Proton transfer from multiply-protonated ubiquitin ions, [M+zH]+z (z=6–12), to 1-butylamine was studied in the gas phase. Absolute reaction rate constant for proton transfer was determined from intensities of parent and product ions in the mass spectra. The reaction rate constant increased rapidly with increase of charge states for parent ions. By changing temperature of collision cell in region from 280 to 450K, temperature dependence of reaction rate constant and branching fractions for proton transfer was measured. Dramatic change was observed for distribution of product ions and reaction rate constant. These results would correlate with conformation change of ubiquitin ions with change of temperature, which originates in self-solvation to protons by hydrophilic residues in polypeptide chains, delocalization of charges with self-solvation, and Coulomb repulsion between charges.