A new procedure is described for identification of disulfide bonds in peptides by fast atom bombardment mass spectrometry (FABMS). Prolonged bombardment of a disulfide-containing peptide in solution by a high-energy xenon beam results in gradual reduction of the disulfide bond. The reduction is the result of reaction intermediates initially produced by the xenon beam. The method for characterization of interchain disulfide bonds is based on the increase in the relative intensity of the pseudomolecular ions of the reduced peptides with a simultaneous decrease in the relative intensity of the protonated molecular ion of the oxidized peptide. This information allows one to identify peptide fragments covalently linked via intermolecular disulfide bonds. The intrachain disulfide bonds are identified by the increase in the relative intensity of the protonated molecular ion of the reduced peptide, relative to the intensity of the protonated molecular ion of the oxidized peptide. These results indicate that this method can be used to detect disulfide bonds of peptides and provides unambiguous information regarding disulfide bond assignment in peptides. Approximately 1 nmol of sample is required.