Recent advances in charting protein–protein interaction: mass spectrometry-based approaches

Cellular functions are the result of the coordinated action of groups of proteins interacting in molecular assemblies or pathways. The systematic and unbiased charting of protein–protein networks in a variety of organisms has become an important challenge in systems biology. These protein–protein interaction networks contribute comprehensive cartographies of key pathways or biological processes relevant to health or disease by providing a molecular frame for the interpretation of genetic links. At a structural level protein–protein networks enabled the identification of the sequences, motifs and structural folds involved in the process of molecular recognition. A rapidly growing choice of technologies is available for the global charting of protein–protein interactions. In this review, we focus on recent developments in a suite of methods that enable the purification of protein complexes under native conditions and, in conjunction with protein mass spectrometry, identification of their constituents.