- by UnknownI don't know if this is the answer to some of my most pressing current problems, but it does seem silly dumping all the data at once into something that can't handle it.Maybe if we treat the data as a stream(?) we can allow it to be progressively processed(?)In their models they get up at a 3-order(!!!) of magnitude(!!!) increase in speed when processing large (and largely simulated) datasets up of tens to hundreds of thousands of proteomics samples.Worth at least thinking about, IMHO.
- by UnknownSince no one asked for it (and ASMS ignored me)! THE Proteomics Show will record live at International HUPO on Monday, November 10th. Main poster/exhibit hall at 2pm (I think!) It'll be me for sure and one super secret special host – and audience participation! Woooo! Toronto!
- by UnknownWhoa! This has been a big week or two for plasma proteomics! And this multi-center evaluation goes after the most important part of it – who gives a rat's ass if we can detect a protein? Not me and not you – what we cant to do is accurately quantify it! Let's spike in all sorts of stuff and have everyone you know run it! All sorts of instruments are employed in this study and -HOT DAMN – Did they get 4,000 proteins in neat plasma?????Oh. Okay, When you put E.coli and Yeast into plasma, even at low concentrations on a […]
- by UnknownOkay y'all. I'm going to approach this one with a healthy pile of skepticism, but I need a solution – and probably you do as well. A small label free single cell study for us – like one 384 well plate is generating maybe 500 – 600 GB in RAW (Bruker .d) data. Then to run our data in SpectroNaut we have do first do the absurdly infuriating process of converting it to a special SpectroNaut format. It's called .HTRMS, which is probably Swiss for "Hard drive (T?) Room Makes no Sense". This takes your .d file and makes a […]
- by UnknownHey you! Do you need to do a big multi-batch TMT study? I've got a couple coming up! What if there was a handydandy GUI that would help you designt that study for getting the maximum quantitative accuracy and least effects from impurities and coisolations fudging all your super cool biological findings?CHECK THIS OUT! Don't want to read? I got you, yo! https://marc-antoinegerault.shinyapps.io/TMT_optimization/
- by UnknownIs your awesome new instrument generating so much data that you can't process it fast anymore? My data density has jumped about 5x from my last hardware to my new stuff and the data processing is correspondingly less faster. A huge thank you to the Director of Proteomic Innovation at Cedar Sinai, Dr. Simion Kreimer for texting me about this new thing called InfinDIA (which is in a free [demo?] for academics in DIA-NN 2.3 that you can get and read about here. I stole one page of the important stuff! How much faster are we talking about? One pseudo-bulk run (25 cells) on […]
- by UnknownEdits 10/2/2025: Thanks for the emails and comments! It looks like this is only the first 1,700 files. Still fun to download and take a look at! Also, it looks like the newest O-Link Explort HT can do 300+ samples/instrument setup per day. That's faster than an Astral at 100SPD. My notes were on the previous O-Link Explore 30something which was 82 samples/plate. That's 82 samples prepared per work day/instrument set but I believe that takes 2 days. Even if it's just that is 410 samples/week compared to 700/week on the Astral. And WAY cheaper on the Astral. WOOOOOOO! This paper […]
- by UnknownEven Doctor Who was like "that IS weird, innit?" when asked about the global declining bee populations (it's the pesticides, some of which are now just as abundant in the air as our friends the polysiloxanes)But declining populations aren't all that we need to know about our stinging little friends, and this very thorough review suggests doing true multi-omics to figure it all out.Really cool, but somewhat strange read, because you'll go a few paragraphs and then remember that it is supposed to be about bees, but then they'll mention them again on the next page somewhere.But, for real, take […]
- by UnknownFuck. This new preprint is awesome. For real….this is really really good, and I saw some stuff about it on LinkedIn and assumed it was blown out of proportion. Its not. It's really really cool. What if you found a really good in vivo model that you could control well to try and dissect what and how single cells actually regulate protein abundance. There are amazing resources for protein turnover and mechanisms in bulk digests, but nothing comprehensive in single cells. I mean…we couldn't actually do that…yet…right? In this case they specifically narrowed in on mouse tracheal cells. Then they metabolically pulsed […]
- by UnknownDue to the dispute between Guugle and Virginia Tech that resulted in – finally, I guess – the loss of my email, I also lost a lot of files linked on this blog that were still in that Googl drive. I'm hoping to find them at some point and put them back up. If you do see a link that is down you could try leaving a comments (it's hard to get through spam) or email me at LCMS methods@gmail.com (remove the space).In basically all mass analyzers, we set the mass resolution at a particular point in the m/z range. The […]
- by UnknownI, for one am glad to see that when I'm not the only one who is at a loss to illustrate deep learning models and resorted to a commercial AI to make some squiggly lines (for the github tutorials).You probably want to read this first before starting to install it!Is this the thing that can take my metabolomics and proteomics of the same exact 800 or so tissues and integrate them properly? …Not out of the box….The current input categories are data that is already processed through R packages such as PharmacoGX and the single cell transcript measurements were processed […]
- by UnknownI'm largely leaving this one for me, but for proteomics people take a think about how value neural networks (like DIA-NN) have helped us in distinguishing signal from noise in low level peptide data.They really are evolving. We constantly do true/false by lying to the neural networks about where and when we have blanks and controls and non-human samples. And even 3 years ago, they weren't nearly as trustworthy as they are now.Now…consider the metabolomics field which doesn't even have a good way for routine false discovery rate estimation in their data….then drop your signal down to just above your […]
- by UnknownLooks like a nice solid workflow (and Shiny App!)
- by UnknownHey you! Did you trick a bunch of …less informed….investors into buying you a bunch of mass spectrometers because you did genomics a while back? Did you already try underpaying a lot of very young and capable seeming scientists with chemistry degrees but no experience, and are SHOCKED to discover content level expertise is required to do mass spectrometry based -omics? After all your …celebrations…that you were now a field leader in proteomics or metabolomics or mass spectrometry of some kind.. do you have just enough money left to finally hire a full time expert for that fleet of instruments? You'll be sad […]
- by UnknownOkay – this has been going on for a while now – you might find 10 posts on this blog about the quest of protein-protein intereactions. Putting protein crosslinkers in to bind proteins together for proteomic analysis! Is this it?!? It looks pretty smart. But I also have a bunch of crap in my freezer that works in a centrifuge tube with 4 proteins (sometimes….) that absolutely does not work in-cell. If so, I'm (…ugh…you work with what you have when you've got 5 minutes for a blog post and a protein bar…)
- by UnknownI've been hanging out with people for the last year or so who are building super high resolution ion mobility systems (at least resolution of 300 while operating, which is significantly higher than any of my TIMSTOFs). So it's funny to see benefits of taking a low resolution IMS (10?) and making it even lower! Anything not getting trhough the FAIMS is going to waste, so this makes a lot of sense. Ultimately you're probably just using FAIMS to get rid of the +1 junk you can't sequence anyway and the PTMs that are much easier in downstream analysis to just […]
- by UnknownTransplantation of organoids serves as a model for understanding the complex development cycle of the the colon, including cancer, and may eventually be a mechanism for building back healthy tissue.In this stunningly beautiful study, this group dissects the process – often at a full single cell level – with striking depth and with cell type-classification.
- by UnknownI've been presenting on this stuff for a while – and I don't think it's a one off observation. A professor in the audience (thanks Vinnie) provided an idea that might help me finally crack this one. Now…gotta talk someone into doing a bunch of cell culture….. Regardless, it's my first use of this particular meme and I'm relatively sure I did it right! https://pubmed.ncbi.nlm.nih.gov/38014353/
- by UnknownIf you're familiar with ETD (electron transfer dissociation)And the much newer and (magical – I still don't get how using large magnets forces more democratic fragmentation, but it's fast as heck, EAD (electron something that starts with an A dissociation)).Here is something called ECD (electron Capture(?) dissociation).Which was equipped here into an Agilent Triple quad wearing an extremely tall tophat.Edit: I have been informed that is a Q-TOF. This appears to allow top down proteomics of little proteins with ECD that is much faster than ETD! It still seems slower than EAD, but might be an attractive solution for upgrading an […]
- by UnknownIf you've ever been to this blog before, you might have encountered the fact that I despite nanoflow liquid chromatography. These authors seem to agree! I rarely quote the text of a paper completely, but I'm going to do it with this great new one. Begin quote: When I started my first proteomics experiment in 2007 or something, I thought "man…these motherfuckers are dumb….this is the shittiest 'separation' I've ever heard of". But you had to do it…probably…because the mass spectrometers needed 4 kilograms of protein separated over 6 weeks of chromatography time to detect 3 proteins besides albumin. Now that mass spectrometers don't completely […]
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