Ruedi Aebersold

Ruedi Aebersold is a Swiss/Canadian scientist trained at the Biocenter, University of Basel, Switzerland, in cell biology and biochemistry. Following postdoctoral research at Caltech, he held faculty positions at the University of British Columbia in Vancouver and the University of Washington in Seattle, WA. In 2000, he co-founded the Institute for Systems Biology in Seattle with Lee Hood and Alan Aderem. In 2004, he joined ETH Zürich to establish the Institute of Molecular Systems Biology. He has co-founded several companies and holds multiple public service appointments. His work has been recognized with numerous national and international awards, including the Biemann Medal of ASMS, the Paracelsus Prize of the Swiss Chemical Society, the Otto Naegeli Prize, the Thomson Medal of IMSF, the HUPO Achievement Award, the Marcel Benoist Swiss Science Prize—the most prestigious science award in Switzerland—and the Heineken Award for Biochemistry and Biophysics in 2024.

The Aebersold group’s research has focused on the proteome. The group pioneered several widely used techniques and developed open-access, open-source software and statistical tools that have helped make proteomic research more transparent, reproducible, and accurate. Collectively, these methods and tools constitute a multiPROTeomic toolkit for investigating biological samples as complex, adaptable systems. Application of this toolkit has advanced the understanding of molecular processes in both basic biology and clinical research.

He entered emeritus status in 2021 and now serves as a member of the board of trustees of several foundations that support life science research and charitable programs.

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.