Proteins control all biological systems in a cell, and while many proteins perform their functions independently, the vast majority of proteins interact with others to execute a full range of biological activities. Characterizing protein-protein interactions through methods such as co-immunoprecipitation (co-IP), pull-down assays, crosslinking, label transfer, and far-western blot analysis is critical to understanding protein function and the biology of the cell. See Table 1 for a list of recommended methods of analysis based on the varying strength of interaction between the proteins under investigation.