Energetics of selective cleavage at acidic residues studied by time- and energy-resolved surface-induced dissociation in FT-ICR MS

Surface-induced dissociation (SID) of four model peptides: LDIFSDF, LDIFSDFR, RLDIFSDF, and LEIFSEFR, was studied using a novel Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. The energetics and dynamics of selective cleavages at acidic residues were deduced by modeling the time- and energy-resolved fragmentation efficiency curves (TFECs) using an RRKM-based approach developed in our laboratory. RRKM modeling revealed that addition of a basic residue-arginine-to the C-terminus of a peptide has a very small effect on the dissociation threshold. However, the dynamics of dissociation is dramatically affected by the presence of arginine. The Arrhenius pre-exponential factor for dissociation of LDIFSDF is two orders of magnitude higher than the pre-exponential factor for dissociation of arginine-containing peptides. The difference in the pre-exponential factors is indicative of a complex rearrangement process associated with selective fragmentation. Molecular mechanics modeling of the four parent ions gives some qualitative insight into the differences in fragmentation mechanisms.