Knowing that a specific protein is present within a cell provides little insight into its function. In a study by Schubert and colleagues, the investigators present a multidimensional method that utilizes fluorescence microscopy and automated antibody introduction and detection, which is potentially capable of localizing hundreds of proteins within individual cells. The method, referred to as multiepitope-ligand cartography, is validated in the analysis of cell-surface receptors in peripheral mononuclear blood cells, and then used to map protein complexes in a series of disease models, including psoriasis and chronic constriction injury. Within each experiment, the locales of each protein are presented in a binary format and the data are interpreted to recognize specific proteins that control the topology of the protein network. The hope is that by identifying partnerships between proteins and those proteins that are most responsible for these interactions, novel diagnostic features and therapeutic targets can be established.