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When I think of proximity extension assays (PEA) which is either famous because of O-Link - or is? O-Link, I think of purely using it for large population studies or for validating discoveries by high depth mass spectrometry based proteomics. But...could you use it in place of mass spec proteomics? Because that is basically what this group did here. Now...if your protein or proteoform isn't in…
Okay. Chemically I do not understand why this would work. That's okay, I don't understand how a lot of things work.... They start out by laser capture microdissecting a pretty big area of cells. Something like 500 micron x 500 in 15 micron cuts. And you stop wondering why the cut is that big when you see the digests are loaded on a Q Exactive Classic. Man, I love those old things, but proteomics…
Hey proteomics people! Did you know that Waters makes mass spectrometers? They totally do and, while I'm not at all sure how this happened, I got invited to drop in and meet scientists and see some talks and touch some instruments. I'm pretty sure I got to visit because of some impressive numbers out of the P10 instrument which looks like a compelling piece of proteomics hardware. I'm trying to…
This is an interesting one. What if it wasn't the most efficient to have proteomics mass spec instruments EVERYWHERE? Rather, what if mass spectrometry proteomics was, instead, a fully centralized system where each sample could be measured comprehensively on multi-capacity hardware without all the compromises that come with solo 150kg - 400 kg vacuum chambers? In the simulations presented here it…
I won't like that picture freaks me out a little, but here we are. 2,800 human samples analyzed at incredible depth. You have to be asking yourself that with a dataset this large and comprehensive, clearly we'll know for sure that the correlation is between transcript abundance from GTEX and this, right? Uuuuummmm..... yeah, it's...the same....though that 0.105 from the pancreas is....special....…
Today I had the privilege of meeting with some fancy people from all over the place to discuss some concerns I have voiced and/or amplified about Bruker Daltronics support system. My concerns largely centered on what looked like a model I've seen before where an LCMS business is the cash cow (wtf is a cash cow?) for a big company to buy a lot of dumb shit. Who cares if a company uses their profits…
Okay. So what if you sent the same single cells out to a whole bunch of labs that agreed to send the data back? Obviously no one would want to play unless they had the very best stuff, right? Or maybe you had to have the stuff to play? I don't know but this is super cool. Now....I am a little confused about the HPLC setup. It looks like they used a bunch of instruments but there is exactly one…
nanoLC System Volume — Flow Path Calculator This is a nanoLC volume calculator inspired by the AMAZING (but dead?) MSBioWorks phone application I miss a lot and made with the frustrating assistance of some AI thing my university lets me use. It's honestly pretty good at color palettes, even if it's bad at math and confident/arrogant about it. nanoLC System Volume To use this, I've assumed some…
Man, I need to start being more collaborative so I can get on these gigantic papers that are going to get a billion lazy citations (that's where you use the title and abstract to make a citation without ever reading the paper). This new one is definitely going to get cited like crazy and since there are people out there who judge you by how many citations you have, each of these people are going…
I was trying to help someone out who, due to the fact the US government is working great, has instruments but can't pay their annual license fee to use the DIA cloud nodes. I was like - how hard could it be to link PD through the node maker things to DIA-NN and then integrate the whole thing. Up until the .parquet thing appears it looked pretty straight-forward if you're smart, but I'm not and it…
