John R. Yates

John R. Yates III is the John Lytton Young Professor in the Department of Integrative Structural and Computational Biology at The Scripps Research Institute. He received a B.A. in Zoology and an M.S. in Chemistry from the University of Maine at Orono, and earned his Ph.D. in Chemistry at the University of Virginia in the laboratory of Donald F. Hunt, where his dissertation focused on protein sequencing by tandem mass spectrometry. He completed postdoctoral training in the laboratory of Leroy E. Hood at the California Institute of Technology.

Dr. Yates previously held faculty positions at the University of Washington, where he was promoted to Associate Professor with tenure, before joining Scripps Research. He is a pioneer in mass spectrometry–based proteomics, serving as the lead inventor of the SEQUEST software for database searching of tandem mass spectra and as a principal developer of shotgun proteomics for large-scale protein mixture analysis. His laboratory has advanced proteomic methods to study protein complexes, post-translational modifications, organelles, and quantitative protein expression, enabling fundamental biological discoveries.

Dr. Yates has received numerous honors, including the ASMS Research Award, Pehr Edman Award, Biemann Medal, HUPO Distinguished Achievement Award, Herbert Sober Award, Christian Anfinsen Award, ACS Award in Analytical Chemistry, Ralph N. Adams Award, Thomson Medal, John B. Fenn Distinguished Contribution Award, HUPO Discovery Award, and the 2024 Pittsburgh Society Award in Analytical Chemistry. He served as an Associate Editor of Analytical Chemistry for 15 years and is currently Editor-in-Chief of the Journal of Proteome Research.

The Work 

John Yates, Ruedi Aebersold, and Matthias Mann collectively established the foundations of modern proteomics -the large-scale study of proteins- by solving three interdependent problems: how proteins can be measured at scale, how those measurements can be made quantitative and reliable, and how complex protein data can be interpreted biologically.  

Yates pioneered shotgun proteomics through the development of the computational methods that interpret tandem mass spectra to identify proteins enabling large-scale, unbiased identification of proteins from complex mixtures, fundamentally transforming biological research.  

Aebersold transformed protein analysis by moving the field from 2D gel electrophoresis to quantitative proteome analysis and later to targeted approaches and to the measurement of the functional state of the proteome, establishing proteomics as a rigorous, systems-level and quantitative science.  

Mann transformed the field through innovations spanning mass spectrometry methods, computational analysis, and biological application. His development of MaxQuant, one of the most widely used computational platforms in proteomics, set new standards for protein identification and quantification. His laboratory pioneered methods that enabled the accurate measurement of over ten thousand proteins and their modifications in single experiments, and extended mass spectrometry-based proteomics into clinical diagnostics through plasma proteomics and into spatial biology through Deep Visual Proteomics.

The Impact 

By making it possible to comprehensively study the molecules and their functionally relevant properties that carry out key cellular functions and serve as targets for many drugs, Yates, Aebersold and Mann made contributions to protein analysis that reshaped biomedical research and medicine. 

Proteomics is now central to understanding disease mechanisms, enabling advances in cancer research, neurodegenerative disease, immunology, infectious disease, and precision medicine. Their collective work has opened new avenues of understanding the biological processes of proteins in the cell and their disruption in disease, enabling drug discovery, and strengthening the pathway for translation of basic research into clinical benefit.