In vivo chemical cross-linking has evolved to provide new insight on proteins, complexes and supercomplex assemblies that exist in organelle, cells and tissues. Our recent efforts have focused on extending chemical cross-linking capabilities to allow quantitative exploration of the interactome. Dynamic cellular interactome measurements made during changing growth conditions, drug treatment, applied stresses, or other perturbations can increase understanding of cellular response and functional regulation. This presentation will discuss advancements in technologies and informatics capabilities we have pursued to help visualize interactome dynamics. These tools are being applied to the study of interactome dynamics involved in mitochondrial dysfunction in heart failure, chemoresistant cancer cells and pharmacological effects on the interactome, bacterial species/strain interactome comparisons and other areas. Efforts thus far have revealed intra- and inter-molecular changes that are chemoresistant phenotype-specific, drug concentration-dependent and mechanism of action-specific, as well as shared or species-specific interactome features among related bacterial strains. For example, molecular interaction changes among mitochondrial permeability transition pore (mPTP) regulators Cyclophilin D (CypD) and oligomycin sensitivity conferring protein (OSCP) in mitochondria from murine heart failure models or from mitochondria subjected to increased Ca2+ stress to cause mPTP activation have been visualized through quantitative mitochondrial cross-linking. Although many challenges yet remain at all levels of interactome dynamic studies, quantitative in vivo cross-linking offers unique opportunities for exploring this exciting frontier.