Just as the Human Proteome Organization is attempting to get its worldwide proteomics initiatives off the ground, a possible rival to one of its projects has sprung up independently. Less than two weeks ago, Leigh Anderson’s Plasma Proteome Institute, based in Washington, DC, initiated a collaboration that some believe will overlap with the Human Plasma Proteome Project HUPO launched earlier this year.
The aim of Anderson’s effort is to assemble a list of proteins found in human plasma by pooling existing data from commercial and academic groups. The project builds on a recent review article by Anderson and his father, published in Molecular & Cellular Proteomics (MCP), in which they list about 300 plasma proteins found in the current scientific literature. Anderson is hoping to expand this list by at least another 200 and up to 500 proteins, depending on how many laboratories sign up and how many proteins they contribute. “It’s a very simple effort to make a unified list of proteins people have detected [in plasma] so far,” Anderson said.
Up to now, he has approached seven companies, including GeneProt, Roche, Celera, Syn X Pharma, and two academic groups, asking them to provide lists of proteins they have identified in plasma. Unlike HUPO’s pilot project, which will provide investigators with standardized samples to analyze, Anderson asks for existing data that could come from any plasma sample, irrespective of the donor’s health. After gathering and analyzing the data in the next few months, Anderson plans a collaborative publication within the first half of next year.
To avoid conflicts arising from intellectual property, participants will not be required to provide any disease information. “Our feeling is that the names of the proteins detectable in plasma are not really valuable IP. It’s the names of proteins that are associated with diseases or drug effects that are, and we are not asking them for that,” Anderson said.
But not all possible participants may find this arrangement workable. Some companies might want to hang on to novel plasma proteins until they have tested their utility — for example as biomarkers — which would enable them to apply for a patent.
Keith Rose, CSO of GeneProt, said that “clearly, we have to protect the intellectual property before we were to [join such a project].” This process would involve consultations with the company’s legal department as well as Novartis, which finances GeneProt’s plasma studies.
As of last week, one academic group at Pacific Northwest National Laboratory had accepted Anderson’s invitation — this group, headed by Joel Pounds, published a list of 490 proteins identified in plasma by LC-MS/MS in MCP last month.
So what is Anderson’s motivation for his project? The value of an expanded list of plasma proteins, he said, would be severalfold: It would allow researchers to group plasma proteins into functional categories; it could serve as a starting point for developing assays to measure plasma proteins; and it would be an extensive resource against which scientists could compare their own lab’s results. “We know already that there are going to be proteins on the plasma list that are unexpected,” Anderson said. “And it helps a lot if more than one person finds these.”
Anderson does not believe, though, that his project is taking away from HUPO’s Human Plasma Proteome Project. HUPO, he said, decided to focus, in its pilot project, on analyzing standardized samples, in order to be able to evaluate various methods. “We thought that in the meantime, we would go ahead and assemble a list, so we could get a little bit greater value out of what’s already been done,” he said. “What we are trying to do and what HUPO is trying to do is, at this point, very synergistic and non-overlapping.” In fact, if the Plasma Proteome Institute already had its own laboratories, he said, it would probably also participate in HUPO’s pilot project.
But according to Gilbert Omenn, who heads HUPO’s plasma project, “the overall goal [of HUPO’s initiative] certainly subsumes what he is proposing to do just by collecting people’s existing information.” Notably, Omenn had not heard about Anderson’s initiative prior to talking to ProteoMonitor.
At HUPO’s recent Versailles meeting, Omenn said, several European groups and companies expressed an interest in joining HUPO’s pilot project. Moreover, the Chinese Academy of Sciences has offered to provide additional plasma and serum samples, which might be used by participating researchers in Asia. This, Omenn said, might solve certain practical issues such as shipping samples between countries, which frequently involves delays at customs.
Though both initiatives may operate peacefully in parallel, it remains to be seen which one will be more successful in engaging researchers, especially from companies, and in coming up with results. HUPO, a large organization that is trying to juggle a worldwide experimental effort, might be at a disadvantage when it comes to speed, compared to Anderson, who asks for existing data.
Rose said GeneProt had not decided yet whether to join the PPI’s initiative, and had requested more details from Anderson. However, it is unlikely to join HUPO’s pilot project, even though Rose believes it is useful. “I do not see GeneProt participating in trying to see how many proteins one can find in one milliliter [of plasma] because that’s not our approach. We have an industrial-scale approach, which involves larger sample sizes,” he said. Hanno Langen, who heads proteomics at Roche, called Anderson’s proposal interesting, but stressed that Roche has yet to discuss the IP issues, and whether or not to share its data.
Though competition is usually healthy, and both initiatives aim to make their data public, not everyone agrees that separate proteomics efforts in the same area are a good idea. “Are we going to see the Liver Proteome Institute, the Milk Proteome Institute, the Urine Proteome Institute?” asked Rose. “Pooling resources from Celera and GeneProt and others, if the companies are prepared to do that, that would better be done, I think, in the context of a worldwide organization.”