PROTEOMICS PROJECTS
ProteomeBinders consortium makes big plans
the human proteome. Although many antibodies have been generated by academic and commercial laboratories over the years, most are directed against relatively few popular targets. Another wrinkle is that some antibodies may be useful for only certain types of applications. For example, an antibody may recognize the denatured form of a protein on a western blot but not the folded form present in a living cell. “I think tailoring the binder to the job will be a very important part of the
reagent base,” she says. Binders will be tested for performance and specificity. The organizers of the ProteomeBinders In addition to producing the reconsortium have their work cut out for source, the group will develop new them. According to Mike Taussig, who binder-based tools for proteomics. is at the Babraham Institute (BI) (U.K.) Participants plan to create various and is the coordinator of the project, assays, including high-throughput participants plan to develop a resource arrays. These techniques will be used infrastructure of binding reagents and in applications, such as biomarker detools for the study of the entire human tection. This activity, therefore, could proteome. He says that such a resource lead to the development of new clinical “would give us the opportunity to disdiagnostics. cover the functions of proteins which, All of the reagents will be made availat the moment, are unstudied” able to researchers at cost, and because of a lack of reagents. data resulting from the project, Currently, the project is funded including quality-control informaby the EU 6th Framework Protion, will be freely accessible in gramme as a 4-year Infrastruclarge databases that are being deture Coordination Action to lay veloped by the bioinformaticians the groundwork and formulate a in the group. These participants sound plan of attack. Funds for also have been working closely the hands-on bench work will be with the HUPO Proteomics Stanrequested at the next EU call for dards Initiative to create a binder proposals. ontology. The consortium has its roots The creation of a proteomein discussions that began 5 wide binder resource itself will be years ago among scientists who a challenge, but before that can were brought together by the begin, ProteomeBinders members European Science Foundation still have a lot to consider during (ESF) program for functional the coordination stage. Plenty of genomics. Their mission was details are still up for debate. For to predict which areas of geno example, now that the researchers mics would be important in the have decided to generate these future. Taussig credits Ulf Lanbinders, which protein targets will degren, who is at the University be first in line? The researchers of Uppsala (Sweden) and is now haven’t agreed on a strategy yet, a member of ProteomeBinders, but Taussig says two prominent with recognizing the need for a views are being considered. “One comprehensive binder collection. view is that we should focus on Bound to the proteome. Members of the ProteomeBinders Spurred on by these discussions, defined protein families of interconsortium plan to assemble a collection of molecules that Taussig started making calls est, such as transcription factors bind to the human proteome. and found that a few small-scale and cell-signaling proteins, and European efforts were generatsystematically produce consistent ing these reagents, but they weren’t work,” says Taussig. But antibodies are and complete sets of reagents for those. coordinated with one another. So he only the beginning. The consortium The other is to focus on those proteins organized two ESF workshops on the also plans to investigate the production for which there are no reagents, to topic and enlisted the participants to of other reagents, such as protein scafmake sure everything is covered,” become members of a pan-European folds, nucleic-acid-based aptamers, and he explains. Regardless of how the effort that eventually became known small molecules. “The idea is to have a researchers eventually tackle the probas the ProteomeBinders consortium. specific reagent, no matter what its nalem, Taussig says that up to 100,000 new The project was officially launched ture is, for every target,” says Taussig. reagents must be generated to cover the in March 2006 as a consortium of 26 Validation is an important part of the proteome, including splice variants and European labs and 2 U.S. labs. (U.S. project, says Oda Stoevesandt, who is posttranslationally modified forms. investigators can attend meetings and at BI and is the administrator for ProProteomeBinders members are unhelp plan the group’s activities, but they teomeBinders. She points out that such daunted by this huge task, says Taussig. are not eligible to receive EU funds.) information is not always available for Participants are taking it one step at a One of the consortium’s main goals the binding reagents that are currently time and are in it for the long haul. The is to organize efforts to produce a colused by scientists. “We will define a project “will be a very long-term effort,” lection of reagents, such as antibodies, set of quality-control methods that are says Stoevesandt. that can bind to proteins that comprise consistently applied across the whole —Katie Cottingham
Journal of Proteome Research • Vol. 5, No. 12, 2006 3237
