- by UnknownWe were JUST talking about this in lab meeting last week! I swear.I said something like "well…sure…we can generate loads of good glycoproteomics data (I've got a tattoo that is almost old enough to drive that shows I've successfully pulled it off at least once on some pretty crappy instrumentation)….but you can't actually interpret what that big pile of glycopeptide stuff means….And….well…there went that argument!
- by UnknownWow…. I do just have to leave this here and move on. I've already forwarded the paper to a bunch of people, though, and can't wait to spend more time on it. We need to figure out how much DDM you can use before it's a bad thing, though! This group used 6-8x more than what we use, and they get a lot more membrane proteins…..Totally worth taking a look at!
- by UnknownOkay, we have to take a look at this for real. I do like the color scheme on these plots, though…As an aside, I ran a commercial program for some people recently and it gave me 20% more protein groups than the ones I currently use. Those extra 20% really annoyed my collaborators. They were …like… biologically very very unlikely…? Not DIA-NN, a commercial thing, but I did re-learn a lesson that more peptides isn't always a better. But DIA-NN has built enough credibility for me to be hesitantly optimistic that I will like this new version. Get it where you […]
- by UnknownFor the first time in a long time, I had to do some EvoSep troubleshooting. Turns out that ceramic needle thing can get clogged! Gabriel at EvoSep led me to this super useful online resource that walks you through step by step to get it all worked out. It's amazingly clear with pictures and "did it work? click here!" AND 4 MILLION PERCENT BETTER than letting Adobe's class trailing LLM help you dig through the user manual. If you see a button to turn that pile of poo off, please let me know where that is!
- by LCMSmethodAdminYeah! I love this new method at JPR! There used to be LCM(s) (laser capture microdissection thingies) everywhere! No joke, they almost died out to the point that one of the leading companies was briefly for sale at the price of a Baltimore/DC suburb house. At ABRF I looked at two very nice new ones and individual systems were in the very nice Pittsburgh house sort of price range. MR-SP2 takes one of the legacy systems that you can't buy new anymore and optimizes it up for spatial proteomics with all the details you'd need to set it up yourself.At 1-2 cell […]
- by LCMSmethodAdminLazy post day! Reviewer comments (….some a little past the due date…sorry….) on ….I shouldn't type how many papers….it'll make me a little stressed out…… on my desktop…..I am legitimately loving recording this new season. Thank you US HUPO and these amazing guests we have lined up. Did you know a brain…just….unfolds….? I did not know this. With the podcast actually now racking up more listens than this blog, I should probably advertise this on the other thing…. But this took 6 minutes and most of that was trying to decide on a gif.
- by LCMSmethodAdminDo you wonder why we don't just do immunopeptidomics by genomics technologies? Besides the obvious fact that it's impossible? Or just wonder what happens after you've spent a really long time working on the crappiest peptides you've ever tried to fragment? Then this is the review for you (and you)!
- 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 […]
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