Current methods for measuring pairwise changes in protein expression involve differential stable isotopic labeling of proteins or peptides either in vivo or in vitro followed by identification and quantification using a mass spectrometer. In these methods, the mass spectrometer detects two different masses, which correspond to a single protein from two different samples that have been labeled with either a heavy or normal isotope. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). This unit describes one of these popular methods for quantitative protein profiling using the isotope-coded affinity tag (ICAT) technique.