Abstract
Protein-protein interactions are essential to various physiological processes in living cells. A full characterization of protein interactions is critical to our understanding of their roles in the regulation of protein functions. Affinity purification coupled with mass spectrometry (AP-MS) has become one of the most effective approaches to systematically study protein-protein interactions. In combination with quantitative mass spectrometry, specific interacting proteins can be efficiently distinguished from nonspecific background proteins. Based on interaction affinity and kinetics, protein interactions can be classified into different categories such as stable and dynamic interactions. Standard biochemical methods are effective in capturing and identifying stable protein interactions but are not sufficient enough to identify dynamic interactors. In this chapter, we describe integrated strategies to allow the identification of dynamic interactors of protein complexes by incorporating new sample preparation methods with SILAC-based quantitation.