proteomics day.You get some super cool insight into running an Exploris with MaxQuant.Live AND expert tips on the TIMSTOF Ultra operations. Great great resource. https://www.youtube.com/watch?v=mMrujxr3JFw
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
