- 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 […]
- by UnknownI didn't know Dr. Amina Woods as well as you'd guess considering the 20+ years we were doing mass spectometry stuff in the same city. We'd spoken a few times, most recently maybe two or three years ago and I was always a fan of her work and presentations of it. What a person she must have been to have inspired such a touching piece from the nitpicky chemistry nerds at JASMS. It's a legitimately nice read and maybe being good and interesting enough to inspire such a thing is something we should all aspire to.
- by UnknownI was initially a little appalled by the amount of optimization of diaPASEF windows in this paper, but I read more of it while walking a mean little dog in the rain and there is a lot here. Food science is very different that your run-of-the-mill proteomics samples. Often the thing you're worried about is the allergenic peptidome, and those sure don't look like tryptic peptides. It's likely that this team ran some baby formula using the default methods on the instrument and they didn't see a single thing of interest.They had to go back to the drawing board do wide […]
- by UnknownWow. Okay, so am I ever confused. Since 2012 or so there has been a constant irrefutable message from one of the world's largest science companies. And that message has been something like "the only way to do good multiplexed quantification is by using an exclusive, incredibly slow, and over all low sensitivity method which can only be performed on our most expensive and complex instrumentation." You've seen that, right? This method relies on doing MS2 fragmentation in an ion trap and then (in later iterations on the Fusion instruments) selecting multiple large fragment ions for MS3 based quan in […]
- by UnknownUmmm….if this is real it could be enormous for a field or two!Yesterday I was reading another paper in this issue of Analytical Chemistry that I was excited (and very skeptical about) and I got to the end before I realized there were no files to support some very lofty claims. I was already really mad about some dumb shit my country was up to and I guess the reviewers and editors were just like – meh – whatever, this is going to be super controversial, so we'll just let you push it through without showing any work. That paper […]
- by UnknownBorrowed this picture from the MicroChem website while I was looking up what a Kirby-Bauer Inhibition assay was. Its a microbial zone of inhibition assay! Paper link!What's a postbiotic? It's a metabolic secondary product of "good" bacteria or other microorganisms. So the question was something like "what would inhibit Salmonella typhimurium" and when we see that inhibition, what is causing that?And since Salmonella is not a fun thing for humans to get, the goal is to find compounds that will inhibit it to limit infections. Interestingly the proteomics from these researchers was performed by sending the samples to the University of Copenhagen […]
- by UnknownUmmm….Wish I'd seen this before US HUPO, because I clearly had an opportunity to ask some questions this week of the PI! (This wasn't me getting mugged for the 3rd time in my life, I'm just never sure what to do with my hands.)Silliness aside this is a really cool top down proteomics study of proteins extracted from single muscle cells (which can be a lot of material…sometimes these are 10x or 100x the size of the typical human cell) but top-down of a single cell of any size is still super cool.And there is bigtime variability across single skinned cells […]
- by UnknownI haven't had the chance to put time into this, but I want to. The abstract suggests that maybe doing all the BCA quan steps might not be necessary for some experiments.
- by UnknownOkay, so I was going to type something like "I don't know where to start" but that's a lie. I should probably start by apologizing for being such a jerk about the city that hosted US HUPO. I'm pretty pissed off about the state of my country basically all the time. I'm particularly frustrated about watching the news and grinding my teeth last week enough that I had to go to the conference with a broken tooth. And some geographic areas are more at fault for the rapid decline of my country than others. Whining about it doesn't change things, […]
- by UnknownWhile I was at the amazing US HUPO conference in …Meh…Souri…which was honestly not as bad as I thought it was going to be, Natalie Porat-Shliom spoke on this amazing new paper at MY University! Stunning amazing, ridiculously great work that blew up our lab Slack channel thing! If you're continuing to look for the applications for single cell proteomics, this and the liver is a great place to start (If you saw my talks at the conference, I'm clearly biased, since this is similar to what my team is also doing). This paper take the work that Florian was doing as […]
- by UnknownWow, there are a lot of liver diseases and we've got decent diagnostics for….well…liver damage…. that's about it. A small panel of liver damage markers finalized around the time Stan Lee and Jack Kirby went on a creative bender and wrote everything from the Fantastic Four, through Spiderman and the X-Man comics. I'm not kidding, there really has been almost zero forward movement in liver diagnostics since the 1960s. The liver protein panel was old when I was running them in the clinic in 2003. And it's still the same thing. Could top down proteomics be the answer? Given the current limits […]
- by UnknownTiming on this one is a little unfortunate, because everyone has schedules, however, we're getting this science fiction sounding new toy and I'm happy to invite you to this webinar next week! Okay, so what if you could do live cell imaging and – not messing around – dose your cells with a drug and then use machine learning tools to go and pick up the cells that meet your criteria. For example, what if I was growing a population of cells – on the instrument(!!) – in the presence of a KRAS inhibitor and then when that annoying subpopulation of […]
- by UnknownThis new preprint is so legit. Not only does it identify a pile of histone post-translational modifications I didn't know about, but it does it fast AND it justifies the chemistry that makes it happen. What if the reason that some of these PTMs aren't visible is that the modification neutralizes that peptide's ability to pick up a charge? Makes sense. A lot of the more awful PTMs do. But what if you could make them visible by adding a boring ol' tandem mass tag? Bonus points for the introduction of an enzyme I didn't know about with an amazing name:Stop, don't […]
- by UnknownIf you are like me and you have a PC in your office that your IT security people don't know about (shhh!) that you just copy your RAW files to in case you need to look at an actual spectrum, do I have great news for you! As of a few months ago Thermo started embracing Windows 11! Check out this list!
- by UnknownLeaving this here so I don't lose it for another week because I am incapable of committing any of these author names to memory.You'd think it would be easy to find something written in the last couple of years that was about tissue-specific proteomics, right? You would be very very very wrong. I have 9 tabs open on just the PC I'm standing in front of in my house (wait. why am I here? I have a meeting in Oakland in like 30 minutes…? TYPE FAST!)In 8 of these papers, the authors who wrote it used the GTEX RNA DATA to […]
- by UnknownIn an interesting recent trend, everyone seems to be emphasizing how small of a cell that they can do single cell proteomics on. Do we have a new winner? No, Akos did single E.coli. Even if it was only like 25 proteins, that's clearly the winner for craziest tiny cell idea.But this group did PBMCs! How much protein is in a PBMC? 14 picograms! (These author's math, not mine). FOURTEEN? My group has recently struggled with some human immune cells… and from the TICs I was guessing we were starting with less than 50 picogram. FOURTEEN? Geez.How'd they get there? NanoPots. Ouch. Okay, so something […]
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