Effect of the basic residue on the energetics and dynamics of dissociation of phosphopeptides

Abstract Time- and collision-energy-resolved surface-induced dissociation (SID) of protonated peptides containing phosphoserine (s) was studied using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer configured for SID experiments. We examined fragmentation of three singly protonated peptides: GGGsGGG, KGGsGGG and RGGsGGG. Fragmentation of GGGsGGG occurs under the mobile proton condition, while the ionizing proton is sequestered by the basic residue, resulting in the nonmobile proton condition in dissociation of the two basic peptides: KGGsGGG and RGGsGGG. RRKM modeling of the experimental data demonstrates that the energetics and dynamics of H 3 PO 4 loss are different under mobile and nonmobile proton conditions. Specifically, fragmentation of GGGsGGG is characterized by a higher dissociation barrier, 1.68 eV, and higher activation entropy, 11 e.u. (e.u. = entropy unit), than fragmentation of the basic peptides. Similar threshold energies of 1.36 eV and 1.40 eV and activation entropies of −4.9 e.u. and 0.3 e.u. were obtained for KGGsGGG and RGGsGGG, respectively. We propose that the loss of H 3 PO 4 from phosphoserine is a two-step process, in which the phosphate abstraction from the phosphorylated side chain is followed by dissociation of the ion–molecule complex.