Michael MacCoss

We're all struggling with this these days.

Huge honor to be recognized by @us-hupo.org! Congratulations to the truly deserving winners - @maccoss.bsky.social, William Noble, @nlkproteomics.bsky.social, Lingjun Li! #USHUPO2026 #USHUPO

Super exiting! What could be better than winning an award? Winning in the same year as a former UW trainee (Nate), one of my closest colleagues (Bill), and two good friends (Neil and Lingjun). See you all in St. Louis!

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...

My favourite attendee feedback:
"I loved this class and I am super excited about Skyline, which is totally new to me. Halfway into the class I'm thinking "I've been living under a rock, this is going to change my life!" Without a doubt this class will have the highest ROI of anything I do this year"

Day 1 of the @asms.org Fall Workshop on "Fundamentals of Instrumentation" and oh boy I am humbled.

www.asms.org/conferences/...

Understanding m/z range settings for MS/MS scans: a case study with intact glycopeptides chemrxiv.org/engage/...

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#proteomics #prot-preprint

We use this strategy to assess the improvement in the Astral Zoom over the original. We also use this strategy to evaluate the effect of different acquisition strategies. Looking forward to seeing others apply this approach in the evaluation of other instruments. Great work by @chrhsu.bsky.social.

Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

Excited to see this published in JPR. For years I've wanted a simple way to standardize the signal between instruments. We use the precision of an intraspectrum ratio to assess the relationship between the reported signal and the number of ions. pubs.acs.org/doi/10.1021/...

It's lossless in the sense that there is no loss in information in counting one ion at a time versus 10^4. When you have a large number of items one should never count them 1 at a time.

Wrapping up the skyline.ms virtual workshop on #MassSpectrometry #proteomics with Advanced Proteomics: data independent acquisition today, post-translational modifications tomorrow. @juank1892.bsky.social @arianashannon.bsky.social @miriamabele.bsky.social (anybody else on bsky?) 🖥️🧬🧪

Lost Science is a new NYT series of accounts from scientists who have lost their jobs or funding. You can send your story to the Times here www.nytimes.com/2025/10/08/c...

Very excited to kick off the annual Skyline Online 2025 Small Molecule course with a keynote lecture by Gary Patti @gjpattij.bsky.social.
Showing how his lab and collaborators are advancing mass spectrometry to achieve parity with sequencing techs, supported by Skyline!

Gearing up for what promises to be an exciting week ahead @crg.eu #CRGtraining #teamMassSpec

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

If those professors are anything like me they probably need the most teaching.

STAFF SCIENTIST OR STAFF SCIENTIST SENIOR We are seeking a highly motivated PhD Chemist to join our laboratory as a Staff Scientist or Staff Scientist Senior and work on lipidomic and LC- MS/MS. Those with experience or willing to be trained ...

Staff scientist position in the Mass Spec Lab at the LSU Health New Orleans Neuroscience Center of Excellence lsuhsc.peopleadmin.com/postings/20349

I would argue this is the same for most proteomics. There are definitely a lot of challenges with experimental design and I think the field in general struggles to understand and how to minimize confounders.

[ASAP] Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00297

(J Proteom Res) [ASAP] Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide: Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00297 #MassSpecRSS

🚨 Webinar Alert! 🚨

Carafe enables high-quality in silico spectral library generation for data independent acquisition proteomics

📅 August 5 - 19:00 Seattle / August 6 - 10:00 Beijing

💡 Don't miss this chance to learn from the experts

#Proteomics

Our CNHUPO OES webinar 7 will be from Bo Wen at MacCoss Lab & Noble Lab at University of Washington, hosted by Wenfeng Zeng at Westlake University (10AM on Aug 6 UTC+8). Mark your calendar to learn more about DIA proteomics! @maccoss.bsky.social @us-hupo.org

Maybe they mean multi-protein profiling?

Just saw it now back to back.

Improvements to Casanovo, a deep learning de novo peptide sequencer www.biorxiv.org/cont...

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#proteomics #prot-preprint

I believe that academic-industry partnerships accelerate science. In the US, the Bayh-Dole Act incentivized the commercialization of discoveries made with govt funds. This is credited with the creation of the US biotech industry. Even better when this feeds back to provide $$ for academic research.

There is pressure for every science job and there can br a COI for job preservation, promotion, helping a colleague, writing a reference letter, etc... We should acknowledge our COIs and ask for guidance in managing them.

I don't think there is a difference. A core lab with a service agreement is under a ton of pressure to deliver results. A CRO performing an analysis on a large contract. A startup struggling to get its next round of VC funding. A PI wanting one more high impact paper for promotion.

I can say that our lab is currently funded mostly (>75%) from NIH, DOE, IARPA, etc... funds. Other than MS core facilities, I believe this is pretty standard. Most of our non-federal funds comes to support the Skyline and Pwiz projects and that supports ~40% of that project.

Asking about total compensation is like asking someone to disclose their salary or the amount of revenue for their company on social media. Even something that I'd regularly discuss with a colleague or is public knowledge, would be completely inappropriate to discuss here.

One thing to keep in mind when you say it is a "joke" is that there are real trainees who have worked hard to get these projects done. They worked hard because they believed in the project and have a manuscript we are proud of. These jokes suggest something nefarious happened.