Author | Lightnews

Brett Phinney @ucdproteomics.bsky.social · 10h

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

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Reposted by Brett Phinney

Dr. Katharine Dickson @metaomicsnerd.bsky.social · 4d

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.

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Brett Phinney @ucdproteomics.bsky.social · 4d

But What if you could run x!tandem on it ?

Reposted by Brett Phinney

John Yates @jyates.bsky.social · 6d

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

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Brett Phinney @ucdproteomics.bsky.social · 5d

My curiosity got the best of me and I searched Grokipedia (Musks AI Wikipedia alternative ) for proteomics . My lord 🙄

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Brett Phinney @ucdproteomics.bsky.social · 5d

Ohh this is awesome , I haven’t heard of this before !

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Brett Phinney @ucdproteomics.bsky.social · 5d

I've tried msrob through MSDAP (which I quite like) . Never heard of mqrobhurdle. When I search for it googles AI tells me there is no person named Mario that is known for hurdling 🙄

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Brett Phinney @ucdproteomics.bsky.social · 5d

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

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Brett Phinney @ucdproteomics.bsky.social · 6d

I really like dia-analyst ! It uses limma and makes things really easy . I used it in my class this summer . The author told me how to get it running in a container so you can run it locally too

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Brett Phinney @ucdproteomics.bsky.social · 6d

Thanks ! I’ve been impressed with limpa so far . The log2 fc ratios seem way more biologically sensible

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Brett Phinney @ucdproteomics.bsky.social · 7d

Oh thanks for the tip !

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Brett Phinney @ucdproteomics.bsky.social · 7d

It was my grandfathers . Original Dobbs 5th avenue. I need to find more places to wear it :)

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Brett Phinney @ucdproteomics.bsky.social · 7d

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

Doing Differential Expression analysis on Proteomics Data using Limpa!!

YouTube video by Brett Phinney

youtu.be

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Reposted by Brett Phinney

ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · Oct 2

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

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Reposted by Brett Phinney

ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 12d

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.

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Brett Phinney @ucdproteomics.bsky.social · 28d

I bought one of these , 1.7 K for 60 TB raid5 www.owc.com/solutions/th... I archived about 50 TB including all of the prg beer raw data (1.6TB) just in case I ever need it 😝

OWC ThunderBay 4: Thunderbolt 4-Bay RAID Storage

Compact, high-capacity RAID storage solution perfect for handling 4K video, audio production, and high-volume photography with confidence and speed.

www.owc.com

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Brett Phinney @ucdproteomics.bsky.social · 28d

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?

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Reposted by Brett Phinney

Brooke @brookegenovese.bsky.social · Sep 19

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 ☺️

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Brett Phinney @ucdproteomics.bsky.social · Sep 18

DTSC ?

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Brett Phinney @ucdproteomics.bsky.social · Sep 18

I haven't..maybe I should !

Brett Phinney @ucdproteomics.bsky.social · Sep 18

Now I just need to get my evotip costs under control, they are just way too expensive right now to scale the way I want .

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Brett Phinney @ucdproteomics.bsky.social · Sep 18

96 & 384 well plates + some sort of robotics or semi-automated prep (King Fisher, Tecan A200) is the only thing that scales in my opinion. Happy to test a cheap 96 well plate DNA miniprep plate. Does anyone know of any?

Brett Phinney @ucdproteomics.bsky.social · Sep 18

I've learned everything has it's trade offs. The trypsin we make is like a billion times cheaper than Promega's but bovine trypsin has a much higher missed cleavage rate than porcine and I have never found a purified porcine trypsin I can reductively methylate like the Worthington's bovine trypsin

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Brett Phinney @ucdproteomics.bsky.social · Sep 18

I don't think I have, thank you!!!

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Reposted by Brett Phinney

Michael MacCoss @maccoss.bsky.social · Sep 15

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

Start Page: /home/software/Skyline/events/2025 Webinars/Webinar 26

skyline.ms

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