E ditor - in - chief
William S. Hancock
editorial
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 Cons u lting E ditor Jeremy K. Nicholson Imperial College London 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 Henry Rodriguez National Cancer Institute 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
Lower-Order versus Higher-Order Proteomics: Time To Move Up?
P
roteomics research presents a myriad of challenges. Although initially these challenges were mostly technical, we are now moving to a phase where we can routinely separate large numbers of proteins, analyze their levels of expression, and identify those of interest to us. In this respect, the proteome is no longer largely unknown. Substantial audits of protein expression have given and will continue to give us insight into which proteins are present in a particular cell or tissue at a certain time and under specified conditions. For the purpose of biomarker discovery, this is of enormous value. Increasingly, many researchers use proteomics technology to understand protein function. In this regard, a challenge we face is that most mainstream proteomics approaches are reductionist in nature. For 2DE gels, scientists use denaturants, detergents, and reducing reagents to enhance analytical reproducibility of individual proteins. Multidimensional LC/MS/MS analyses require the complete dissociation of proteins before they are digested into as many peptides as possible. In both cases, methods are designed to completely eliminate all covalent and noncovalent associations between proteins. The data produced from 2DE gels and LC/MS/MS can be near-global, in that information such as expression data can be produced for a very large number of proteins. But the information is of “lower order” in that it does not generate insight into the functional organization of proteins into complexes and supercomplexes. This valuable context for each protein is lost. Unfortunately, the data that are generated do not easily lend themselves to alternative interpretations that would provide glimpses into or enhance our understanding of the “higher order” of the proteome. Large-scale studies of protein complexes (the “complexome”) are beginning to be reported. Interestingly, these researchers have used affinity purification and simple MS identification methods that are, in some respects, quite low-tech approaches. With these methods, two research teams have unequivocally shown that the proteome exists as a large collection of complexes (Nature 2006, 440, 631–636; 637–643). In Saccharomyces cerevisiae, ~500 of these have been defined, and it is estimated that there are ~800 complexes in total. These complexes, from dimers and tetramers up to supercomplexes, such as ribosomes, represent the higher order of the proteome. It is how the cell organizes itself to deliver function at a molecular level. This new definition and view of the cell, which is likely to approximate biological reality, presents challenges and opportunities for proteome research. Technology in which large numbers of protein complexes are purified in parallel and in a way that is amenable to downstream MS analysis is required. Blue native PAGE and iterations of this technique are likely to play a role. Mass spectrometers tuned to analyze massive protein complexes are also needed. Conceptually, we need to move from thinking about proteins as individual molecules and toward thinking of them as being parts of molecular machines. These advances in concepts and technology, no doubt in association with a smorgasbord of other advances, may well usher in a new era of higher-order proteomics. Changes in protein expression, the focus of much current research but whose functional impact is difficult to discern, might then be evaluated at the level of the protein complex. Do protein complexes still form and is function still performed when protein levels change? Or do proteins expressed at varying levels form different complexes? With respect to our understanding of disease, this concept brings new avenues of investigation. For example, is the genesis of disease associated with a loss or gain of protein–protein interactions? Higher-order proteomics, when realized, should present the opportunity to answer some of these important questions. Marc R. Wilkins School of Biotechnology and Biomolecular Sciences University of New South Wales, Australia Journal of Proteome Research • Vol. 6, No. 7, 2007 2403
