- by UnknownThis came up when some old friends were visiting my lab this week. Where do I get these estimates for how much protein concentration should be in each single human cell? A couple of places, but the best organized place to start is the amazing Human Cell Tree Map – https://humancelltreemap.mis.mpg.de/Is is the topic of this recent PNAS paper. Now – they did this the hard way. They took tissue from people counted the cells and weighed them. For real. It was an amazing amount of work. Supplemental File 3 is an amazing resource for getting these numbers. They didn't just come frome one white […]
- by UnknownThere is a lot to love in this short new preprint! Let's count them!1) This uses a NIST reference material and uses a very standard analytical approach to tell if one of these "next gen" proteomics things actually has quantitative accuracy. As an aside – this is one way to approach the easy and obvious SomaScam experiment that I've been searching for and pleading for – for nearly a decade. The authors spiked in a some proteins into plasma and then used the O-Link assay and made sure that -in a complex matrices like a human plasma pool (wonders and wonders!!) the numbers […]
- by UnknownAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHH!!!One of the biggest challenges in adopting a new piece of hardware is that you might lose access to software that you've used for years and are very comfortable using. Losing MetaMorpheus by adopting TIMSTOFs hurt. For real. And this isn't a dig on other great software out there – I just know how to use MM and how to read the data and how to make MM do what I want it to do. I have whole downstream pipelines for HLA peptide analysis that uses MM scoring output as the input. This week when I thought I was seeing artifacts […]
- by UnknownThis isn't the first study of it's type but this digs into more variations of how to fix cells. Something everyone doing single cell proteomics (SCP) has struggled with is HOW TO GET THE FREAKING CELLS TO THE MASS SPEC LAB.At ASMS, I detailed my adventures preparing EvoTips and driving them across the completely insane and poorly maintained Pennsylvania Turnpike. In case you were wondering – I have far better luck keeping the tips at a stable temperature and being on wet ice seemed to be a detriment to the tips. n=1.Meh. I was typing about something….THIS!Okay, so there are obviously […]
- by UnknownTesorAI has been on the blog somewhere before. As an academic I very much approve of the fact I can now process up to 500 Thermo RAW files/month! Edit/corrections – when I first starting using TesorAI it was only Thermo RAW file compatible. I'm punishing it right now and this is clearly no longer the case. The link above will take you to a high speed 45 second video demonstrating what you can now do with TesorAI processed data. You can tell a freaking chat bot to make your data into heatmaps and then just tell it to change the colors or […]
- by UnknownThis new tool may only be exciting for a small group of people – but holy cow, yo – this is a just visually stunning. Maybe I'm just used to the fact that all LCMS proteomics figures generally come off the software looking like crap, but graph based algorithms seem like a great idea. You will need variant input sequences from transcript level data. And proteomic data. And someone who can use python – and can install a docker. All that magic stuff is here.
- by UnknownWatch out UK Biobank – Pennsylvania is coming for you with 2 HUGE proteomics initiatives!Geisinger Health is well known for monitoring the genomics of my …neighbors who prefer to use horse drawn carriages over motorized vehicles. Due to the limited speed of …horses….people don't end up too far from home so it's easy to track geneology over time. Geisinger does other things, but that's what they're well known for. And Regeneron has the deep proteomics know how to pull off a 200,000 patient cohort!! Press release is here.
- by UnknownI just upgraded to the fancy new SpectroNaut 20 and was flipping through all the things! Here are the release notes (in screenshot form, which is by far, the most convenient way to share text!) And I'm having the guys at the HPC upgrade FragPipe Academic and DIA-NN Academic to the newest ones for me as well (I don't have permission) and in the latter case (DIA-NN Academic) there are a lot of shared concepts!In case it needs to be typed, I'm not accusing anyone of sharing notes. These teams are very user centric and we are all probably complaining about the […]
- by UnknownWow. Sort of short notice, but this looks like an amazing use of a few days in Boston/Cambridge. This wasn't on my radar for the summer. The program is a little vague, but the organizers are some of the best scientists in proteomics and have picked extremely relevant topics. Definitely something to think about! Edit: I found the list of speakers as well. I was just on the wrong page. Geez. Check it out, the week is stacked. Here are the main themes.
- by UnknownI gotta move fast, but for those of you on the TMT32plex or 35plex or whatever it is, I think you'll really like this screenshot! How? What? I don't know! Check it out here!
- by UnknownOkay – somewhere on this blog a few years ago is a post that is called something like "what the hell is ion mobility"? And I'm continually learning – or trying to – and might have just given 3 talks doing proteomics with ion mobility devices. I might still only partially know what it is and I certainly couldn't build you one.However, I'm occasionally surprised by measured versus predicted ion mobilities. And I'm often troubled by how ion mobility clouds are altered by things like isobaric tags. And for the former problem….this new preprint is really really interesting.Why couldn't a […]
- by UnknownGuess who finally got the ASMS PRESS PASS! Now….would….it have been an easier conference to have given 3 separate talks and not had a bunch of press responsibilities? Yes. it would have been. Waters saved me a bunch of time by inviting me to their conference but then not letting me in, so I used that to sit in my room for just a few and stare at the wall in the dark to recenter, and I sincerely appreciated that time. I don't think they had anything in proteomics to show off. I just went to be polite. On the proteomics side […]
- by UnknownAs my very first takeaway from ASMS2025, I'd like to start with this paper that is just a little bit older than I thought it was when it came up in my talk on Monday. Oh man, did we ever see some awful chromatography this week. Whole proteomics on 5cm columns was often higher resolution LC separations. There are 4cm columns and probably shorter. And often at low pressure. Now, maybe all the hardware advances that have happened on the gas phase should negate the statements in this commentary? But I'm skeptical that is truly the case. And maybe I'm just […]
- by UnknownConflict of interest statement on this one – I'm both a compensated member of the Proteomics Advisory Board for Mobilion Systems and the first author of this preprint met weekly with me for 4 or 5 years while getting her PhD. I'm even more impressed by her work than by the quality of her education. ;)Okay, but here is the real question and I know I've certainly wondered about this….. at what point would ion mobility and quadrupole isolation overlap? Or maybe this? Could you crank up your ion mobility resolution to a point you could widen your quadrupole and […]
- by UnknownJust stealing Chris's post! Bonus, if you see Ian watch what he's eating and model your diet after it. He's at least 114 and he's out there on stage giving talks at 8 in the morning? Oh! Website went up on the Astral 2 "Zoomie"270 Hz and the resolution to do TMT 32-plex (I thought it was 35? Does anyone know?) Big question should be – can it do the 32-plex at the highest acquisition rate? Or do you need to slow it down? We're going to see a lot of 300SPD proteomics on it, I guess. Probably with a 4cm column so […]
- by UnknownIf you've seen me talk about single cell proteomics, I like to point out the proteins I can see (50,000 copies and up) and I make a joke suggesting you come back in a decade if you're interested in transcription factors.They turn on transcription at your DNA…you only have a couple copies of each gene. In many, most cases, we only expect a few copies of each of those proteins in each cell – certainly not tens of thousands! Yes this preprint demonstrates measuring them in global single cell data! How? Well…it's complicated. But basically it looks like we've got MS1 – […]
- by UnknownHardware is already leaking to the media? Here is the first one – and a surprisingly well-written article with insight from a bunch of early adopters and/or beta testers. Oh crap, and my news feed was like "oh, so you like mass spectrometers? First I've ever heard you mention that… here's another! Looks like it's a top-down focused instrument with MSn(?) capabilities and some electron transfer thingamabobs, but I'm excited to see what it can do in the area of PTMs in bottom up as well. There area lot of PTMs that are just no fun at all to do with MS2 […]
- by UnknownRead more here! It sure makes the Illumina protein prep 384 samples/week seem even sillier…..
- by UnknownHeading into ASMS shortly and there will be lots and lots of places where business and science interact. We'll see a load of vendor talks where the two things are clearly working together to make things better… but we'll also see… the other thing.Case in point – An e-Mission EXD cell equipped after the quad on an Orbitrap UHMR can stablize the hell out of large proteins going into the Orbitrap for "single ion" detection (it's not really single ion, it's crappy signal measurements for deconvolution and enough combined to make it deconvolutable and since the mass accuracy is phenomenal it […]
- by UnknownMy first thought when I saw this new preprint was something like "I've been working on these IRB documents for my clinical trial for waaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaay too many hours, cause I can't figure this out at all." I honestly might still not get it, so the less I type the better, but this is probably the best figure for driving the idea home in the preprint. I do think it is an interesting idea, and I'm all about getting extra throughput. Multiple samples running with time delays are demonstrated as being deconvolute-able using retention time re-alignments. From a practical standpoint – Since 2020 I think […]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
