Proteins perform essential cellular functions as part of protein complexes, 
often in conjunction with RNA, DNA, metabolites and other small molecules. The 
genome encodes thousands of proteins but not all of them are expressed in every 
cell type; and expressed proteins are not active at all times. Such diversity of 
protein expression and function accounts for the level of biological intricacy 
seen in nature. Defining protein-protein interactions in protein complexes, and 
establishing the when, what and where of potential interactions, is therefore 
crucial to understanding the cellular function of any protein-especially those 
that have not been well studied by traditional molecular genetic approaches. We 
generated a large-scale resource of affinity-tagged expression-ready clones and 
used co-affinity purification combined with tandem mass-spectrometry to identify 
protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting 
protein complex "map" provided a blueprint of metazoan protein complex 
organization. Here we describe how the map has provided valuable insights into 
protein function in addition to generating hundreds of testable hypotheses. We 
also discuss recent technological advancements that will be critical in 
addressing the next generation of questions arising from the map.