Systematic studies of the organization of biochemical networks that make up the living cell can be defined by studying the organization and dynamics of protein interaction networks (PINs). Here, we describe recent conceptual and experimental advances that can achieve this aim and how chemical perturbations of interactions can be used to define the organization of biochemical networks. Resulting perturbation profiles and subcellular locations of interactions allow us to 'place' each gene product at its relevant point in a network. We discuss how experimental strategies can be used in conjunction with other genome-wide analyses of physical and genetic protein interactions and gene transcription profiles to determine network dynamic linkage (NDL) in the living cell. It is through such dynamic studies that the intricate networks that make up the chemical machinery of the cell will be revealed.