Cells contain numerous supramolecules, such as the nuclear pore complex, proteosome, chlorosome, ribosome, and flagellar motor complex, and these are used to carry out a wide variety of complicated functions. A supramolecule usually consists of a population of diverse biomolecules, and these biomolecules are organized in such a way that their contributions to the function of the supramolecule are coordinated spatially and temporally. Understanding the protein organization of a supramolecule is thus essential for fully understanding the molecular mechanism by which the supramolecule functions. Several powerful techniques, such as nuclear magnetic resonance, cryoelectron microscopy, x-ray crystallography, and chemical cross-linking, have been used to investigate the protein organization of supramolecules. Here we report a novel methodology that was designed to distinguish proteins lining the surface from those embedded in the interior of supramolecules. After verification with a synthetic multilayered protein complex of known structure, this methodology was used to investigate the protein organization of a landmark structure of the asymmetric synapses in the mammalian central nervous system, the postsynaptic density (PSD).