Abstract
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.  Advances in multi-dimensional separations as well as mass spectrometry have improved the scale of experiments for protein identification.    This has improved the analysis of protein complexes, and more complicated protein mixtures. Subtractive data analysis approaches have also improved the ability to identify the components of large structures such as the centrosome and proteins associated with chromatin.  Experiments to identify centrosome proteins and chromatin associated proteins using subtractive approaches will be described.

Background
Professor John Yates received his Ph.D. in Chemistry at the University of Virginia under Professor Donald Hunt.  His graduate research involved the development and application of tandem mass spectrometry for sequence analysis of proteins.  Following a Biotechnology Fellowship at the California Institute of Technology, he moved to the Department of Molecular Biotechnology at the University of Washington where he attained the tenured rank of Associate Professor.  He is now a Professor in the Department of Cell biology 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 proteomics.  He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and principle developed of the shotgun proteomics technique for the analysis of protein mixtures.  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 has published over 354 scientific articles.