Proteolytic cleavage of neuropeptide precursors is a major post-translational modification that is essential for the production of all biologically active peptides. Differential processing of precursors can produce peptides with unique biological activities. Even differences of a single amino acid can cause large changes in biological activity. Therefore, it is important to understand the precise molecular form of the peptide that is produced in a particular cell or tissue. For this, mass spectrometry-based peptidomic approaches are ideal. Unlike older radioimmunoassay-based detection techniques, peptidomics methods can measure the precise form of each peptide and can readily distinguish between longer and shorter forms of the same peptide. In addition, peptidomic methods are not limited to known peptides and can detect hundreds of different peptides in a single experiment. Comparison between two or more groups of samples is possible with quantitative peptidomic methods. The use of quantitative methods allow for differences in levels among tissues, cell types, or between wild-type and mutant animals to be determined. This review describes a method for quantitative peptidomics using isotopic labels based on trimethylammonium butyrate, which can be synthesized in five different isotopic forms, allowing multivariate analysis of five different samples in a single liquid chromatography/mass spectrometry run.