The gas-phase fragmentation mechanisms of small models for peptides containing intermolecular disulfide links have been studied using a combination of tandem mass spectrometry experiments, isotopic labeling, structural labeling, accurate mass measurements of product ions, and theoretical calculations (at the MP2/6-311 ϩ G(2d,p)//B3LYP/3-21G(d) level of theory). Cystine and its C-terminal derivatives were observed to fragment via a range of pathways, including loss of neutral molecules, amide bond cleavage, and S-S and C-S bond cleavages. Various mechanisms were considered to rationalize S-S and C-S bond cleavage processes, including charge directed neighboring group processes and nonmobile proton salt bridge mechanism. Three low-energy fragmentation pathways were identified from theoretical calculations on cystine N-methyl amide: (1) S-S bond cleavage dominated by a neighboring group process involving the C-terminal amide N to form either a protonated cysteine derivative or protonated sulfenyl amide product ion (44.3 kcal mol Ϫ1 ); (2) C-S bond cleavage via a salt bridge mechanism, involving abstraction of the ␣-hydrogen by the N-terminal amino group to form a protonated thiocysteine derivative (35.0 kcal mol Ϫ1 ); and (3) C-S bond cleavage via a Grob-like fragmentation process in which the nucleophilic N-terminal amino group forms a protonated dithiazolidine (57.9 kcal mol Ϫ1 ). Interestingly, C-S bond cleavage by neighboring group processes have high activation barriers (63.1 kcal mol Ϫ1 ) and are thus not expected to be accessible during low-energy CID experiments. In comparison to the energetics of simple amide bond cleavage, these S-S and C-S bond cleavage reactions are higher in energy, which helps rationalize why bond cleavage processes involving the disulfide bond are rarely observed for low-energy CID of peptides with mobile proton(s) containing intermolecular disulfide bonds. On the other hand, the absence of a mobile proton appears to "switch on" disulfide bond cleavage reactions, which can be rationalized by the salt bridge mechanism. This potentially has important ramifications in explaining the prevalence of disulfide bond cleavage in singly protonated peptides under MALDI conditions. [6,7] in the MS/MS of protonated peptides are indicators of phosphorylation and methionine sulfoxide formation, respectively. Progress has been made in understanding the factors that govern these reactions through a combination of mechanistic studies [1,2,6,8] and interrogation of databases of tandem mass spectra [7]. Several different types of mechanisms may operate depending on the structure and properties of the peptide. For example, studies on simple derivatives of O-phosphoserine reveal that H 3 PO 4 loss can occur via the following: charge directed neighboring group process (path A of Scheme 1, X ϭ H 2 PO 4 ); and charge remote internal elimination reaction to form a dehydroalanine residue (path B of Scheme 1, X ϭ H 2 PO 4 ) [8]. These different pathways can