Steering the scientific direction of proteomics is not an easy task, but participants at “Defining the Proteomics Agenda,” a conference held by the American Chemical Society Oct. 7-10 in Leesburg, Va., made tentative steps toward laying out what the field should try to accomplish.
Rather than undertake a massive international effort to catalog every protein in the human body, the 250-odd conference participants, led by Human Proteome Organization (HUPO) president Sam Hanash, coalesced around the idea of assembling a consortium of academic and industry researchers to take on medium-scale projects, such as analyzing the proteome of one type of cell system, or of one model organism.
Such a project requires leadership, and HUPO seems poised to take on that role. Although the organization initially struggled to find its purpose, in June the 24 council members elected a president, University of Michigan Medical School researcher Hanash, who expects to hash out an agenda over the course of the fall.
In a brainstorming session as the conference came to a close, Hanash solicited ideas for how HUPO could satisfy what he defined as the primary needs of the proteomics community: to develop an accessible knowledge base, to develop technology for cataloging and quantifying proteins in various cell systems, and for describing protein function.
Hanash suggested that HUPO could take a role in creating a knowledge base modeled after the Alliance for Cellular Signaling, a public-private partnership sponsored by the National Institutes of Health and six pharmaceutical companies. The organization, launched in September of last year, consists of 52 primary investigators at 21 research institutions who have pledged to jointly study G-protein-mediated and related signaling systems.
But finding a similar goal in proteomics will not be easy. With many researchers neck-deep in studies of specialized proteins systems, conference attendees had trouble finding a system that might serve as common ground. Hanash suggested analyzing the proteome of the lymphoid cellular system in humans as a candidate public-private project, but others expressed the desire to work with a simpler system, such as E. coli.
In the short term, the National Human Genome Research Institute (NHGRI), an arm of the NIH, is promising to fund databases that catalog information on all human proteins, much like SwissProt, a database administered by the Swiss Institute for Bioinformatics. In a keynote address at the conference, Francis Collins, the director of the NHGRI, said his institute would release a request for applications (RFA) within the next few weeks to fund “one large protein database” already in existence.
As for the role of HUPO, other conference attendees suggested that the organization sponsor training workshops to help disseminate knowledge on challenging areas of proteomics research, such as analyzing membrane or phosphorylated proteins. “The information is there, but not the education, or the access to that information,” said Ian Jardine, the president of Thermo Finnigan.
Hanash, however, is thinking in grander terms. Building a proteomics knowledge base, he said, is much like constructing the International Space Station. “It wasn’t built overnight, and it wasn’t by just one party. There should be a coming together.”