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
Contemplating this as my facilities new logo. What do you think?
February 17, 2026 at 11:16 PM
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 🙄
February 8, 2026 at 9:06 PM
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 🙄
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...
January 28, 2026 at 5:58 PM
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 😜
January 27, 2026 at 11:46 PM
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
January 26, 2026 at 7:30 PM
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
www.youtube.com
January 23, 2026 at 12:00 AM
Nice Phosphorylation enrichment Video from ISB and Affinisep about a year ago . www.youtube.com/watch?v=pFfC...
Reposted by Brett Phinney
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
--> computationalproteomics.khoury.northeastern.edu
May Institute – Computation and statistics for mass spectrometry and proteomics
computationalproteomics.khoury.northeastern.edu
January 20, 2026 at 11:26 PM
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
--> computationalproteomics.khoury.northeastern.edu
Reposted by Brett Phinney
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-...
🎧 Listen or read the transcript: magazine.eacr.org/using-ai-to-...
January 21, 2026 at 10:01 AM
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-...
🎧 Listen or read the transcript: magazine.eacr.org/using-ai-to-...
Reposted by Brett Phinney
This might be the problem.... #TeamMassSpec
January 16, 2026 at 7:35 PM
This might be the problem.... #TeamMassSpec
Reposted by Brett Phinney
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...
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...
www.biorxiv.org
January 15, 2026 at 7:24 PM
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...
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...
Reposted by Brett Phinney
A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#proteomics #prot-paper
January 14, 2026 at 3:01 PM
A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#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...
January 14, 2026 at 10:25 PM
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...
Reposted by Brett Phinney
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
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
January 13, 2026 at 11:28 AM
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
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
Reposted by Brett Phinney
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
January 12, 2026 at 10:10 PM
How does COVID affect hamsters?!? Proteomics answers the question at the front of all of our minds today. proteomicsnews.blogspot.com/2026/01/how-...
Reposted by Brett Phinney
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.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
January 13, 2026 at 12:30 AM
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.ly/4qQruIe
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?
January 8, 2026 at 7:05 PM
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?
January 8, 2026 at 6:06 PM
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 :(
. Maybe someday we will discuss the illusive beer paper @benneely.com :(
January 8, 2026 at 12:24 AM
For the Local UC Davis peeps
. Maybe someday we will discuss the illusive beer paper @benneely.com :(
. 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?
January 7, 2026 at 5:43 PM
So I'm genuinely curious , how is it over there on X for those Proteomics people that stayed?
Reposted by Brett Phinney
#THEProteomicsShow is back and now we’re talking about #USHUPO2026. Me and Ben @proteomicsnews.bsky.social got to talk to Mike MacCoss @maccoss.bsky.social and it’s everything you’d want: quant, mentoring and car discussions. Find it wherever you find fine podcast or here anchor.fm/theproteomic...
December 12, 2025 at 1:14 PM
#THEProteomicsShow is back and now we’re talking about #USHUPO2026. Me and Ben @proteomicsnews.bsky.social got to talk to Mike MacCoss @maccoss.bsky.social and it’s everything you’d want: quant, mentoring and car discussions. Find it wherever you find fine podcast or here anchor.fm/theproteomic...
Reposted by Brett Phinney
Excited 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
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
December 15, 2025 at 8:09 PM
Excited 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
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
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
December 11, 2025 at 1:00 AM
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.
Nanotrap Protein Enrichment Affinity Kit | Ceres Nano
Nanotrap® Protein Enrichment Affinity Kits (PEAK) use the Nanotrap hydrogel particle technology to capture and concentrate low abundance, low molecular weight proteins and peptides while simultaneousl...
www.ceresnano.com
December 4, 2025 at 6:17 PM
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)
December 2, 2025 at 10:18 PM
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)