- 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 […]
- by UnknownI'd seen this one months ago, and didn't dig into it until I had reason to send out some updated reviews. If you're trying to catch up on proteomics as of February 2025, it's worth the read.
- by UnknownI totally hoped this was going to be an untargeted plasma proteomics at low resolution/high speed paper, but that's okay, it's still pretty cool.Now…if the price of this fast little ion trap would come down to an appropriate price range… we'd be in business. Do you want 5ppm mass accuracy on a benchtop Orbi that's WAY slower? Or 15ppm mass accuracy on a TOF that is the same speed as this cool little ion trap? Or is 800ppm an okay trade off for fast and sensitive? I'm not willing to pay the same price (or more!) for unit resolution, and […]
- by UnknownI'm going to leave this here. I think it's a really intesting study, but I'm a little surprised by the conclusions. Caution is always good, and this paper is all about limitations of blood (spot?) forensics. While machine learning classifiers appear underpowered to make accurate determinations, I really wonder if a targeted analysis of specific proteins and peptides – in this same set of data – would come up with the same limitations…. Also – in case you haven't seen it, last week we dropped a new podcast that was also on Proteomic Forensics (in wildlife!)! Get it wherever you get […]
- by UnknownThis paper took me some time to dig through, with the majority of the time focused on PUBLICLY AVAILABLE SOMASCAN DATA!Paper first. It's here! What's it about? It's about how to change the output data from SomaScan into something useful. In this case the authors walk you through a large pile of separate R Scripts that will take you from your Somamer output and will get you to a gene identifier for each one….cause…obviously….that's not what you get from the vendor….Here is what you'll need to take these output data and get to pathway analysis….they all won't fit on the screen….Now….you […]
- by UnknownThis idea has been proposed to me a few times recently and I thought something like "oh, sure, and exactly how TF would you do it in practice??"Not sure it's the solution, but I sure need to leave it here so I can look at it later!
- by UnknownWow, I've been slammed lately! Okay, if you haven't seen this, get out from under your rock and check this out. It's stunning.
- by UnknownI only have a second to drop stuff here so I can close another of the zillion tabs open on my desktop! These are going to be intrinsically controversial, so the data we have the better!
- by UnknownDisclaimers! I've had this open on my desktop since I got back from vacation and I do not get it. We're way way out of my wheelhouse. I do think it's worth posting here, though, for people to think about, if only so I can close the tab and reference it here later. Ultimately, I don't think it has any real overlap with what most of us do PTM-wise with mass spectrometrs. We're looking at how all the acetylation sites (for example) change in appearance and abundance when we put drug A into some cells when compared to control cells. However, the interest […]
- by UnknownThis one had so many steps to get behind the paywall of that I thought I was trying to find a certain global leader's name thousands of times in files about a certain island. It was totally worth it though, because this is GREAT! KRAS does so many things and has so much redundancy that you can fill entire buildings full of RAS researchers for decades and they still haven't sorted it all out.Now there are these awesome little small molecule inhibitors, but you're still looking at a big matrix of effects. Tubingen was like – fuck it, we'll just use them […]
- by UnknownUmmmmm…..okay…..so when I saw the first preprint with a similar concept, I thought something like "that's a weird idea that probably looks okay on paper but will absolutely never ever work in practice".And….here is a bunch of top notch scientists like Dan frickin' Polasky, himself, demonstrating a very similar concept? Between the 2 studies there are 15 or so authors and I'm pretty sure that means 22 of them are smarter than me – so… …wait. That's upside down. Do we revisit this idea? It might be like the single ion mass spectrometry thing that I really couldn't figure out, that – to […]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
