In January, HUPO appointed chairs for each of five committees: protein bioinformatics, new technology, a plasma proteome project, cell models, and antibody initiatives. Last week, after input from meeting attendees during two-hour breakout sessions, the committee chairs presented their agenda items to the meeting as a whole. A summary of the action items follows:
Led by chairperson Rolf Apweiler of the European Bioinformatics Institute in Cambridge, UK , the HUPO bioinformatics committee announced its plans to develop standards for proteomics data, akin to the efforts of the MGED consortium with DNA microarray data, Apweiler said. The committee first plans to tackle protein mass spectrometry and protein-protein interaction data, by assembling a panel of academic and industry scientists to devise annotation and data format standards. Apweiler plans to have an initial group of advisors in place by June, and convene a meeting in August. The protein standards group also plans to meet during the HUPO Congress, its first independently-organized meeting, to take place in November in Versailles, France.
Richard Simpson of the Ludwig Institute for Cancer Research, in Melbourne, Australia, said one of the primary goals of the new technology committee will be to develop workshops for disseminating technical knowledge and protocols for performing proteomics experiments. Specifically, Simpson singled out studies of quantitative protein expression, protein-protein interactions, and phosphoproteins as topics around which to build a seminar series. Rather than dictate what technologies to fund or adapt, Simpson, who chairs the new technology committee, said HUPO should “act as a facilitator to bring people together to learn and decide what technology they want to use.”
Last January in San Diego, HUPO president Sam Hanash proclaimed that HUPO would undertake a project to study the plasma proteome. Last week, Gil Omenn of the University of Michigan Medical School, the chairperson of the committee overseeing the project, presented its plans to provide about 30 to 50 laboratories with 1 mL of serum or plasma, taken from healthy males and females representing at least three global geographic ethnic groups. Omenn said the committee favored studying serum over plasma, because the anticoagulants in plasma could cause sensitivity problems, but that ideally the project would involve both serum and plasma. To remove the high abundance proteins, such as albumin and immunoglobulin, which make up at least 90 percent of the biological mass, Omenn invited companies to provide technical guidance or equipment, such as customized chromatography columns. As a potential second phase to the project, member groups could examine a greater number of biological variables in the serum and plasma proteomes, such as age and disease state.
The chairs of the cell models group, Peipei Ping of the University of Louisville, and Ron Taussig, of the Alliance for Cell Signaling, recommended heart, liver, breast, and immune cells as candidate cell model projects for HUPO. Taussig and Ping said HUPO should develop standard procedures for cultivating the cell models, and that rather than issue edicts, HUPO’s role should be to “rally the troops” to specific projects.
As chairman of the committee on antibody initiatives, Matthias Mann, of the University of Southern Denmark and MDS Proteomics, proposed four pilot projects that HUPO could support or endorse: a GenWay initiative to produce polyclonal IgY antibodies in chicken eggs; a research program led by Matthias Uhlén of the Royal Institute of Technology in Sweden to produce polyclonal rabbit antibodies; an effort to produce human single chain antibodies in yeast at the Pacific Northwest National Lab; and a German Society for Proteome Research (proposed) 80 million euros project to produce monclonal human antibodies in mice. [For more details on HUPO’s antibody initiatives, see story p. 3]