Category Archives: Uncategorized

Add another huge set of techniques to the list of things I had NO IDEA that we could do or were important, and now I do to a great new preprint! Where to start? Let’s go first sentence. …so…what’s going on with the cysteines and what is stuck to them is some critically important thing.Continue reading “Quantitative proteomics of cysteine activation in T-cells!”

I’m in complete awe of what an absurd amount of work this new preprint represents, but even more than that — wow — what a shining example of how we need to move to the surfacome to figure how how cells are responding stuff….. So much work here…where to start…. Okay — so they usedContinue reading “Dramatic remodeling of 700 proteins in the surfaceome when messing with 6 oncogenes!!”

Have you got a beautiful output out of your favorite software with thousands of quantified proteins but you’re still at this point? Do I ever have amazing news for you! What if you could just take that quantitative output (for real — your MaxQuant or mzTab output CSVs) and reinterpret that quantification side of itContinue reading “Need more power out of that protein quan output? Reinterpret with MSQRob!”

I am ALWAYs up to add another “-omics” as long as you don’t mean you did a western blot or set up an SRM experiment for 4 small molecules and are going to call it “-omics”. I need a hard cutoff where I do/don’t make fun of the suffix….. This amazing open resource deserves farContinue reading “Integration techniques for "multi-omics" data! — INTEGROMICS!”

This new resource presented in JPR is a simple and great idea! It also might explain a lot of things you might have seen using big databases for proteomics. When Amol’s team at OptysTech started building their cloud based search engine, they kept coming up with tons and tons of cow proteins. Like — wayContinue reading “Are your collaborators growing cells? You need the cRFP!”

I don’t get the maths in this new study, but I do like getting more peptide identifications. What is a sequence-mask-search hybrid de novo peptide sequencing framework? No idea. I assumed the 3 hyphenated words were a stats or math thing I’ve never heard of, but if it is, Google also hasn’t heard of it.Continue reading “Sequence-mask-search-hybrid thing finds more HLA peptide IDs!”

For those of us on the edge of our seats for this — the new HPP Data Interpretation guidelines are finally available. The big highlight is probably how to incorporate Data INdependent Acquisition (DIA) data into our biggest effort to map the human proteome. How many proteins are we up to that have significant evidenceContinue reading “Human Proteome Project Guidelines version 3.0!”

Electrospray ionization isn’t perfect, but it sure has been an amazingly flexible solution for an absurd number of things! This short comment at Nature Communications is a great history and perspective of the 30 years since it was first shown to ionize without destroying everything!

I’ve spent a lot of time with this great paper this week, and even though I posted it on another blog a long time ago I just realized yesterday how useful it is for scheduling PRMs for proteomics. Here is the scenario — you discover all this cool stuff with your super cool ultra highContinue reading “Scheduling PRMs for lots of metabolites and/or phosphopeptides!”

This image of how BioID works was brazenly stolen from Creative Biolabs — sorry, please let me know if you want me to take it down — because they already offer this BioID service! I’m using this because the preprint has some strict copyright statements on their pictures, however — this is worth checking out.Continue reading “A proximity biotinylation map of human cells!”