Looking forward to ASMS! Here are highlights of the presentations from our lab (not including all the collaborations). Definitely don't miss the Skyline User Group Meeting on Sunday skyline.ms/project/home/s…
Michael MacCoss Deanna Bo Chris Hsu

Friends, #FragPipe 22 has been released, and it's a big update! diaTracer enables spectrum-centric analysis of diaPASEF data. Skyline integration. Koina server for more deep-learning prediction options. DDA+ mode for ddaPASEF. DIA glycoproteomics and new chemoproteomics workflows

New preprint! This has been how our lab has developed targeted peptide assays for years. Using gas phase fractionation DIA is a great strategy for building targeted SRM assays -- cost effective and fast. Thanks to Deanna for putting this together. biorxiv.org/content/10.110…

Let the debate on best new features in FragPipe 22 begin. My vote (to be tested this AM) 👇

🔓 #OpenAccess + Most Read in the past 30 days: 'Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition'
go.acs.org/9qI

'It's Elisabeth Bik and her AI tools again, pointing out some minor errors'.
Some serious concerns about this Nature Neuroscience paper from a Stanford University Nobel-Prize-winner in
pubpeer.com/publications/9…

Graduate student Amie Solosky will be talking about our updated lipid database and how she used it to analyze sea lion plasma for biomarkers. Don’t forget to sign up!!

Our #FragPipe team is thrilled to work with the Skyline team to streamline visualization of FragPipe results (MS1, DIA, PTM/glyco searches etc) in Skyline. We will present a talk at the Skyline user meetings, and the entire program looks terrific. Register if there is space left!

new lab preprint - using proteomics and protein co-variation to infer protein association networks across 11 human tissues to study what determines tissue differences and to prioritize disease genes in GWAS linked genes through tissue specific networks biorxiv.org/content/10.110…

Don't forget to register for the Skyline User Group Meeting at Am Soc for Mass Spec in Anaheim! Sunday prior to the meeting we have a fantastic lineup of speakers and lots of new features to announce!
skyline.ms/project/home/s…

Excited to announce the inaugural AIMBA (AI Meets Biology of Aging) 2024 meeting on May 22, 2023, 9-2pm PT, organized by University of Washington Nathan Shock Centers !

Featuring four keynote speakers: Profs Maria Brbic, Anne Brunet, Vadim Gladyshev, James Zou.

Check it out! sites.google.com/cs.washington.…

Thank you Retraction Watch for covering our letter to the nature editors about the lack of AlphaFold3 code retractionwatch.com/2024/05/14/nat…

The story contains perspectives from letter authors Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social Stephanie Wankowicz (she/her) and a response from nature Editor in Chief Magdalena Skipper.

My team (Astral) is expanding and looking for new talent. We're hunting software, instrumentation and application experts. Have a look!

jobs.thermofisher.com

230864BR Senior Software Scientist
230865BR and 230863BR Senior Scientist
230862BR Staff Scientist

I've been playing around with AlphaFold3 since the server was released and, like others have noted, I'm seeing a lot of odd pathological behaviors. For instance, when given 2 copies of this particular protein (+lipids), it more or less just superimposes the structures 1/n

Dr. Maitreya Dunham (Maitreya Dunham ) shares stories of her path to becoming a yeast geneticist and her passion for teaching and science outreach. Written by Yimei (Cindy) Wan and Kate Jiang 🧬 :
transcripts.blog/2024/05/12/con…

Only one week left to register for this amazing event organized by Britta Eggers RUB, Kathryn Lilley, JesperOlsenLab, Bavarian Center for Biomolecular Mass Spectrometry! Don't miss out this great opportunity and join the Summerschool brixenproteomics.org🥳

Demis -- I think AlphaFold3 is really exciting. As Reviewer #3, I got great results from the server. I tried hard to get nature to urge you to release the code but was unsuccessful. I did not get it for re-review so I don't know if you responded. So why no code? Google DeepMind

We were incredibly disappointed with the lack of code or executable accompanying the publication of AF3 in nature . This contradicts scientific principles of the ability to evaluate, use, and build upon existing work. zenodo.org/records/111798…

if you're concerned that the new AlphaFold3 is totally closed source and doesn't even share executables, sign the letter to Nature that is being put together - see the thread quoted here. The link to the letter is the 2nd tweet in the thread.

View from our house in Seattle tonight. Pretty spectacular Aurora Borealis!