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The Human Proteome Project: Current State and Future Direction balt3/zjw-macp/zjw-macp/zjw00711/zjw3889-11a xppws Sϭ1 3/6/11 8:30 4/Color Figure(s) F1 ARTNO: M111.009993 Research © 2011 by The American Society for Biochemistry and Molecular Biology, Inc. This paper is available on line at http://www.mcponline.org The Human Proteome Project: Current State and Future Direction Pierre Legrain‡q**, Ruedi Aebersold§, Alexander Archakov¶, Amos Bairochʈ, Kumar Bala**, Laura Beretta‡‡, John Bergeron§§, Christoph H. Borchers¶¶, Garry L. Corthalsʈʈ, Catherine E. Costelloa, Eric W. Deutschb, Bruno Domonc, William Hancockd, Fuchu Hee, Denis Hochstrasserf, Gyo¨ rgy Marko-Vargag, Ghasem Hosseini Salekdehh, Salvatore Sechii, Michael Snyderj, Sudhir Srivastavak, Mathias Uhle´nl, Cathy H. Wum, Tadashi Yamamoton, Young-Ki Paiko,q**, and Gilbert S. Omennp,q** AQ: A After the successful completion of the Human Genome initiatives and a chromosome-centric protein mapping Project, the Human Proteome Organization has recently strategy, termed C-HPP, with which many national teams officially launched a global Human Proteome Project are currently engaged. In addition, numerous biologically (HPP), which is designed to map the entire human protein driven and disease-oriented projects will be stimulated set. Given the lack of protein-level evidence for about 30% and facilitated by the HPP. Timely planning with proper of the estimated 20,300 protein-coding genes, a system- governance of HPP will deliver a protein parts list, re- atic global effort will be necessary to achieve this goal agents, and tools for protein studies and analyses, and a with respect to protein abundance, distribution, subcellu- stronger basis for personalized medicine. The Human lar localization, interaction with other biomolecules, and Proteome Organization urges each national research functions at specific time points. As a general experimen- funding agency and the scientific community at large to tal strategy, HPP research groups will use the three work- identify their preferred pathways to participate in aspects ing pillars for HPP: mass spectrometry, antibody capture, of this highly promising project in a HPP consortium of and bioinformatics tools and knowledge bases. The HPP funders and investigators. Molecular & Cellular Pro- participants will take advantage of the output and cross- teomics 10: 10.1074/mcp.M111.009993, 1–5, 2011. analyses from the ongoing Human Proteome Organization Fn1 From the ‡CEA, Life Sciences Division, Fontenay-aux-Roses, The success of the Human Genome Project (HGP)1 has France; §Department of Biology, Institute of Molecular Systems Biol- provided a blueprint of genes encoding the entire human ogy, ETH, Zu¨ rich, and Faculty of Science, University of Zurich, Swit- protein set potentially expressed in any of the ϳ230 cell zerland; ¶Institute of Biomedical Chemistry of the Russian Academy types that comprise the human body (the human proteome). of Medical Sciences, Moscow, Russia; ʈSwiss Institute of Bioinfor- matics (SIB) and University of Geneva, Geneva, Switzerland; **Bio- At present, we have at least limited knowledge about the technology at Bridge4Bio, San Francisco, CA, USA; ‡‡Fred Hutchin- proteins of approximately two-thirds of the 20,300 protein- son Cancer Research Center, Seattle, WA, USA; §§McGill University, coding human genes mapped through the HGP. Based on Montreal, Canada; ¶¶Proteomics Centre, University of Victoria, Ge- the UniProtKB/Swiss-Prot database content, about 6000 nome British Columbia, Canada; ʈʈTurku Centre for Biotechnology, (30%) of these genes currently lack any experimental evi- University of Turku and Åbo Akademi University, Turku, Finland; aBoston University, HUPO President (2011–2012), Boston, MA, USA; dence at the protein level; for many others, there is very little bInstitute for Systems Biology, Seattle, WA, USA; cLuxembourg Uni- information related to protein abundance, distribution, sub- versity, Luxembourg; dNortheastern University, Boston, MA, USA; cellular localization, interactions, or cellular functions. e f Beijing Proteome Research Center, Beijing, China; Geneva Univer- The Human Proteome Project (HPP) is designed to map the sity, Geneva, Switzerland; gLund University, Lund, Sweden; hRoyan entire human proteome in a systematic effort using currently Institute, Tehran, Iran; iNational Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA; jStanford University, available and emerging techniques. Completion of this project Palo Alto, CA, USA; kNIH/NCI, Bethesda, MD, USA; lRoyal Institute of will enhance understanding of human biology at the cellular Technology, Stockholm, Sweden; mProtein Information Resource level and lay a foundation for development of diagnostic, prog- n (PIR) and University of Delaware, Newark, DE, USA; Niigata Univer- nostic, therapeutic, and preventive medical applications. The sity, Niigata, Japan; oqYonsei University, HUPO President (2009– 2010), Seoul, Korea; pqCenter for Computational Medicine and Bioin- formatics University of Michigan, Ann Arbor, MI, USA 1 The abbreviations used are: HGP, Human Genome Project; Received April 5, 2011, and in revised form, April 29, 2011 HUPO, Human Proteome Organization; HPP, Human Proteome Proj- Published, MCP Papers in Press, April 29, 2011, DOI 10.1074/ ect; KB, knowledge base; SRM, selective reaction monitoring; C- mcp.M111.009993 HPP, chromosome-centric HPP. Molecular & Cellular Proteomics 10.7 10.1074/mcp.M111.009993–1 • balt3/zjw-macp/zjw-macp/zjw00711/zjw3889-11a xppws Sϭ1 3/6/11 8:30 4/Color Figure(s) F1 ARTNO: M111.009993 The Human Proteome Project C O L O R FIG.1.The HPP vision. The HPP is driven by two major scientific forces on top of the three pillars of MS, protein capture, and protein information databases: biology-powered projects and proteome activity mapped to a chromosomal orientation (see http://hupo.org/research/ AQ: B hpp/and Fig.). The HPP will deliver a comprehensive map of human proteins in their biological context. proteomic space generated from these gene products is enor- The Three Pillars of the HPP—The HPP will deliver a com- mous, including up to an estimated one million different protein prehensive map of the human proteins in their biological isoforms derived by DNA recombination, alternative splicing of context. It will generate publicly accessible data and informa- primary transcripts, and numerous post-translational modifica- tional resources supporting further exploration of the human tions of many types that vary with time, location, and physio- proteome by basic and clinical scientists. The HPP will be logic, pathologic, and pharmacologic perturbations. These built on the three major technological pillars of shotgun and modifications expand the proteomic space by altering the pri- targeted MS, polyclonal and monoclonal antibodies (Ab), and mary products in a combinatorial manner. In early 2010, HUPO an integrated knowledge base (KB) (Fig. 1). The HPP will use F1 proposed a gene-centric approach to generate a human pro- the output and cross-analyses (see below) from the ongoing teome map with an “information backbone” that would display HUPO initiatives that have focused on tissue- and biofluid- the proteins expressed from each gene locus (1). A working based proteomes, as well as much other published work. The groupq for an HPP was created in October 2009 by the HUPO HPP will provide tools and reagents (e.g. cDNAs, peptides Council to build an international consensus and a long-term and their corresponding reference fragment ion spectra, re- plan for this project. We concluded that recent substantial ad- combinant proteins, antibodies, and annotation software) for vances in proteomic technologies including quantitative mass the scientific community that will enable all researchers to spectrometry, protein capture with antibodies, and bioinformat- design and perform hypothesis-driven and hypothesis-gener- ics for global exchange of large primary data sets and data- bases make the generation of such a human proteome map ating experiments to enhance existing knowledge, as has feasible (2, 3). As was done for the HGP, gene-centric human occurred with the HGP. The availability of reference samples proteome mapping will be complemented with in-depth studies and standardized informational resources will contribute to of protein variability in response to various physiologic and creating proteomic data with improved quality and compara- pathologic states. Supportive interest for the HPP has been bility. Furthermore, the HPP will provide a blueprint for fast- expressed by the international scientific community, major sci- track analogous projects in other species, again following the entific journals, industrial representatives, and funding agencies path of the HGP. around the world. The overall plan for the HPP was launched at Regarding the MS pillar, the HPP will track the development the 9th Annual HUPO World Congress in Sydney, Australia, on of and access to robust selected or multiple reaction moni- September 23, 2010. The presentation from that plenary ses- toring (SRM/MRM)-based assays of proteotypic peptides, in- sion is available on the HPP web page at the HUPO website cluding stable isotope-labeled peptides, which enable high- (http://hupo.org/research/hpp/). throughput, targeted, quantitative protein measurements at a 10.1074/mcp.M111.009993–2 Molecular & Cellular Proteomics 10.7 balt3/zjw-macp/zjw-macp/zjw00711/zjw3889-11a xppws Sϭ1 3/6/11 8:30 4/Color Figure(s) F1 ARTNO: M111.009993 The Human Proteome Project high degree of reproducibility.
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