Methods for protein-protein interaction analysis

Protein-protein interactions (PPIs) play key roles in various aspects of cellular regulation. Accordingly, PPI analysis is crucial for systems-level understanding of any biological process. This chapter describes two major methods for PPI analysis, namely, mass spectrometry (MS)-based approaches and yeast two-hybrid (Y2H)-based ones. Both methods have been the major driving forces of interactome mapping to reveal the characteristics of global PPI networks. Furthermore, MS-based methods enable a quantitative analysis of interaction, thereby providing insight into system dynamics. Alternatively, Y2H-based methods provide interaction- defective and separation-of-function alleles, which are useful for system perturbation. These two methods would thus contribute not only to system identification but also to system analysis, thereby serving as invaluable tools for systems biologists.