Protein complexes may well be the most relevant molecular units of cellular function. The activities of protein complexes have to be regulated both in time and space to integrate within the overall cell programs. The cell can be compared to a factory orchestrating individual assembly lines into integrated networks fulfilling particular and superimposed tasks. Recent proteome-wide studies provide insight into the properties of cellular protein complexes, their modular nature, their interaction with other complexes and the resulting preliminary organization chart of the proteome.