- by LCMSmethodAdminBrazenly borrowed from this whitepaper. If I have a super power as a person or a scientist, it is that I'm very okay with being wrong. It helps that it happens all the time and the fact that I have friends and a domestic partner who are way way way smarter than me. I'm used to be the dumbest person in the room and I can just discover that I'm wrong.And boy – was I wrong about this new Illumina Protein Prep thing. I thought it was just a repackaging of SomaScan, a product that has had the strangest propensity for avoiding […]
- by UnknownThis is the first time ABRF has happened in a city that I live in! Man, once upon a time there were so many proteomics people that we had competing initiatives. We were standardizing methods and standardizing standards and comparing software and it was all a lot of fun and it all kind of stopped. But you know what you can talk about anywhere you want to? Single Cell Proteomics! Dr. Kyle Swovick, photo taken from the front row, organized a session and, for a small conference with 3 competing sessions at a meeting with sessions with riveting titles like "asset […]
- by Unknown4 people have sent me this new preprint and I've had to go "…oh…it's in my draft's folder…" but the power went out in my building while I was at a conference and it's sort of a mess and I'm grumpy, so Imma post this. So…sometimes I see these papers where someone does something like – 1) Get better results than anyone in the world has ever gotten with that instrument (or at all) 2) And when you do that…if you don't make the data publicly available, I have to think….Let's do background first! THE number one challenge in single cell proteomics (or any […]
- by UnknownIn this US HUPO sponsored season (thank you!) we're being serious scientists who are asking the big questions of bigtime experts of specific tissues and organs. Neely kicks it off in this week's episode with "…What…IS…hair…?" And one we just recorded features a guest who speaks to our level when referencing the activity of adrenaline as – and I quote – "Yo, get down there and dilate, we gotta go!" US HUPO is letting us do a big unsupervised season and so far, I'm happy to say I'm enjoying it. Listen to Episode 101 with Glendon Parker, wherever you get podcast […]
- by LCMSmethodAdminOh. This. Is. Sick.Matt Foster and I were JUST talking about this at US HUPO. Sometimes blood gets frozen in transit, y'all. And sometimes it probably sits around on some phlebotomist's cart for a whole day and then gets frozen. The last paper I could find on this weird stream of consciousness website was almost 10 years old. Wait. How long have I been doing this? That seemed like a recent paper… Whatever. It was before all these fancy nanoparticle thingamabobs showed up.Actually, I'm procrastinating – here is a rant. I'm convinced that absolutely no one understands how these nanoparticles work. […]
- by LCMSmethodAdminI don't have my notebook on me but someone who was on The Proteomics Show dropped a knowledge bomb on us about cysteines a couple of years ago. She said something like only 12% of cysteines are involved in those disulfide bridges we're all so worried about. Might have been a he and might have been 2 or 40%. So…when this PI is in the lab, he commonly skips the alkylation and reduction steps. Not just because he doesn't know where the reagents are, but also because I spent a couple of years studying drugs that bind cysteines. True story, about […]
- by UnknownOkay, so this might be more interesting to me right this second than it normally would be, but I'm very glad to have this group's notes and findings! There is a paywall on this, but if you were a little sleuthy you might find an earlier version of it that isn't quite as polished that is not.
- by UnknownY'all know what organoids are, right? Some people got together like 20-ish years ago and were like "yo, I wonder if it actually makes sense that all these human cells are growing in 2 dimensions…?" For real, like, they don't grow like that inside a human being, outside of perhaps Lady Cassandra….So they make cells grow in little balls instead. Still…not…like normal…but if you give people a dose of a drug and measure a response and you work out that same dose for cells growing in 2 dimensions vs growing in the little balls of cells (organoids) the latter is closer […]
- by LCMSmethodAdminOkay, so maybe what we actually need is 500 parallel ion traps within our instruments!!! This is just an early proof of concept of teeny tiny ion traps operating under the control of individual (or individual clusters?) of GPU (CUDA-type?) cores. I've never seen anything at all like this so it jumped the queue of things I meant to type about this week.
- by UnknownYikes. Okay, so if there is legitimate instrument competition across the board, I think there should be some seriously competitive pricing in the LCMS space this year. If you're not seeing it, demo something else and let them know about it because – holy cow…I had a super early version of the 7600. I had it before it could do ZenoPulsing/ ZenoTrapping in DIA. It was a nice instrument and super ridiculoulsy great at targeted proteomics. That PRM thing (mRmHR?) loved Skyline and it processed data super fast. But it wasn't up there with my TIMSTOFs. Not really. You could […]
- by Unknown…well…this is frustratingly brilliant….So why we're all messing around trying to figure out how to do a better job deep learning endogenous peptides, this group decided to just cut out the middle of the plan completely.This system relies on using E.coli to generate the peptides that you think are there which can be directly informed from your genomics data – to actually make the endogenous peptides that you might be able to see – if they are there. Double dash! Then you can have the real spectral libraries for that mutant form that would be really super amazingly cool to see […]
- by UnknownThis is a solid new study with a noteworthy method combination.The global proteomics was done one a TIMSTOF with diaPASEF and analysis in SpectroNaut. The glycoproteomics was done following some sort of chemical enrichment thing followed by TMT proteomics. It's a big 'ol pile of files.I was looking for how they would normalize the glycopeptides against the whole protein concentrations and they actually include that part in the method section! Our puppy just scratched our kid, sounds minor, but I've got to stop typing here even though I haven't got to how they used some combination of ETD and HCD […]
- by Unknown…well…I didn't know that you could do this….And – wow – has ChemRXIV gotten a glow up! It used to be the ugliest duckling of the preprinting world, but now it's totally modern and legible! For this study something called a Q Exactive HUMR with charge detection was used to work out these assembled protein complexes. Flipping everything I know about Orbitrap intact protein work on it's head, this group ran the charge detection thingy at 200,000 resolution with direct nanoinfusion for possibly as long as 30 minutes. I've done a lot of intact mAB work, somehow almost always out of the […]
- by UnknownI missed this recent study and it's ridiculously cool! I'm going to start by just stealing this line in the conclusions by the authors: "…From an ecological-evolutionary perspective, a post-transcriptional mechanism that modulates rapid variation of the venom phenotype can potentially confer adaptive advantages in response to environmental changes…."…right??? because of course it would. 'Cause if you're a snake and you want to spread across a mountainous region where some of your 94th cousins live close to the ocean and you live at 3,000 meters you and your cousins have different things that you need to need to defend your self from, […]
- by UnknownThis was the first poster I hunted down after Day 2 Lightening Talks at US HUPO 2026, and now I can share it with you guys! It's great because another SCP Biorxiv preprint came out this week and my opinions on that that one definitely have to stay in my drafts folder. This is a place for positive commentary, mostly! Proteomics has a very strange relationship sometimes with the concept of zero. I get it, dividing by zero is not allowed in Excel, and that's probably a significant part of the problem, so there are piles of smart-ish ways to not […]
- by UnknownGiven the sheer multiplicity of peptide level data, we're probably approaching a point where just trying to do metagenomics classification seems silly compared to the metaproteomics stuff, right? The way I think of it – Yo, is this species A or species B? I've got 20 bases of relatively fragile oligonucleotides, so 4 bases ^20 is what I'm working off of to make that species ID. That's a big number. Something in the e12s according to some extremely sleepy Excel thing that took 11 seconds and might not be right at all. Or. I've got some collagen which can have a half life […]
- by UnknownOkay, so everyone else should be really embarrassed they didn't put together a preprint and get credit for "ChatDIA". I just submitted a one paragraph "paper" to Biorxiv on my lunch break, so ChatDDA is mine in the next 72 hours or so.That's not to say that this doesn't have merit. This thing appears to fare well against DIA-NN!
- by UnknownYou know what proteomics needs more of? Accessible data interrogation and interpretation tools, like the new SAINTexpress portal! For some people they just really need tools online because it takes them 6 months to get permission to install things. Not me, I hang out with the IT Director whenever I can. SAINT (Significance Analysis of INTeractome) (whoa. my font went all funny, that's what I get for copy/pasting. Come on, Ben you can absolutely spell Sigifnivcance on the first try. Wait. Maybe not.) is a great way to take your immunoaffinity, affinity enrichment, pull-down, IP-MS, AE-MS (wait, maybe thats what one of […]
- by UnknownOkay, so I went back and forth on posting this one for a while, but I might honestly be missing something. I'm certainly missing the RAW data files, because those weren't deposited… but the initial idea seems clever…until you try to design something that can multiplex more than 3 samples at a time….The basic idea is something like "why swap isotopes around when you could SWAP AMINO ACIDS AROUND?"As shown in figure 1 – if you had INFINITELY LARGE PEPTIDE LINKED TAGS! …attached to your tryptic peptides…. (wait. what?) …you could have INFINITE MULTIPLEXING! Y'all don't line up immediately to add a 2,000 Da multiplexing […]
- by UnknownOur library doesn't subscribe to this journal, and I don't have $50 to spend on one paper, so it sure was handy for the authors to put links in the abstract to the -OpenLC Github! There is a repository with .STL files you'll need to print adapters and the code you can use to over-write the original OpenTrons one.There are a couple of related papers that I can access as well, such as this one that can probably provide a starting point on useful details like this.What's the point of these super fast LCMS methods if your HPLC only has room for […]
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