Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla Mass Spectrometry Reviews, EarlyView.

(MS Reviews) Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla: Mass Spectrometry Reviews, EarlyView. #MassSpectromRev #MassSpecRSS

UW graduate student deported through SEA as protesters demand answers A union representing University of Washington graduate student workers says Kennedy Orwa’s student visa was rescinded without explanation.

Our PhD student Kennedy Orwa, who studies applications of AI to health care, was hastily deported today to Kenya along with his 13-year-old son without opportunity to speak to legal counsel.

King 5 reports that he held a valid visa that was rescinded without explanation.

Getting the ol' grad school gang back together with Carafe2 -- Bo Wen (@maccoss.bsky.social and Bill Noble) and @jspaezp.bsky.social (@willfondrie.com at @talusbio.bsky.social) teamed up for essentially some late night hackathons to build out Carafe for @brukercorporation.bsky.social timsTOF data.

📢 Publication alert🌶️! Congrats to the @maccoss.bsky.social lab who show the use #Mag_Net for enrichment of EV's from #serum to study the effects of monoclonal antibody therapy on the fate and function of T-cells in people with type 1 diabetes! biorxiv.org/content/10.6...

Congratulations to John R. Yates III, Ruedi Aebersold and Matthias Mann, recipients of the 2026 Canada Gairdner International Award.

Prof. Yates: www.gairdner.org/winner/john-...
Prof. Aebersold: www.gairdner.org/winner/ruedi...
Prof. Mann: www.gairdner.org/winner/matth...

#2026GairdnerAwards

I haven't seen that poster, but the optimal selection of entrapment sequences is something that should be investigated. I wonder how much their data is a result of such a strong dependence of MS1 on the Spectronaut scoring. Other tools are less dependent on MS1.

Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies A recent clinical study tested the effects of two different monoclonal antibodies (mAbs) (siltuximab, anti-IL6; tocilizumab, anti-IL6R) on the fate and function of T-cells in people with type 1 diabetes. While both mAbs affect the response of T-cells to stimulation, they have very different, sometimes opposing mechanisms. Here, we use mass-spectrometry based proteomics to analyze longitudinal serum samples (baseline and two weeks post-treatment) from 20 clinical trial participants to examine the effects of siltuximab and tocilizumab on extracellular vesicles. To accomplish this, serum samples were enriched for extracellular vesicles with Mag-Net and analyzed by LC-MS/MS to identify significantly differentially abundant protein groups and pathways. Proteome analysis confirmed highly reproducible measurements across multiple draw dates. In total, we quantified 3300 protein groups of which 46 protein groups had significantly altered abundance after mAb treatment. Tocilizumab altered pathways associated with proteostasis (neddylation) and pre-notch transcription and translation. Siltuximab altered FCGR activation pathway members. In addition, quantitation of the monoclonal antibody therapies themselves enabled the measurement of the correlation between drug amounts and impacted proteins. Taken together, this work demonstrates the utility of the Mag-Net method to evaluate the impacts of therapeutic interventions on serum extracellular vesicles.

(BioRxiv All) Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies: A recent clinical study tested the effects of two different monoclonal antibodies (mAbs) (siltuximab, anti-IL6; tocilizumab, anti-IL6R) on the fate and function… #BioRxiv #MassSpecRSS

📢Publication Alert🌶️! #IRCCS developed a #multiomics workflow for #lipidomics and EV #proteomics analysis of very preterm infants using just 10 µl of plasma with #Mag_Net (from the lab of @maccoss.bsky.social) #TeamMassSpec #TeamReSynBio www.medrxiv.org/content/10.6...

#ushupo2026 huge congratulations to Mike @maccoss.bsky.social for winning the @us-hupo.org Don Hunt Distinguished contribution in Proteomics award - so well -deserved! 👍🙌🎉 Also congrats to Bill Noble for receiving Omenn Computational proteomics award and Nathan for Cotter New investigator award🥇 🎉🙌👍

Excited we renewed our long-term relationship with Sciex to ensure our software tools Skyline, MSConvert, Panorama, AutoQC, etc... work seamlessly with Sciex hardware. We have big plans for Skyline in the upcoming year.

Looking forward to hearing how @talusbio.bsky.social is using Skyline in their latest applications.

Also, happy to work with other groups to calculate the alpha on their instruments. We just need a file that contains MS/MS of a peptide or similar from a continuous infusion over say 1000 spectra.

We have data from Sciex and Bruker platforms. We are working on something. I agree that it would be good to be able to compare signal intensities directly between platforms.

Its not "in your day" ... its "today". The Nyquist–Shannon sampling theorem hasn't changed.

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...