A little while ago FragPipe overtook the always-amazing MaxQuant in terms of number of global users. While there are probably some level of error bars, such as maybe the old server I have offline because it doesn't have a CMOS(?) battery in it's motherboard so it thinks it is 2018 and exactly zero of my annual licenses on anything have expired (it runs MaxQuant 1.6.17, which was one of my very favorites). No Fragpipe on that, it has 32 bit Java.  That was a joke. AND 1) That probably wouldn't work and 2) No sane person would admit to that if it did work.  However, Fragpipe i ..read more

 A whole international consortium got together in 2022 and found something like 10% more human proteins!  Does that mean that you now have a FASTA you can reprocess your data with and get like 10% more IDs?  ...not exactly...at least not yet....but it's super cool! Here is the preprint! Wow. That's a lot of names, including some of the wettest blankets in all of proteomics - "false discovery" this" "analytical metrics of precision" that - "standard pipelines and data storage types" on an on. Names you may not recognize are even worse - they're RiboSeq people.... (I wrote up som ..read more

Didn't I just post an MS1 only based prediction paper? I sure did, but here is another!  Have you ever just thought we're doing a little too much stuff? How many degrees of certainty do you need that the peptide you're interested in is the one you're looking at. MonoMS1 takes a step back and asks this question: If I have Solid chromatography High resolution ion mobility And a high resolution precursor Do I need everything else? Can I just predict where my peptide is going to elute, how many charges it will pick up and what the isotopic envelope - and here is the twist - predict a solid ..read more

  It's on, y'all! Can we do single cell proteomics (SCP) in the core where cost recovery is always hanging around in the background getting on your nerves? Let's find out at ABRF 2025 March 23-26 in Las Vegas!  Justin Walley just committed as my first invited speaker (I'm session chair! What?!?)  And Justin's team's paper on Arabidopsis root biology by single cell proteomics is out now! You can check out the published paper here.  ..read more

30 years ago today some guy said the word "Proteomics" at a conference. It was THE first term used to encapsulate all of the versions of a specific class of molecules in an organism. Transcriptomics Followed. Then Metabolomics. Etc. Etc., We sat down with the man himself, Dr. Marc Wilkins to talk about it. This is the kick off for the next season of THE Proteomics Show "What is a proteomics?"  Check it out, and happy birthday proteomics!  ..read more

  For some reason I thought lupine had something to do with werewolves, but if that connection exists, I couldn't sort through Google's ads to get there. You can find some pretty colored flower things, though.  Lupine is the topic of this new preprint where a deep learning model applied to 1,000 or so of the samples in the CPTAC project.   CPTAC has been going on for a long time and that puts a lot of confounding variables - that's beside even the fact that these proteomes are from diverse cell types and cancer types. So...Figure 5 is pretty darned impressive ..read more

  Is there finally a small weird splintery group of proteomics people out there who are starting to think about "The Cloud Computing?" Probably not, but this new preprint is really cool!  As in any bioinformatics paper there are very boring flow charts everywhere BUT they did us all a favor and kept their equations to themselves. No one likes you showing off how many Greek letters you know.  Why does it belong on this awful blog, though? There are so....many....tools.... Well, I took a dataset that I know exceptionally well and I ran those files in it, and it looks legit. AN ..read more

  I know a guy who got a nasty version of hepatitis mouth pipetting in the 1980s, but this is still funny to me.  Borrowed from the great  r/proteomics community, which is rapidly becoming THE place to take your questions about anything that isn't FragPipe. You go here for that.  ..read more

  This at first sounds sorta sketchy until you read the rest of the title (...confidence evaluation with MS2 information....).  Which then makes it sound like a new twist on the classical way of doing these things.  Clustering potential glycans sounds super smart and MS2 confirmation - great - but what I really like about this paper is that it leads you to this great data portal!  GlyCosmos is loaded with tools and great information - and you can evaluate your data with GRable on the portal!  ..read more

  This is just a solid all-around story on how having just a little extra dimension in your data can help you see some past ions that have the same exact mass and charge (and darned close retention times!)  The figure above at the top is my favorite part. The ions in panels A, B and C all come off the column at right about 26.80 minutes. And they're all +3 ions at 548.658.  Check out how different the 1/K0 values are for A and B! Something weird is up there, right? A is at/around 0.82 and B is about 0.9. That's well outside the 0.05 window that people seem to beo okay with ..read more