© 2010 by Imperial College Press. All rights reserved. The development of soft ionization techniques has made it possible to examine biological macromolecules using mass spectrometry. Proteomic approaches have been developed which are capable of identifying and chemically characterizing a wide variety of biological molecules in an efficient manner. A variety of mass spectroscopic experimental approaches have been developed which allow the investigator to obtain information about protein structure, dynamics and protein/protein interactions. This review focuses on the application of these techniques to the study of viral replication.