How Useful Will Functional Proteomics Data Be?

Large-scale protein interaction maps are, with gene expression profiles, among the first examples of data sets generated without specific knowledge on functions of genes. These are technology-driven experiments rather than hypothesis-driven experiments. They are valuable tools for protein function prediction, despite the occurrence of typical artifacts. These approaches are still in their early stages. Related bioinformatics tools are also primitive and require much more independent experimental validation before becoming useful predictive tools. Functional annotations based on predictions cannot replace primary experimental sources of information that should also be accessible through functional databases available on the web. Ultimately, functional annotation asserting a putative function for a protein will certainly be replaced by a more precise description of experimental data on this protein, helping users of databases to build new hypotheses that still will have to be experimentally proven.