The myriad events that occur in living cells (replication, organellar assembly, transport, genome organization, transcription etc.) are to a large extent carried out through dynamic associations and assemblies of macromolecules. I will describe our efforts to develop and integrate sets of tools that are designed to throw light on the evolution, structure and function of these macromolecular machines. To do this, we are developing approaches for elucidating proximal, distal, and transient protein-protein interactions in cellular milieus, as well as for determining distance restraints between amino acid residues within large protein assemblies by chemical cross-linking and mass spectrometry. The long-term goal of this research is to develop what I loosely term a “molecular microscope” for defining cellular systems with scales spanning all the way from dimensions of the cell to atomic resolution of molecules.