"We don't want to say that we will do the whole proteome in the next 18 months," says Hanash, a professor of pediatrics and communicable diseases at the University of Michigan. "That's impossible. But at the same time, it's not true that there's nothing you can do."
Industry groups have lofty aspirations as well as proprietary concerns. Myriad Proteomics proclaimed last year it would complete a map of every human protein-protein interaction by 2004.2 Information-based biotechs are increasingly steering into pharmaceutical development making it imperative for them to patent newly generated data, a practice that might not mesh with the HUPO vision.
Complex Project, Complex Issues
Some HUPO members say they hope the organization will foster collaboration and education programs and set standards, but not oversee or fund projects. "We don't want to come across as the organization that's driving proteomics and you're either in or you're out," says Emanuel F. Petricoin, codirector of the Food and Drug Administration-National Cancer Institute Clinical Proteomics Program. Nevertheless, he says, data must be shared. "If you're going to want to be included, then you're going to have to offer full data access," he says.
Some HUPO members from biotech companies say the rules should accommodate proprietary interests. Pierre Legrain, vice president of science and technologies at Hybrigenics, a Paris-based proteomics company and a member of HUPO's committee on informatics, says, "I think we would be very pleased to see people working with some of our data as soon as we've made patent applications." Patented data would be made available for research, Legrain says, but not for commercial applications.
Big pharmaceuticals, on the other hand, have long supported the creation of free immediate-access databases. "Traditionally, companies like Merck & Co. have had the attitude that they like the basic information to be out there," says Matthias Mann, professor of bioinformatics, University of Southern Denmark and chair of the HUPO informatics committee. Petricoin, HUPO treasurer, says concessions may have to be made: "It's what makes proteomics daunting."
A Consortium of Coalescence
Many in basic research would welcome an antibody initiative. "Whenever ... we find 10 proteins involved in something, we have to send off for 20 peptides and 20 rabbits to be immunized," Mann says. "For all we know, 23 other labs may do the same thing ... that's clearly a duplication of effort." Hood says the effort to please all sides might be the hardest part. "How are you going to get strong-willed people that are going in a lot of different directions to see in what I would call an integrated vision?"
1. D. Steinberg, "Is a human proteome project next?" The Scientist, 15:1 April 2, 2001.
2. D. Steinberg, "Industry group to map proteome," The Scientist, 15:13 Apr. 16, 2001.