I wonder what type of proteomics data this is ? Olink ? Anyone know ?

Satoshi Yoshiji, MD, PhD@satoshiyoshiji.bsky.social · last mo.

NIH All of Us has just released a massive multi-omics dataset, including: • 535K WGS (120K+ added; now larger than UKB) • ~10K proteomics + RNAseq + long-read • ML-curated clinical notes • 68K with Fitbit data Kudos to this great initiative and to the participants for advancing science

My daughter (now a 2nd year grad student at Irvine) found this yesterday. She made it in 1st grade for a school project. Stick around until the last page you won't be sorry 🤣😂

I just used Sage to search 120 Astral DDA files in 12 minutes my cluster. I honestly don't understand what Thermo's Ardia thingy does or why it's even needed

It's that time of year again for are Annual proteomics chart course! Going on almost 20 years! Honestly it's a good class for those wanting to add proteomics to your research. And Proteomics really is the best Omics if I don't say so myself #proteomics #massspec #proteome #massspectrometry

I seem to have acquired and kept over 233K mass spec files over there years. Here is a breakdown

See I Knew I would have some use for keeping every qc file I ever created 😁 I'll have more in a day or two

Well, I apparently saved over 32K BSA QC files from my LTQ era. Now I need to figure out what to do with them lol

I really like having a computer cluster. I have been using it a crazy art more since I have switched to claude code. Currently - 2048 cores running running (across 259 jobs)- 283 jobs pending - 1 GPU-A100 job pending

Claude Code and I whipped up some software for running DIA-NN and LIMPA. I kinda like it so far. Has a lot of features I've always wanted and now I can make it myself !!, well with Claude Codes help ;) youtu.be/lXxqDpCHXOA

De-LIMP Proteomics Analysis Software Part1

YouTube video by Brett Phinney

youtu.be

I guess we should have companion papers. Need to update that pile of blood papers I sent @ucdproteomics.bsky.social www.nature.com/articles/s41...

This is truly hilarious , and accurate !

Never disappointed when I go to #ushupo , always a great conference

Matt Foster@mattwfoster.bsky.social · 5mo ago

Another awesome #USHUPO in the books. @ucdproteomics.bsky.social is already planning the tour of “Better Call Saul” filming locations for next year in Albuquerque.

Contemplating this as my facilities new logo. What do you think?

You know you’re a mass spec person when you are watching Olympic skating and every time they say quads you think about how yours probably needs to be cleaned 🙄

Yikes ! Speed running the AI apocalypse i see . This can’t be real right? www.moltbook.com

moltbook - the front page of the agent internet

A social network built exclusively for AI agents. Where AI agents share, discuss, and upvote. Humans welcome to observe.

moltbook.com

If you're interested in how I did this. It wasn't that hard. The github site is here github.com/bsphinney/DI... You can find the original version if you want the ASCII charts that only seem to run locally. And here is my work being GeminiAI's assistant gemini.google.com/share/d0e59c...

GitHub - bsphinney/DIA-NN-QC-Streamlit

Contribute to bsphinney/DIA-NN-QC-Streamlit development by creating an account on GitHub.

github.com

Brett Phinney@ucdproteomics.bsky.social · 6mo ago

Want to make your DIA-NN QC reports in a web browser and then go back in time to the 80's and 90's? Now you can with my completely AI vibe coded streamline app! dia-nn-qc.streamlit.app You're welcome 😜

Want to make your DIA-NN QC reports in a web browser and then go back in time to the 80's and 90's? Now you can with my completely AI vibe coded streamline app! dia-nn-qc.streamlit.app You're welcome 😜

Last minute Candlelight vigil in Davis last night for Alex Pretti organized by Indivisible Yolo. It was a good turnout

Nice Phosphorylation enrichment Video from ISB and Affinisep about a year ago . www.youtube.com/watch?v=pFfC...

Affinisep webinar "Exploring Sample Prep and Instrument Parameters for Phosphoproteomics"

YouTube video by AFFINISEP

youtube.com

Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social ! --> computationalproteomics.khoury.northeastern.edu

Explore how AI can be used to bridge chemistry, proteomics and precision medicine in our latest podcast episode with Bernhard Küster, who will be speaking at the 2026 EACR Congress. 🎧 Listen or read the transcript: magazine.eacr.org/using-ai-to-...

This might be the problem.... #TeamMassSpec

How do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data? Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback! www.biorxiv.org/content/10.6...

Empirical-Bayes and Bayesian Hierarchical Modelling for Missingness and Differential Expression in Proteomics

Mass spectrometry-based label-free proteomics data often suffer from missing values, especially for low-abundance proteins or when a protein is completely absent in one condition. This makes it challe...

biorxiv.org

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs pubs.acs.org/doi/10.... --- #proteomics #prot-paper

I made a google notebook llm based on this www.nature.com/articles/s41... and new data concerning mRNA - Protein expression correlation over the last year. It even wrote a grant , which you can find in there if anyone wants to submit it ! notebooklm.google.com/notebook/2c7...

Does enzyme quality matter in #proteomics? New study in JPR w/ @jesperolsenlab.bsky.social shows: LysC-Trypsin reduces missed cleavages from 30% → 15% KPL's A. lyticus LysC achieves >90% efficiency in systematic comparison. Congrats to the authors! pubs.acs.org/doi/10.1021/... #TeamMassSpec

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows

This study presents a comparative analysis of three LysC endopeptidase homologues from Achromobacter lyticus (A. lyticus),Pseudomonas aeruginosa and Lysobacter enzymogenes for mass spectrometry-based proteomics. Utilizing a protein aggregation capture workflow with HeLa cell lysates, we assessed the enzymes’ cleavage specificity, digestion efficiency, and performance across various experimental conditions. Results showed that while all three LysC homologues exhibited high cleavage specificity at lysine residues, A. lyticus LysC outperformed the two others with superior peptide identification, digestion efficiency, and protein coverage, especially at shorter digestion times. Our experiments using a combination ofA. lyticusLysC and trypsin demonstrated the importance of employing LysC for significantly minimizing missed cleavage rates in tryptic digests, especially with regard to lysine-containing peptides. This study underscores A. lyticus LysC’s potential as an optimal choice for enhancing mass spectrometry-based proteomics.

pubs.acs.org

How does COVID affect hamsters?!? Proteomics answers the question at the front of all of our minds today. proteomicsnews.blogspot.com/2026/01/how-...

a close up of a hamster with its mouth open and a pink nose .

ALT: a close up of a hamster with its mouth open and a pink nose .

media.tenor.com

New globally representative vaccine screening method from the Foster lab uses 30 diverse cell lines + LC-MS/MS to identify broadly protective antigens. Analysis via EASY-nLC 1000 + timsTOF Pro with Aurora Ultimate 25x75 CSI column, identified 18 common binding motifs. bit.ly/4qQruIe

Preprint: A globally representative immunopeptidomics approach to identify population-wide vaccine candidates - IonOpticks

This Foster lab study into population-wide vaccine candidates by Baker et al. used IonOpticks Aurora Ultimate 25×75 CSI UHPLC columns.

bit.ly

I'm not sure what I think bout this new Nature Spatial proteomics paper. www.nature.com/articles/s41... . They ID peptides from their MALDI image by matching MS1 in a standard LCMS bottom up library. This has been tried forever right? But the data somewhat validates, so maybe this is okay now?

I've been having weird issues getting access to Journals here on campus. I think I have narrowed it down to Safari. Has anyone else had this issue? left is Chrome and one the Right is Safari . chatGPT gave me a log list of things to try, but nothing has worked yet. Anyone solve this?