and Mass Spectrometry

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Protein Quantitation Using Stable Isotope Labeling in Mammals (SILAM) to Understand Human Disease and Injury

presented by

John Yates III
Ernest W. Hahn Professor
The Scripps Research Institute

April 18, 2013

The Scripps Research Institute Auditorium


Dr. Yates is a Professor in the Department of Chemical Physiology at The Scripps Research Institute. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has developed the use of proteomic techniques to analyze protein complexes, posttranslational modifications, organelles and quantitative analysis of protein expression for the discovery of new biology. Many proteomic approaches developed by Yates have become a national and international resource to many investigators in the scientific community. Dr. Yates led an NIDCR funded Center to characterize the Saliva proteome and has been involved in an NCRR funded Research Resource Center for the last 15 years and was involved in an NSF funded Science and Technology for 10 years. He has received the American Society for Mass Spectrometry research award, the Pehr Edman Award in Protein Chemistry, the American Society for Mass Spectrometry Biemann Medal, the HUPO Distinguished Achievement Award in Proteomics, Herbert Sober Award from the ASBMB, and the Christian Anfinsen Award from The Protein Society. He was ranked by Citation Impact, Science Watch as one of the Top 100 Chemists for the decade, 2000-2010. He has published over 600 scientific articles.


A component to understanding biological processes involves identifying the proteins expressed in cells as well as their modifications and the dynamics of processes. Several major technologies, but especially mass spectrometry, have benefited from large-scale genome sequencing of organisms. The sequence data produced by these efforts can be used to interpret mass spectrometry data of proteins and thus enables rapid and large-scale analysis of protein data from experiments. This has improved the analysis of protein complexes and more complicated protein mixtures. Quantitative mass spectrometry can be used to study biological processes. We developed methods to label rats and mice with 15N for use as internal standards for complex tissue samples 1. This allows the study of animal models of development and disease2-4. The advantages and disadvantages of the approach in the study of several different disease and injury models will be discussed.

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