Characterization of Disulfide Bonds in Cyclic Peptides Using Electron Transfer–Ultraviolet Photodissociation Mass Spectrometry

Analysis of peptides with multiple disulfide bonds can be challenging because of the complexity of deciphering fragment ions originating from dual backbone and disulfide bond cleavages required to release fragment ions from the regions spanned by disulfide bonds. Two ion activation methods, electron transfer dissociation (ETD) and ultraviolet photodissociation (UVPD) have demonstrated the ability to cleave disulfide motifs, either via C-S or S-S bond cleavages, resulting in diagnostic fragment ions that can help localize disulfide bonds. Here, these MS/MS methods are examined in comparison to a hybrid method, ET-UVPD, for the characterization of peptides containing multiple disulfide bonds. Fragment ions arising from S-S and C-S bond cleavages, both with and without hydrogen atom transfer and with dual S-S and C-S cleavages, were searched based on a list of possible products generated from alternative cleavage pathways. Identification of these low-abundance fragment ions can facilitate the characterization of peptides constrained by multiple disulfide bonds.