Brett Phinney
@ucdproteomics.bsky.social
Scientist, still hanging around the UC Davis Genome Center. I guess I currently have 11 protons, because people keep telling me i'm Sodium Fine ;)
Does anyone else feel like they need to take a shower after browsing LinkedIn?
November 13, 2025 at 6:23 PM
Does anyone else feel like they need to take a shower after browsing LinkedIn?
wow! apparently UC Davis doesn't have access to Journal of Proteome research any more . @jyates.bsky.social do you know if this is a permanent thing ?
November 13, 2025 at 6:12 PM
wow! apparently UC Davis doesn't have access to Journal of Proteome research any more . @jyates.bsky.social do you know if this is a permanent thing ?
Reposted by Brett Phinney
Congratulations to Mike MacCoss on receiving the Donald F. Hunt Distinguished Contribution in Proteomics Award from US HUPO!
us-hupo.org/Distinguishe...
us-hupo.org/Distinguishe...
US HUPO - Distinguished Contribution Award
us-hupo.org
November 12, 2025 at 5:12 PM
Congratulations to Mike MacCoss on receiving the Donald F. Hunt Distinguished Contribution in Proteomics Award from US HUPO!
us-hupo.org/Distinguishe...
us-hupo.org/Distinguishe...
Reposted by Brett Phinney
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
November 10, 2025 at 4:39 PM
May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu
How to run dia-nn on your cluster the easy way using slurm youtu.be/TLijSR_RPRE?...
Running Dia-NN 2.3 on your universities computer cluster using slurm
YouTube video by Brett Phinney
youtu.be
November 10, 2025 at 7:58 PM
How to run dia-nn on your cluster the easy way using slurm youtu.be/TLijSR_RPRE?...
After all this time , Finally have the evotip loading protocol working on the #Opentrons Flex, so far so good ! @evosep.bsky.social
November 7, 2025 at 8:17 PM
After all this time , Finally have the evotip loading protocol working on the #Opentrons Flex, so far so good ! @evosep.bsky.social
Thinking about putting this sign outside my facilities door . 🤔
November 5, 2025 at 2:13 AM
Thinking about putting this sign outside my facilities door . 🤔
I try the newest version of DIA-NN, version 2.3 and its new Infini search approach on some Lumos and tismTOF HT datasets. If you're new to DIA-NN this might be a good video to watch. youtu.be/MIMnDw0loCk
We try the new DIA-NN 2.3 (November 2025)
YouTube video by Brett Phinney
youtu.be
November 3, 2025 at 8:01 PM
I try the newest version of DIA-NN, version 2.3 and its new Infini search approach on some Lumos and tismTOF HT datasets. If you're new to DIA-NN this might be a good video to watch. youtu.be/MIMnDw0loCk
Reposted by Brett Phinney
If you are in Davis and will be affected by the SNAP benefits cut, go to Central Park at 9 pm on weekdays for the Night Market. It’s run by good people, I’ve checked it out and gotten a couple of things from it myself, and there was plenty of food - they collect surplus food from nearby restaurants.
October 30, 2025 at 7:14 PM
If you are in Davis and will be affected by the SNAP benefits cut, go to Central Park at 9 pm on weekdays for the Night Market. It’s run by good people, I’ve checked it out and gotten a couple of things from it myself, and there was plenty of food - they collect surplus food from nearby restaurants.
Reposted by Brett Phinney
Hey @asms.org peeps. I’m running for VP for programs and I’d like your vote. Check out the asms web site for details and you will see an email with voting instructions in the near future. I approach this position with lots of experience organizing scientific conferences & I ❤️ asms. Please re-sky.
a spongebob squarepants scene with a mailbox and a flower
ALT: a spongebob squarepants scene with a mailbox and a flower
media.tenor.com
October 28, 2025 at 4:39 PM
Hey @asms.org peeps. I’m running for VP for programs and I’d like your vote. Check out the asms web site for details and you will see an email with voting instructions in the near future. I approach this position with lots of experience organizing scientific conferences & I ❤️ asms. Please re-sky.
My curiosity got the best of me and I searched Grokipedia (Musks AI Wikipedia alternative ) for proteomics . My lord 🙄
October 29, 2025 at 8:55 PM
My curiosity got the best of me and I searched Grokipedia (Musks AI Wikipedia alternative ) for proteomics . My lord 🙄
Want to turbo charge your R skills? The Bioinformatics online R courses here are very good I hear. It will definitely help you know when your AI generated R code is actually stupid registration.genomecenter.ucdavis.edu/events/r_nov...
Genome Center Event Registration
registration.genomecenter.ucdavis.edu
October 29, 2025 at 5:50 PM
Want to turbo charge your R skills? The Bioinformatics online R courses here are very good I hear. It will definitely help you know when your AI generated R code is actually stupid registration.genomecenter.ucdavis.edu/events/r_nov...
Need to do some cutting edge Proteomics Differential expression? Maybe give Limpa a try! Guaranteed to rise to the occasion ...despite its name !
youtu.be/vqeOT8xcycc
youtu.be/vqeOT8xcycc
Doing Differential Expression analysis on Proteomics Data using Limpa!!
YouTube video by Brett Phinney
youtu.be
October 27, 2025 at 5:03 PM
Need to do some cutting edge Proteomics Differential expression? Maybe give Limpa a try! Guaranteed to rise to the occasion ...despite its name !
youtu.be/vqeOT8xcycc
youtu.be/vqeOT8xcycc
Reposted by Brett Phinney
GO FAST with InfinDIA!! proteomicsnews.blogspot.com/2025/10/tire...
Tired of slow DIA search times? Try DIA-NN 2.3 with InfinDIA!
Is your awesome new instrument generating so much data that you can't process it fast anymore? My data density has jumped about 5x from my...
proteomicsnews.blogspot.com
October 2, 2025 at 11:01 AM
GO FAST with InfinDIA!! proteomicsnews.blogspot.com/2025/10/tire...
Reposted by Brett Phinney
Are you going to the International Human Proteomics Organization World Congress? Are you traveling with your (electric?) guitar? Do you have a few free minutes on Monday early afternoon? I have a great idea! Please reach out. Bonus points if you tune down to drop C.
October 22, 2025 at 4:25 PM
Are you going to the International Human Proteomics Organization World Congress? Are you traveling with your (electric?) guitar? Do you have a few free minutes on Monday early afternoon? I have a great idea! Please reach out. Bonus points if you tune down to drop C.
Going through trying my hardest not to delete my old data. Found some ABRF RG data from 2009 and 2011. Doesn't look like we did very good. Wonder if we are any better now?
October 6, 2025 at 5:20 PM
Going through trying my hardest not to delete my old data. Found some ABRF RG data from 2009 and 2011. Doesn't look like we did very good. Wonder if we are any better now?
Reposted by Brett Phinney
Thanks to @ucdproteomics.bsky.social & the team at our core facility for training me from the ground up in all things proteomics & to the wonderful @nistara.bsky.social for everything I now know about using R ☺️
September 19, 2025 at 6:47 PM
Thanks to @ucdproteomics.bsky.social & the team at our core facility for training me from the ground up in all things proteomics & to the wonderful @nistara.bsky.social for everything I now know about using R ☺️
Reposted by Brett Phinney
Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Start Page: /home/software/Skyline/events/2025 Webinars/Webinar 26
skyline.ms
September 15, 2025 at 8:26 AM
Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Reposted by Brett Phinney
@lindsaykpino.com talking about the power of using proteomics to measure the regulome of live cells using our platform here at Talus Bio, and how far we have been able to scale this platform up to further cancer drug discovery and more. #regulomesummit
September 15, 2025 at 4:35 PM
@lindsaykpino.com talking about the power of using proteomics to measure the regulome of live cells using our platform here at Talus Bio, and how far we have been able to scale this platform up to further cancer drug discovery and more. #regulomesummit
Thanks to everyone that attended our #proteomics Short course last week ! We generated over 150 GB of timsTOF HT data comparing different proteomics sample
Prep methods .
Prep methods .
September 4, 2025 at 9:01 PM
Thanks to everyone that attended our #proteomics Short course last week ! We generated over 150 GB of timsTOF HT data comparing different proteomics sample
Prep methods .
Prep methods .
Reposted by Brett Phinney
We have updated our Slice-PASEF preprint! It's a result of a large collaboration where we highlight its advantages for single cell proteomics. Or any other applications benefiting from sensitivity. For example, major gains for ubiquitinomics:
September 2, 2025 at 5:58 PM
We have updated our Slice-PASEF preprint! It's a result of a large collaboration where we highlight its advantages for single cell proteomics. Or any other applications benefiting from sensitivity. For example, major gains for ubiquitinomics:
Reposted by Brett Phinney
The article here in, very well discusses the importance of randomisation, power analysis for designing meaningful experiments..there was also a JPR perspective on block randomisation for proteomics experiments..together make a nice primer..
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
August 10, 2025 at 8:17 AM
The article here in, very well discusses the importance of randomisation, power analysis for designing meaningful experiments..there was also a JPR perspective on block randomisation for proteomics experiments..together make a nice primer..
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Brett Phinney
New spatial proteomics workflow maps 1,047 proteins in atherosclerotic plaques using laser-capture microdissection + timsTOF Pro with Aurora Rapid 5x150 columns. Reveals plaque heterogeneity & rupture-prone regions.
A powerful tool for identifying therapeutic targets.
Learn more: bit.ly/4eTRKwv
A powerful tool for identifying therapeutic targets.
Learn more: bit.ly/4eTRKwv
Spatial proteomics of the human atherosclerotic microenvironment reveals heterogeneity in intra-plaque proteomes and extracellular matrix remodeling - IonOpticks
Jokumsen et al.'s study into intra-plaque proteomes uses 5 cm x 150 μm IonOpticks Aurora Rapid 5x150 UHPLC columns.
bit.ly
August 11, 2025 at 2:46 AM
New spatial proteomics workflow maps 1,047 proteins in atherosclerotic plaques using laser-capture microdissection + timsTOF Pro with Aurora Rapid 5x150 columns. Reveals plaque heterogeneity & rupture-prone regions.
A powerful tool for identifying therapeutic targets.
Learn more: bit.ly/4eTRKwv
A powerful tool for identifying therapeutic targets.
Learn more: bit.ly/4eTRKwv
What the heck ? Found this in the lab today. What old instrument could this possibly be for?
August 8, 2025 at 2:45 AM
What the heck ? Found this in the lab today. What old instrument could this possibly be for?
I thought this was super interesting. re-analyzed a DIA data file I originally processed with encyclopedia in 2018 with Spectronat 20. Encyclopedia really held up! At least on the protein level. Peptides are more difficult to compare. Surprised me
August 7, 2025 at 11:21 PM
I thought this was super interesting. re-analyzed a DIA data file I originally processed with encyclopedia in 2018 with Spectronat 20. Encyclopedia really held up! At least on the protein level. Peptides are more difficult to compare. Surprised me