Tandem MS sequencing of peptides that contain a disulfide bond is often hampered when using a slow heating technique. We show that complexation of a transition-metal ion with a disulfide-bridge-containing nonapeptide yields very rich tandem mass spectra, including fragments that involve the cleavage of the disulfide bond up to 56% of the total product ion intensity. On the contrary, MS/MS of the corresponding protonated nonapeptides results predominantly in fragments from the region that is not involved in the disulfide bond. Eleven different combinations of three nonapeptides and three metal ions were measured using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) combined with sustained off-resonance irradiation collision induced dissociation (SORI-CID). All observed fragments are discussed with respect to four different types of product ions: neutral losses, b/y-fragmentation with and without the disulfide bond cleavage, and losses of internal amino acids without rupture of the disulfide bridge. Furthermore, it is shown that the observed complementary fragment pairs obtained from peptide–metal complexes can be used to determine the region of the binding site of the metal ion. This approach offers an efficient way to cleave disulfide-bridged structures using low energy MS/MS, which leads to increased sequence coverage and more confidence in peptide or protein assignments. Copyright © 2007 John Wiley & Sons, Ltd.