Most proteins function through protein complex assemblies. Defining and mapping protein complex networks are crucial elements in the fundamental understanding of biological processes. The ability to measure protein-protein interactions in biological systems has undergone significant advances in the past decade due to emergence and growth of numerous new molecular biology and mass spectrometry technologies. Chemical cross-linking, along with yeast two-hybrid, fluorescence resonant energy transfer (FRET), and co-immunoprecipitation have become important tools for detection and characterization of protein-protein interactions. Individual protein members in a noncovalent complex assembly remain in close proximity which is within the reach of the two reactive groups of a cross-linker. Thus cross-linking reactions have potential for linking two interacting proteins which exist in close proximity. In general, chemical cross-linking experiments are carried out by first linking the interacting proteins through covalent bonds followed by a series of well-established protocols -- SDS-PAGE, in-gel digestion, and shotgun LC/MS/MS for identification of the cross-linked proteins. These approaches have been employed for both mapping topology of protein complex in vitro and determining the protein interaction partners in vivo.