Lab News & Updates

ACS Publications has announced that Mike MacCoss has been appointed the next Editor-in-Chief of Journal of Proteome Research (JPR). He will begin his term on January 1, 2027, succeeding Professor John R. Yates III, who has led the journal since 2016.

JPR is a monthly, peer-reviewed journal reporting on global protein analysis and function, with an emphasis on a multidisciplinary approach to the life sciences through the synergy between the different types of “omics.”

Mike’s vision for the journal is for JPR to be an outward-facing hub for pioneering methods, computational tools, and biological discoveries, while expanding its reach into clinical and translational medicine. He also wants the journal to be welcoming to researchers outside the proteomics community and to serve as a knowledge base for the next generation of proteomics and metabolomics scientists, with field-defining perspectives, tutorials, and reproducible protocols that make complex omics technologies accessible to any laboratory. These goals will be anchored by an author-first review experience that is fast, constructive, and respectful of the reviewers who make the community possible.

Read the full announcement on ACS Axial.

The Analytical Scientist has published a feature article, “Vibe Coding Moves Beyond the Proteomics Prototype”, describing how the MacCoss Lab used Claude to build and validate Osprey, a new open-source, peptide-centric search tool for data-independent acquisition (DIA) proteomics. The article includes interviews with Mike MacCoss and Brendan MacLean.

Osprey detects and scores peptides in DIA data, then writes out peak boundaries and a spectral library that Skyline reads directly. Mike built the original version entirely through natural-language prompting with Claude: roughly 30,000 functional lines of Rust plus about 12,000 lines of tests. Brendan then ported Osprey to C# for integration with ProteoWizard and Skyline, and neither of them typed a line of the code by hand.

The article focuses on what it takes to move AI-generated code past the prototype stage. An early translation looked convincing because identification counts matched, but deeper problems in the pipeline only surfaced weeks later. To catch issues like these, Brendan divided the pipeline into seven stages and compared the C# and Rust implementations at each one, moving on only when a stage produced virtually identical results. As Mike puts it, “Generating code is the easy part now. Knowing whether the code does what you asked is the hard part.”

A key motivation for the project is reproducibility. Quantitative DIA analysis is currently dominated by closed-source tools, and Osprey is intended to provide a fully open alternative that integrates with the Skyline ecosystem.

Read the full article at The Analytical Scientist, and find the Osprey source code on GitHub.

Congratulations to Lauren Fields, a postdoctoral fellow in the MacCoss Lab, who has been selected as a 2026 Schmidt Science Fellow! The Schmidt Science Fellowship is a highly competitive program that supports the next generation of science leaders working on the world’s most pressing problems. Fellows are chosen for their potential to make a significant impact through interdisciplinary research.

As a Schmidt Science Fellow, Lauren will use advanced mass spectrometry and protein analysis of clinical blood and cerebrospinal fluid samples to search for earlier diagnostic markers for amyotrophic lateral sclerosis (ALS). This work could pave the way for earlier intervention and the development of therapeutics that alter the trajectory of the disease.

Lauren earned her PhD in Chemistry from the University of Wisconsin-Madison in December 2025, where she worked with Professor Lingjun Li on neuropeptide detection strategies using mass spectrometry. As a Schmidt Science Fellow, she will pivot from analytical chemistry into proteomics and genomics, bringing her expertise in mass spectrometry to bear on one of the most challenging problems in neurodegenerative disease research.

Read more about Lauren’s work in the UW-Madison Graduate School press release and learn about the full 2026 cohort of Schmidt Science Fellows.

The TaMADOR consortium has launched a new website at tamador.org. TaMADOR — Targeted Mass Spectrometry Assays for Diabetes and Obesity Research — brings together research groups funded by two NIDDK programs to develop and disseminate targeted mass spectrometry assays for the diagnosis and monitoring of Type 1 Diabetes and Obesity.

The consortium includes four participating institutions:

• University of Washington (PIs: Andrew Hoofnagle, Michael MacCoss) — Quantifying proteins in plasma to democratize personalized medicine for patients with Type 1 Diabetes
• PNNL & University at Buffalo (PIs: Jun Qu, Wei-Jun Qian) — Robust mass spectrometric protein/peptide assays for Type 1 Diabetes clinical applications
• Cedars-Sinai Medical Center (PI: Jennifer Van Eyk) — Design and validation of easy-to-adopt mass spectrometry assays of importance to Obesity
• Pacific Northwest National Laboratory (PI: Wei-Jun Qian) — Multiplex mass spectrometric protein assays for precise monitoring of the pathophysiology of Obesity

The site features publications, datasets, meeting information, and links to the Panorama data repository. Check it out at https://tamador.org.

We are pleased to announce an all-new advanced course: Frontiers in Proteomics: Advanced Skyline Applications, taking place July 6–10, 2026 at the Foege Building, University of Washington, Seattle.

This year’s curriculum has been completely redesigned for experienced Skyline users looking to deepen their expertise across advanced quantitative proteomics topics. Through lectures, hands-on exercises, and guided discussions, participants will explore:

• System suitability and quality control strategies
• Statistical methods for designing and analyzing advanced DIA experiments
• AI-driven workflows
• The Skyline software ecosystem and integrating external tools effectively
• Experiment design tailored to your own research goals

The instructor list includes researchers and software developers from the MacCoss Lab, alongside experts with extensive experience in targeted and quantitative proteomics — a unique opportunity to learn directly from the creators of Skyline.

• Who: Experienced Skyline users
• When: July 6–10, 2026
• Where: Foege Building, University of Washington, Seattle
• Cost: Academic: $500 | Industry: $1250
• Participants: 30
• Apply by: April 1, 2026

Registration includes course materials, refreshments, and a course dinner. Participants are responsible for their own travel, lodging, and meals.

Apply now or see the full course details and schedule.

At this week’s US HUPO 2026 conference in St. Louis, Missouri, three members of our extended community officially received their awards. Congratulations to Mike MacCoss, Nate Basisty, and Bill Noble!

Mike MacCoss received the Donald F. Hunt Distinguished Contribution in Proteomics Award, recognizing his outstanding contributions to the field of proteomics, including his scientific achievements and dedication to mentorship and improving equity and inclusion within the community.

Nate Basisty, a former MacCoss lab trainee who completed his Ph.D. at UW co-mentored by Peter Rabinovitch and Mike MacCoss, received the Robert J. Cotter New Investigator Award. Nate is now an NIH Distinguished Scholar and Tenure Track Investigator at the National Institute on Aging, where his Translational Geroproteomics Unit works at the intersection of proteomics and translational aging biology.

Bill Noble, one of our closest colleagues in the Department of Genome Sciences, received the Gilbert S. Omenn Computational Proteomics Award, recognizing his tremendous contributions to machine learning and statistical methods for analyzing shotgun proteomics data.

We are incredibly proud of all three awardees. What a wonderful representation of our community!

Deanna Plubell’s paper on Development of highly multiplex targeted proteomics assays in biofluids using a nominal mass ion trap mass spectrometer is now published in Molecular & Cellular Proteomics. This work was done during Deanna’s postdoc in the lab and was a fantastic collaboration with our Thermo colleagues Phillip Remes, Cristina Jacob, and Lilian Heil, as well as our neurodegeneration collaborators Kathleen Poston and Tom Montine. The paper demonstrates the generation of large-scale targeted assays using the Stellar mass spectrometer, with applications to cerebrospinal fluid and Mag-Net enriched plasma extracellular vesicles for neurodegenerative disease research.

Mike MacCoss was recently interviewed on “The Proteomics Show” podcast leading up to USHUPO 2026. The discussion covers topics in proteomics research and mass spectrometry.

The episode is available wherever you get your podcasts, or you can listen directly on Spotify.

We hosted our third Skyline webinar of 2025 with over 153 participants joining Michael MacCoss and Nick Shulman on December 11th. The webinar introduced the newest Skyline tutorial on Peak Boundary Imputation for DIA Data.

Mike presented a case for imputing boundaries for missing DIA data, and Nick demonstrated the technique using Skyline. The session concluded with a great Q&A that generated many excellent questions and will lead to more discussion in a future webinar.

The webinar recording, slides, tutorial, and data set are available on the Skyline Webinar 27 page.

Michael MacCoss and Brendan MacLean have been recognized on the 2025 Clarivate Highly Cited Researchers list. This list identifies researchers who have demonstrated significant and broad influence in their fields through the publication of multiple highly cited papers over the last decade.

The University of Washington had 56 faculty and researchers named to this year’s list across various fields. The Clarivate Highly Cited Researchers list recognizes world-class researchers selected for their exceptional research performance, demonstrated by production of multiple highly cited papers that rank in the top 1% by citations for their field and year.

This recognition reflects the significant impact of the MacCoss Lab’s work in mass spectrometry and proteomics, particularly the development of widely-adopted tools like Skyline and contributions to quantitative proteomics methodology.

Read more about the 2025 Clarivate Highly Cited Researchers at UW.