The utility of capillary electrophoresis (CE) for assessing the purity and stability of pharmaceutical peptides is investigated. The degradation of nisin, a pentacyclic peptide antibiotic, depends upon sample preparation and storage conditions and is followed by CE. With conventional UV detection, peaks are not identified and unresolved components are not detected. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) of isolated CE fractions provides molecular mass information that aids in identification of the nisin degradants and determination of peak purity. The purity of pure and degraded nisin in the absence of any separation is also determined using electrospray ionization mass spectrometry (ESI-MS) and MALDI-TOFMS.