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Molecular & Cellular Proteomics 6:1110-1111, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.
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From the Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, ¶ Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90075, and || Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 2B2, Canada
This year's HUPO World Congress, Bench to Bedside, captured the excitement within the proteomics community over current developments and the anticipation of applying these developments to fundamental and clinical questions. This was best reflected in the organizers' intention that the Long Beach meeting was not going to be "just another mass spectrometry meeting." Vertical integration of the program captured the breadth of developments in the fast moving proteomics field and illustrated the power of current technologies to better understand both basic biological functions and the pathogenesis to disease phenotypes. The opening keynote address by Dr. Anna Barker highlighted the congress theme on translating proteomics technologies to advance medicine and to benefit society.
The breadth of research featured in this congress is best illustrated by two lectures presented at the meeting. Mike Tyers encapsulated the breadth of modern technologies applied to the protein interactome, and Donald Hunt described new developments in mass spectrometry technologies that can be used to better understand regulation of transcription. The network of >12,000 protein interactions in yeast curated from the primary literature (see BioGRID (General Repository for Interaction Datasets), www.thebiogrid.org) forms a dense, uniform network that contains more hub-hub interactions than the sparsely connected networks derived from initial high throughput studies. Recent high throughput (HTP)1 proteome-wide surveys by the Greenblatt and Superti-Furga groups support the notion that biological networks are highly interconnected. Similarly the exhaustive analysis of the phagosome presented by Michel Desjardins and of the nuclear pore presented by Brian Chait supported the notion that biological processes are controlled by a dense and dynamic web of protein interactions. An important discussion point raised by John Yates, namely the reliability of individual interactions in an HTP dataset versus the same interaction studied in depth "by a postdoc at the bench" elicited divergent views from the HTP and small scale camps. Regardless it is clear that the yeast interactome is far from complete as, for example, less than 30% of literature protein interactions are found in all HTP data combined. Tyers also cited examples of well studied signaling pathways for which less than 5% of known interactions are found in an HTP dataset. Reinterrogation of the protein interactome using rapid magnetic bead-based isolation methods developed by Brian Chait holds promise of detecting the transient signaling interactions that underlie cellular dynamics. Given the evident density and redundancy of biological networks, Tyers argued that systematic collections of small molecules will be needed to precisely modulate the proteome. An initial matrix of >4,000 chemical-genetic interactions has enabled successful prediction of small molecule-small molecule interactions. Such interactions may enable highly specific antifungal and anticancer therapeutics.
Proteomics has been heavily driven by technologies such as mass spectrometry. New developments in mass spectrometry can have a significant impact on the quality of mass spectrometry data but can also enable new or improved strategies. Donald Hunt described developments in the dissociation of peptides in tandem mass spectrometers using a new method called electron transfer dissociation (ETD) in a session called Pioneers in Proteomics. ETD dissociates multiplying charged peptide ions in tandem mass spectrometers by transfer of an electron to create an unstable radical cation. Peptide ions fragment and do so very evenly across the amide backbone of the peptide. Because the method works best on multiply charged peptide ions (+3 and greater), the method is effective at dissociating larger polypeptides. To this end Hunt showed the use of ETD to dissociate larger pieces of histones to identify post-translational modifications. Histone proteins are heavily modified, and the pattern of modification is important for the regulation of gene transcription. Hunt showed by using ETD in simple ion trap mass spectrometers that modifications contained within long stretches of histones could be readily identified. In particular ETD is useful to identify phosphorylation sites as ß elimination of phosphate from Ser and Thr residues does not occur in ETD spectra. Hunt also described implementations to perform ETD that do not require extensive modification of the mass spectrometer, a development that will allow wider adoption of the process on a larger variety of mass spectrometers.
The meeting stimulated vibrant discussions regarding the future directions of proteomics sciences. Emerging approaches parallel mass spectrometry such as antibody-based arrays, large scale characterization of protein structures, nanotechnology, and high resolution imaging were among the hot topics. The over 1,000 abstracts presented showcased the tremendous contributions of proteomics sciences to advance biology and medicine. Additional newsworthy papers include the release of the second version of the Human Protein Atlas by a Swedish team led by Dr. Mathias Uhlen and the well developed Proteomics Standard Initiatives (PSI) led by Dr. Rolf Apweiler at the European Molecular Biology Laboratory-European Bioinformatics Institute.
Ostensibly the meeting marked an exciting milestone where proteomics-supported developments of novel technologies, proteomics-based discoveries in expanding our knowledge base to biological systems, and proteomics-enabled advancements in personalized and predictive therapies have begun to see fruition. Moving forward, HUPO has established a set of goals to ensure a continuation of the current success achieved in the proteomics community. At the technology front, The HUPO Technology Committee is leading the effort in the scientific community by an emphasis on standardization with a new Initiative on Protein Test Samples. At the education front, HUPO is engaged in activities to enhance public awareness on the social benefits of proteomics sciences; in addition, HUPO continues to promote the careers of young scientists in the community and is committed to place education and training as its key focus areas. To further promote interactions of academia, institutions, and industry, HUPO created the Industrial Advisory Board (IAB) to facilitate collaborative efforts of industry partners to support the proteomics community.
There are obvious challenges ahead; yet the enthusiastic participations from investigators of academic institutions, federal funding agencies (e.g. National Institutes of Health and European Union), and industrial partners as evidenced in the congress clearly demonstrate a consensus in the proteomics community that joint efforts and team work are the key to success.
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FOOTNOTES |
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Co-organizers of the HUPO World Congress at Long Beach, CA.
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