Brett Phinney
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
- Yikes ! Speed running the AI apocalypse i see . This can’t be real right? www.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...
- 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...
- Reposted by Brett PhinneyApplications 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
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- 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...
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- 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?
- For the Local UC Davis peeps . Maybe someday we will discuss the illusive beer paper @benneely.com :(
- So I'm genuinely curious , how is it over there on X for those Proteomics people that stayed?
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- Reposted by Brett PhinneyExcited to share our work at @natcomms.nature.com We used single cell proteomics to define the functional heterogeneity of human neutrophils in glioblastoma, finding pro and anti-tumorigenic effector states invisible to scRNAseq. SCP will revolutionise immunology, this is just the start
- Happy to share our latest preprint doing low cell number (mini-bulk) and single cell #proteomics on tumour associated neutrophils from human glioblastoma where we find multiple functional states that would be invisible to scRNAseq, some showing pro-tumoural states with potential therapeutic value
- I don't know exactly what this all means, but I'm running cascadia github.com/Noble-Lab/ca... on my genome centers A100 80GB GPU so it's probably really cool I'm guessing
- I've been very impressed with the Ceres Nano-Trap enrichment beads so far. www.ceresnano.com/nanotrap-peak . I just quantified over 2200 proteins from Dog Plasma. Including reliably seeing KITLG (Stem Cell Factor) which is in the pg/ml range I think. Let's see O-link do that in in dog ...Pfft.
- This is our loading buffer on our Exploris 480 /U3000 system today. Coming to Nature Methods ASAP: The Proteomics S.P.I.D.E.R. Method (Suitability Protocol Integrating Dead Eight-legged Reference)
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- Holy crap the new AI's are scary . I uploaded a dataset and asked gemini 3.0 what proteins should not be in the list based on the biology and what it told me sounded really plausible. The trick is figuring out if it's right I guess....
