The collision-induced dissociations are reported for Cu(II) complexes containing 1,4,7-triazacyclononane (tacn) as the auxiliary ligand and a peptide containing one cystine residue. For six of the complexes examined, cleavage of the S–S bond in the peptide was the dominant fragmentation pathway. The exceptions were for complexes containing the largest peptides, (GlyCys′Gly)₂ and (GlyGlyCys′)₂ (Cys′ = NHCH(CH₂S)CO, one half of the cystine residue; terminal H and OH are implicit), for which proton transfer to the auxiliary ligand was the major channel. Cleavage of the C–S bond was observed, but was a minor channel for all complexes. The radical cation (Cys′)₂˙⁺ was not observed although the complementary ion [Cu^I(tacn)]⁺ was present in moderate abundance. Density functional calculations (at B3LYP/6-311++G(d,p)) gave low barriers to fragmentation of (Cys′)₂˙⁺ by homolytic fission of the C–S bond of the canonical ion (barrier 16.5 kcal mol⁻¹) and of the structure at the global minimum, a captodative ion (barrier 17.2 kcal mol⁻¹). Peptide radical cations (GlyCys′)₂˙⁺, (GlyCys′Gly)₂˙⁺, (GlyGlyCys′)₂˙⁺ and (GlyCys′(Cys′)Gly)˙⁺ were observed in low abundances; the first two of these ions dissociated predominantly by fragmentation of the S–S bond, while the other two preferentially cleaved at an amide bond. No cleavage of the C–S bond was observed for the peptide radical cations. Density functional calculations at B3LYP/6-31G(d) established that the cystine in [Cu^II(tacn)(Cys′)₂]˙²⁺ is bound as a zwitterion through the carboxylate anion with the proton on the distal amino group. The lowest energy complex containing a canonical cystine, coordinated through the carbonyl oxygen and the amino group of the same Cys′, is 8.3 kcal mol⁻¹ higher in enthalpy.