If you've never done it, it absolutely sucks to kill a lab animal to get samples. Not only is it awful but an increasing body of evidence suggests that those millions of years or evolution make it not make very much sense at all to do it for many mechanisms. However, there are some systems where you absolutely have to do it to get that information. What if instead of needing to murder dozens of animals you could learn everything you wanted from just one?  Hey, wait, this is one of the few labs on earth who are doing real single cell proteomics with mass spectrometers? What are ..read more

  Well....at the top of the "I'd rather not talk about this one, but I know we absolutely need to have this conversation..." list!  Unlike some of the other times this has come up in the literature where someone is like "omg, I can totally figure out who this person is from this dandruff we found!" This one suggests some well-considered solutions.  ..read more

Thanks r/massspectrometry! I didn't know about this. I have Gary's Mass Spectrometry for Biotechnology which was a key part of Iulia Lazar's class on bioanalytical instrumentation when I was in grad school.  This is on an obviously inferior -omics but I bet it's a solid read and it's like $14 in paperback!  ..read more

  There it is! It was ASAP when I read it on my phone the other day and it moved to this month's issue.  I might be getting old because the HF-X and Lumos both seem pretty recent to me, but in a review we're putting together we refer to them as "previous generation instruments" and that does appear to be the case. So...what if that's what you have and someone wants you to run 1 nanogram of peptides or less? Do you want an okay number of peptides and proteins? Or would you rather have 15-fold MORE? Probably the latter, but you do you, yo.  The reason I took screenshots of the ..read more

  I read this while not even Jalen Brunsen dismantling the Pacers could keep me from falling asleep (rough spring so far) but it is totally worth thinking about.  Coincidentally, this paper prominently features another New Yorker (AOC) which is the only abbreviation I'll now ever remember for antibody oligonucleotide conjugates. There are a whole ton of single cell technologies where you put an oligo on an antibody and you mix that with your single cells and analyze them. In our experience with these so far - THEY ARE NOWHERE NEAR AS TURNKEY AS SALESPEOPLE WHO WANT TO USE UP YOUR ..read more

  Now, this study is very clear that this workflow is simple for me or you to add into your or my workflow by just following 3 steps in the materials and methods section and Imma take that as face value.  because I really like the conclusions. Such as - and  as well as  So when we get through the very last set of mass spectrometry experiments that I will ever run at the Johns Hopkins University (on the systems right now! eeeeeeeeeek! cross your fingers for us that we can get just a couple more weeks without another flood) I'd really like to try this out.  ..read more

  If you're just wondering if the guys in suits who say words like "depreciation" and "gestation lag" (and might seem like the sort of guys having fun in college while you were doing enzyme kinetic curves) are just making stuff up - they do appear to have some math to rely on here and there. This comes from what might be the worst name of an academic journal I've ever heard of, but it's funny how much (what I can understand of it) seems to line up with reality. That Orbitrap Velos didn't get more valuable while you were using it. It likely got less. And how long was it before you felt ..read more

As part of a big review we've been working on for a while, and might be a little late (sorry) we've been really digging into the data behind "single cell proteomics" studies. I really really like this review from friends in Austria because I don't know how to do these publication search term analyses and I can just steal theirs. To people in the outside world it probably looks like we've completed hundreds - or at least....dozens.... of studies where single normalish-sized single cells were analyzed by LCMS.  Our list does not have even 2 dozen actually studies. I'm sure that will cha ..read more

This is a thoughtful addition to the challenges with carrier channel boosting proteomics samples. The isotopic impurities are something you can largely ignore when your signal is roughly equivalent, but when it isn't, it's a big problem. It does make you wonder if there might be a way to make expensive multiplexing tags that are...I dunno.... actually pure...?  ..read more

  Ready to get super pumped about leaving the lab and not thinking about proteomics for a few days? I'll help you get started with  QUAAAAAALLLLIIIIIIIITTTTTYYYYYY  COOOOONNNTRRRROOOOOLL PREEEPRIINNNTTS! Let's start with this great new Primer!  Just like how you have to put primer on right after you sand most things and before you do the actual hard part of applying the paint people will see --- this'll get you ready for the this bit of important misery ..read more