- by UnknownI received some questions about my longer term impressions of the amazingly sensitive and somewhat fast TIMSTOF Ultra2. It's been a year already? Yikes. I guess I'll reference my earlier TIMSTOF reviews.Great stuff!1) The sensitivity of this thing is still absolutely unreal. Multiple people are writing up papers on single cells ran on it with DIA label free and the numbers are cell type specific and amazing.Even with a high loss, but very inexpensive and very fast sample prep, most cancer cell check in at well above 2,000 protein groups per cell and human hepatocytes are around 2,500. Throw in a […]
- by UnknownThis new paper maybe isn't for everyone, but I'm excited to look at these scripts. There are a very small number of supported software packages out there in the world (approaching zero) that can make sense out of direct infusion of flow injection analysis quantitative data. We used to have a pile of them. Ion A is 10x higher than ion B in these two matrices, you could extract that a bunch of ways, but that's largely fallen off.I'm also excited to see how many metabolites look real in direct injection in an Exploris 480. The intrascan linear dynamic range of a […]
- by UnknownFor real, I've been telling people about this conversation since we recorded it a while back. Snot is way cooler than you'd guess.
- by UnknownThe fact that some labs have some weird background ions that other labs don't (check my repositories for Pug keratin! There's tons of it!) isn't news. Someone a while back showed they could tell when a study was done in the winter due to the amount of wool peptides ionized in their deposited data. I forget who that was.But this new paper in JASMS shows that it's not just proteomics and peptides. It can even be those nasty adduct things that everyone outside of one group in Madison, Wisconsin ignores is even a thing in proteomics. This is the first time […]
- by UnknownMaybe this was here before? I'm not going to look, but it's definitely out now in JPR.It makes sense in my head, though. The same way that a single population of a million ions ionized at the exact same second might end up being distributed between mostly +2 charged, some +3 and maybe a barely detectable number of +4. Why wouldn't that population of peptides dissolved in acidic buffer also have 2 different possible shapes (or more?) Is that charge linked in some way? Would make sense. The authors suggest a simple calculator for predicting both modes – which would […]
- by UnknownI'm legitimately knocking out a couple of blogposts to get my brain fired up for writing and my hands used to the new (quieter) keyboard I brought to a super intensive 3 day writing camp. R01 resubmit peer pressure time! As you might guess, both R01s I should be writing on are about the human liver and not honey bees, but you probably have a dumb way of doing things as well. Where the f' is the control key? I'd rather look for it here. AND honey bees are super cool! Did you know that worker and drones (which I thought were […]
- by UnknownInteresting! When this group talks about -omics they even include lipids and metabolites. Worth taking a look at for sure. Figure 2 is one of the clearest descriptions I've ever seen of machine learning classifiers. The link to the web portal in the paper appears to need a user name and passcode, but I ain't got time for that.Probably faster to pull the code from this Github anyway.
- by UnknownI had a really weird conversation this week when people were talking about how many "tokens" they were using for making AIs do things poorly for them.Look, I'm also getting AIs to poorly do things for me that I don't know how to do. What I'm not doing is 1) Paying for them…2) Letting some money hoarding corporate weirdos see what I don't know how to do by sending my prompts off to some AI datacenter they knocked down a park to build.And the LLMs on modern hardware can run faster than the cloud based ones because the upload/download speed can […]
- by LCMSmethodAdminI love when a proteomics study makes my newsfeed! Did I know what a gastruloid was before yesterday? Related, do you have gastroids? Here is a link and there are reasons this ultracool study is making the popsci popups!This is one of the earliest stages of mammalian development – studied at ridiculously high depth here by RNA-Seq, proteomics (by TMT SPS RT MS3) and phosphoproteomics by the same.Don't feel like reading? Check out this awesome interactive webpage with protein networks and protein by protein visual analysis. Edit: I thought it had phosphopeptide interactions mapped, but I think I just clicked on a bunch of […]
- by LCMSmethodAdminOkay, so here we go – a real question for proteomics scientists.WTF is in that weird yellow stuff you put in the cell culture media? Apparently it comes from a cow. And – even if you don't have it in your database to look for it, it probably has an effect…Super cool idea for a study. https://pubs.acs.org/doi/10.1021/acs.jproteome.5c01097
- by UnknownWhew…what a month….. if only the highest numerical % of your grant was the one that got you funded, I'd be looking at catching my breath and starting a deep dive into some amazingly cool single cells for a couple of years. It is, however, the lowest number that gets funded, which is both seemingly weird (totally weird….nerds….) and it's funny to joke about it and not funny to be a little sad.While I was doing ALL THE THINGS the world kept moving and I kept mostly meeting my daily reading goal, so I'll back print some things like -SINGLE […]
- by UnknownThis is amazing. Not only did this group use a commercial DESI equipped instrument, they found an Orbi XL somewhere and put a DESI on it, AND they put one on an Exploris 240!
- by UnknownSo…this came up with some incredible scientists I met at the University of North Carolina this week…And here is a really cool review/perspective on the same issues. UNC's core is getting WAY higher plasma proteome coverage than I ever have with their amazing robots and magic nanoparticle things. But when they do quantitative comparisons and have rigorous restrictions on their quantitative accuracy, the numbers drop.Is it as bad as an aptamer? Of course not. Nothing is as bad at measuring the abundance of a protein as an aptamer. Might as well flip a coin 😉 But this is a smart look at […]
- 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)!
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
