Abstract

Protein complexes perform many important functions in the cell. Large‐scale studies of protein–protein interactions have not only revealed new complexes but have also placed many proteins into multiple complexes. Whilst the advocates of hypothesis‐free research touted the discovery of these shared components as new links between diverse cellular processes, critical commentators denounced many of the findings as artefacts, thus questioning the usefulness of large‐scale approaches. Here, we survey proteins known to be shared between complexes, as established in the literature, and compare them to shared components found in high‐throughput screens. We discuss the various challenges to the identification and functional interpretation of bona fide shared components, namely contaminants, variant and megacomplexes, and transient interactions, and suggest that many of the novel shared components found in high‐throughput screens are neither the results of contamination nor central components, but appear to be primarily regulatory links in cellular processes. BioEssays 26:1333–1343, 2004. © 2004 Wiley Periodicals, Inc.