Functional proteomics: Systematic characterization of the physical and functional organization of cell systems

Unbiased elucidation of the networks of physical and functional interactions in cells is fundamental to understanding the molecular organization of biological systems, the mechanistic basis driving essential and disease-related processes, and the assignment of functional annotations to previously uncharacterized gene products via guilt-by-association. Over the last decade, the Emili laboratory has participated in the rapidly evolving field of “functional proteomics” that has in turn driven the discovery of large collections of physically and functionally associated proteins in a variety of organisms whose genomes have been sequenced. Here, we recount our past and ongoing experimental and computational efforts to generate, interpret, and report proteome-scale maps of interaction networks encompassing stable multiprotein complexes and other types of functional associations in yeast, Escherichia coli, and human cells as model systems.