Brett Phinney

Brett Phinney

@ucdproteomics.bsky.social

Scientist, still hanging around the UC Davis Genome Center. Really concerned with the state of things these days so you may see occasional political posts here or there

1K followers537 following657 posts

Brett Phinney
@ucdproteomics.bsky.social

I asked Claude to make podcast where a statistician and biologist discuss the proteomics results run through my claude proteomics skill and while it's not as good as @benneely.com podcast, but it's not bad either :) it's in the newest version of the skill github.com/bsphinney/DE...

github.comGitHub - bsphinney/DE-LIMP: LIMPA DAVIS Proteomics PipelineLIMPA DAVIS Proteomics Pipeline. Contribute to bsphinney/DE-LIMP development by creating an account on GitHub.
Brett Phinney
@ucdproteomics.bsky.social

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

Satoshi Yoshiji, MD, PhD@satoshiyoshiji.bsky.social

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

Brett Phinney
@ucdproteomics.bsky.social

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

Brett Phinney
@ucdproteomics.bsky.social

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

Brett Phinney reposted

Ben Neely
@benneely.com

Replying to @benneely.com

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...

nature.comA standardized framework for circulating blood proteomics - Nature GeneticsThe field of blood proteomics faces an upsurge of data with the challenge of cross-study comparisons. This Perspective offers an in-depth analysis and proposes reference materials to enhance data inte...
Brett Phinney
@ucdproteomics.bsky.social

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

Matt Foster@mattwfoster.bsky.social

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.

Brett Phinney
@ucdproteomics.bsky.social

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.comGitHub - bsphinney/DIA-NN-QC-StreamlitContribute to bsphinney/DIA-NN-QC-Streamlit development by creating an account on GitHub.
Brett Phinney@ucdproteomics.bsky.social

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 😜

Brett Phinney
@ucdproteomics.bsky.social

My buddy who works for an AI company says Claude Code is what everyone is using, but I used GeminiAI as you can get a pro account free with an edu email address . Seemed to work okay I think

Brett Phinney reposted

Matthias Trost
@mtrost.bsky.social

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...

biorxiv.orgEmpirical-Bayes and Bayesian Hierarchical Modelling for Missingness and Differential Expression in ProteomicsMass 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...

Brett Phinney reposted

KPL ApS
@kplaps.bsky.social

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

pubs.acs.orgComparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics WorkflowsThis 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.

Brett Phinney reposted

IonOpticks
@ionopticks.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

bit.lyPreprint: A globally representative immunopeptidomics approach to identify population-wide vaccine candidates - IonOpticksThis Foster lab study into population-wide vaccine candidates by Baker et al. used IonOpticks Aurora Ultimate 25×75 CSI UHPLC columns.
Brett Phinney
@ucdproteomics.bsky.social

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?