Michael MacCoss

Totally agree.

The US HUPO sponsored "Pony Express" series highlights speakers at the upcoming #USHUPO2026 meeting. Ben and Ben sit down to talk with Dr. William Noble, University of Washington, recipient of the 2026 Gilbert S. Omenn Computational Proteomics Award.

Listen Now: https://ow.ly/XiBa50Y6o4m

Same with code. I might not have written any of my students programs but I've helped evaluate them, document, and confirm how the algorithms work.
I totally agree w/ your hammer metaphor. I'm totally worried about LLMs impact but people are still going to use power tools. Hopefully we do it safely.

I should clarify. I'm not saying LLMs are like a student. I find I interact with them like I would a trainee. I would never let text from a student get submitted without significant time editing & revising. As a student gets more experienced there is less revision. These tools will get better soon.

I'm personally much more against kits with mystery reagents than AI methods.

We've been through similar transitions in the past. Should we let trainees use kits, calculators, Google searches, Intellij, etc... These tools have the potential of advancing science significantly but we all have concerns about whether we could be creating a gap in the institutional knowledge.

Everything we do is based on building on the existing literature. The responsibility is still on the author for ensuring the content is accurate and appropriately cited. If the content is BS then the community/reviewers, etc... need to call it out. It doesn't matter how the content was written.

These tools aren't going away and they will get much more accurate and powerful. The real question is what's the best way to use them. Just like how we need to be skeptical with everything we get from Google or even the literature; this doesn't change that.

I'm not sure we need 1000s of AI generated scripts or web apps in the literature but I'm supportive if those help an individual QC, visualize, or interpret their data. We do need to think about the best ways to use these tools and how to train future scientists on how to use them appropriately.

I find the process of using AI similar to mentoring a trainee. You get drafts that need revision and implementations of algorithms that produce results that don't make sense. That said, AI methods are improving exponentially and becoming very useful. Claude Opus 4.5 appears on a different level.

Special Issue on Women in Proteomics www.mcponline.org/ar...

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#proteomics #prot-paper

I definitely don't need a TV that big. 😂

Development of highly multiplex targeted proteomics assays in biofluids using a nominal mass ion trap mass spectrometer The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale c…

It took a while for us to get this paper finalized! Pretty excited for this to be out.
www.sciencedirect.com/science/arti...

That's what I use my 49" monitor for!

We can start the rumor that Skyline is named after the Nissan Skyline if it would help 😀.

#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...

Comic. Panels up to the 10-year point are grayed out. New panels since the Ten Years comic, which chronicles the first ten years of PERSON 1's journey with cancer: (1) [two people in bed] PERSON 1 (woman): One more chapter? PERSON 2 (man): Don’t we both have to get up early? PERSON 1: Nnnnnggggh PERSON 2: Sure, good point. (2) [many people wearing masks, walking while looking at graphs on their phones] (3) [birds landing on people] PERSON 2 in beanie and scarf: Hah! They like *my* seeds best. PERSON 1 in scarf holding phone with a bird sitting on it: Wait, how do I take a picture of this one? (4) [two people rowing boats with tree landscape] (5) [Person 1 carries overflowing stack of things to Person 2 in bed] PERSON 1: I brought you honey lemon tea, more pillows, a cinnamon roll, Tylenol, another blanket, a– PERSON 2: It was just Appendicitis, I’m really– PERSON 1: *It is my turn to take care of you and I am going to do it right!* (6) [Two people in car] (7) [still in car) PERSON 1: Oh my god. PERSON 2: Oh my god. (8) [car driving] PERSON 1: Pull over! PERSON 2: I am! (9) [both people get out of car] (10) [Large colored panel of aurora borealis over water with both people looking on] (11) [Person 1 sits against tree while Person 2 lies on the ground] PERSON 1: Fifteen years. No sign of the cancer. (12) I *am* having some weird symptoms. Joint pain. Fatigue. I think I’m losing my close-up vision. PERSON 2: Yeah. Me too. (13) PERSON 2: I think we’re getting old. (14) PERSON 1: I guess that’s okay. PERSON 2: It’s all I wanted.

Fifteen Years

xkcd.com/3172/

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!