With the completion of full genome sequence for several model organisms, new approaches are emerging to comprehensively characterize the function of gene products. In these so-called functional proteomics approaches, large-scale assays on the complete set of proteins of a given organism — the proteome — enable the study of the function of proteins in their context, rather than individually. The recent emergence of high-throughput techniques to systematically identify physical interactions between proteins has opened new prospects. Not only can an important part of what is now referred to as the “function” of a protein be characterized more precisely through its interactions, but networks of interacting proteins also extend this purely local view of function by providing a first level of understanding of cellular mechanisms. In short, protein interaction maps can provide detailed functional insights on characterized as well as yet unannotated proteins, along with an information base for the identification of biological complexes and metabolic or signal transduction pathways (for review, see Walhout and Vidal 2001).