Amos Bairoch (Swiss Institute of Bioinformatics, Geneva, Switzerland), whose group administrates the SwissProt/UniProt protein database, announced that the number of human protein-coding genes was currently estimated to be 20,400, although this number is likely to change over the next few years. Interestingly, he reported that for almost 9,000 (44%) of these genes, there is still no experimental information about the proteins they encode. This emphasizes the need for a systematic effort to characterize human proteins to leverage information from the genome project and to form a basis for further studies. At the conference, the possible launch of a Human Proteome Project to systematically map the proteome was discussed with representatives from funding agencies from Europe, USA, Canada and Asia. John Bergeron (McGill University, Montreal, Canada) proposed a gene-centric approach based on three technology platforms (mass spectrometry, antibodies and interaction analysis) to characterize at least one representative protein variant from every gene locus. Several participants pointed out the difficulty of a gene-centric approach for mass spectrometry, whereas such an approach is more feasible for antibody- and interaction-based analysis. The shortcomings of previous systematic proteomics efforts were brought up, emphasizing the need for increased precision of protein identification by mass spectrometry. Representatives of several funding agencies pointed out the importance of focused pilot projects to show the feasibility of the different parts of the effort, and emphasized the need for clear end-points and international coordination.
The conference demonstrated that proteomics research has entered a new era of biology-driven applications, with studies of signal pathways and protein profiles in various cells and tissues based on advances in the use of proteomics tools. The rapid development of mass-spectrometry based, immuno-based and gene-tagging technologies has opened up the possibility of whole-proteome analysis. The challenge for the proteomics community now is to show how the human proteome can be experimentally annotated, and to deliver a human proteome 'parts-list' with data on localization and function within a reasonable time-frame. Such a list, with its accompanying resources of protein-specific probes (antibodies), proteotypic peptides and cDNA clones, would provide a valuable asset for hypothesis-driven research into human biology and disease. Such efforts will no doubt be discussed at the next HUPO conference, to be held in Toronto, Canada, in September 2009.