Extending the Chain: Thermochemical and Mechanistic Studies on the Collision-Induced Dissociation of Protonated...

In this work, guided ion beam tandem mass spectrometer (GIBMS) studies are extended to a peptide length of four amino acids long in order to begin to probe the reaction mechanisms for dissociation in longer peptides, approaching what would typically be seen in a tryptic digest, bottom-up sequencing study. Threshold collision-induced dissociation in a GIBMS was performed on protonated tetraglycine (H⁺GGGG) by using Xe as the collision partner. The kinetic energy dependence of five primary product ion channels ([b₃]⁺, [b₂]⁺, [y₃ + 2H]⁺, [y₂ + 2H]⁺, and loss of water) were reproduced using the modified line-of-centers model including RRKM kinetic theory in order to determine experimental threshold energies. Energies for reactants, products, and intermediates were calculated using multiple methods (B3LYP, M06-2X, CAM-B3LYP, MP2), and transition states between intermediates were located using relaxed potential energy scans. Calculated global minima for rate-limiting transition states (loose phase space limited for [b₃]⁺, [b₂]⁺, and [y₂ + 2H]⁺ and tight transition states for [y₃ + 2H]⁺ and loss of water) show good agreement with experimental thresholds. To accurately model the cross section for [b₃]⁺ and [b₂]⁺, a secondary loss channel for [b₃]⁺ decomposing to [b₂]⁺ was also included. The loss of water was explored theoretically and two tight transition state pathways were located. Both pathways were required to accurately reproduce the cross section for this reaction channel, which confirms previous studies that have concluded that multiple fragmentation pathways occur for this channel. Here, we provide the first accurate energetics for each pathway as well as insight into the competition between them.