E ditor - in - chief
editorial
William S. Hancock
Barnett Institute and Department of Chemistry Northeastern University Boston, MA 02115 617-373-4881; fax 617-373-2855
[email protected] Associate E ditors Joshua LaBaer Harvard Medical School György Marko-Varga AstraZeneca and Lund University Martin McIntosh Fred Hutchinson Cancer Research Center
Proteomics: You Say Functional, I Say Structural
Cons u lting E ditor Jeremy K. Nicholson Imperial College London
n the field of proteomics, it is interesting to note that structural proteomics is generally not included in the description of “proteomics” for meetings or in the titles and scopes of journals, although it is sometimes included in web-based definitions. One explanation for the origin of this separation dates back to the use of the phrase “structural genomics” when the field was being organized. A simple definition that distinguishes between genomics and proteomics is that genomics focuses on genes on an organism scale, whereas proteomics focuses on proteins or “the total protein complement of a genome” (Wikipedia). Structural proteomics can be considered the systematic study of relationships among biological macromolecules—such as the entire protein complement of a genome, protein family, pathway, or protein-fold space—and how these components are interconnected on a proteome scale. Interestingly, only in the U.S. is the term structural genomics still used, mostly for historical reasons but also in part to emphasize the more bioinformatics-driven focus. The European efforts now consistently use the term structural proteomics, and Japan has recently renamed its effort the Riken Structural Genomics/Proteomics Initiative. It is likely that in a few years, everyone will be referring to the large-scale study of protein structure families and their relationships as structural proteomics. There is value in how we define scientific activities, because definitions can influence who joins organizations, attends meetings, or ultimately collaborates. The 2006 HUPO conference in Long Beach, Calif., was very functional and clinical in its program, but it offered only one lecture on structural proteomics out of 150. In contrast, the recent (December 2006) Asia Oceania HUPO (AOHUPO) meeting in Singapore was held jointly with the Fourth Structural Biology and Functional Genomics Conference. As a result of the joint nature of the conference, the meeting had a very different look and feel. In particular, it offered an equal balance of MS-based proteomics, functional analysis, and structural proteomics. From a structural and functional proteomics perspective, AOHUPO was a great meeting because multiple groups interested in studying an entire proteome were in one place, and diverse topics, ranging from large-scale data-management issues to biological discovery on a proteome scale, were discussed. Proteomics should be recognized as a continuum of activities, from identifying proteins in a given proteome and the functional roles of these proteins to detailing the mechanisms that carry out those functions. A startling outcome of the Human Genome Project was how few genes are present and, thus, how important the structural variations created by alternate splicing and covalent modifications must be in the generation of functional diversity. Only through a combination of efforts along the “Proteomic Continuum” will we learn how structural variations and modifications in proteins can have the necessary pleiotropic effects to evolve wonderfully complex organisms such as ourselves. A small but necessary step to achieve this goal is better integration of conferences. This will naturally lead to more collaboration and integration of efforts.
E ditorial adv isory board Ruedi H. Aebersold ETH Hönggerberg Leigh Anderson Plasma Proteome Institute Rolf Apweiler European Bioinformatics Institute Ronald Beavis Manitoba Centre for Proteomics John J. M. Bergeron McGill University Rainer Bischoff University of Groningen Richard Caprioli Vanderbilt University School of Medicine R. Graham Cooks Purdue University Thomas E. Fehniger AstraZeneca Catherine Fenselau University of Maryland Daniel Figeys University of Ottawa Sam Hanash Fred Hutchinson Cancer Research Center Stanley Hefta Bristol-Myers Squibb Denis Hochstrasser University of Geneva Michael J. Hubbard University of Melbourne Donald F. Hunt University of Virginia Barry L. Karger Northeastern University Joachim Klose Charité-University Medicine Berlin Matthias Mann Max Planck Institute of Biochemistry David Muddiman North Carolina State University Robert F. Murphy Carnegie Mellon University Gilbert S. Omenn University of Michigan Akhilesh Pandey Johns Hopkins University Aran Paulus Bio-Rad Laboratories Jasna Peter-Katalini´c University of Muenster Peipei Ping University of California, Los Angeles Michael Snyder Yale University Clifford H. Spiegelman Texas A&M University Ruth VanBogelen Pfizer Global Research & Development Timothy D. Veenstra SAIC-Frederick, National Cancer Institute Scot R. Weinberger GenNext Technologies Susan T. Weintraub University of Texas Health Science Center John R. Yates, III The Scripps Research Institute
© 2007 American Chemical Society
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RAYMOND C. STEVENS Department of Molecular Biology, and JOHN R. YATES Department of Cell Biology, The Scripps Research Institute
Journal of Proteome Research • Vol. 6, No. 3, 2007 927
