G O V E R N M E N T It’s a HUPO jamboree! On June 1–4, about 85 scientists from around the world took over the University of Michigan Media Union for a different kind of meeting—a jamboree, in fact. Instead of gathering to hear rehearsed spiels, the researchers, who are involved in the Human Proteome Organization’s (HUPO) Plasma Proteome Project (PPP), rolled up their sleeves and got their hands dirty. The jamboree “was an intensive, hands-on probing of the dataset,” says Gil Omenn of the University of Michigan and director of the PPP. “We had break-out sessions in rooms with highpowered computers where people could really call up the whole dataset and work on [it].” Attendee Bill Hancock of Northeastern University says the jamboree’s strength was its collaborative nature. “They hammered into the detail and really figured out what one lab did versus another.” The work was split into four main categories—specimens, bioinformatics, protein identification, and cost-effectiveness. The specimens group discussed whether to use plasma or serum samples. They also considered factors
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affecting the stability of the proteins in the specimens. Some researchers in the bioinformatics group compared search engines and databases, while others worked on annotating the proteome and assigning biological functions to the thousands of proteins identified so far. In the protein identification group, researchers discussed ways to determine whether a protein’s identification is credible. Techniques such as LC/MS/ MS, surface-enhanced laser desorption/ ionization, antibody arrays, and fractionation methods were evaluated and compared across labs and specimens. The group charged with considering cost-effectiveness debated the financial investment needed for labor, sample preparation, and data analysis. Jamboree participants have enough material for 15–20 manuscripts, according to Omenn, who says that these papers will appear in the journal Proteomics, and perhaps other publications, later this year. Although Omenn prefers to wait until the manuscripts are published, he divulged a few tidbits about the researchers’ conclusions. He says that the PPP may propose a few guidelines on
Journal of Proteome Research • Vol. 3, No. 4, 2004
how to establish whether a protein has been correctly identified. “We didn’t want to overcall this,” Omenn points out. “We want to be appropriately conservative, but we don’t want to miss important things.” He also predicts that no single technique will be declared the best. Instead, a combination of instruments and methods will likely be the most appropriate approach. As Hancock says, “There was no bolt of lightning from the sky to say this is the method.” Standard operating protocols, which will ease the comparison of data between laboratories, will be proposed, Omenn says. Hancock says the jamboree experience was a good one, and it has made him more optimistic that progress can be made on the plasma proteome. “I’ve been a great supporter of HUPO, but I was even more so after the jamboree,” he says. “I think a very reasonable position with today’s technology is that the plasma proteome is impossible, but when you get 40 of the best labs together, you start finding that we can actually make a pretty reasonable cut of this problem.” —Katie Cottingham
