Classical trajectory simulations are performed to study energy transfer in collisions of protonated diglycine, gly2-H+, and dialanine, ala2-H+, ions with a fluorinated octanethiol self-assembled monolayer (F-SAM) surface for collision energies Ei in the range of 5-70 eV and incident angles θi of 0 and 45° with respect to the surface normal. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface. The simulations show the distribution of energy transfer to the peptide-ion's internal degrees of freedom, ΔEint, to the surface, ΔEsurf, and in peptide-ion translation, Ef, are very similar for gly 2-H+, and ala2-H+. The average percentage energy transferred to ΔEsurf and Ef increases and decreases, respectively, with an increase in Ei, while the average percentage energy transfer to ΔEint is nearly independent of Ei. Changing θi from 0 to 45° decreases and increases the percentage of energy transfer to ΔE surf and Ef, respectively, but has little change in the transfer to ΔEint. Average percentage energy transfer to the surface is found to approximately depend on Ei according to exp(-b/Ei). Comparisons with previous simulations show that peptide-H+ collisions with the EA F-SAM model transfer approximately a factor of 2 more energy to ΔEint than do collisions with the hydrogenated SAM, that is, H-SAM. Replacing the mass of the F atoms by that of a H atom in the simulations, without changing the potential, shows that the different ΔEint energy transfer efficiencies for the F-SAM and H-SAM surfaces is a mass effect. The simulations for ala2-H + colliding with the EA F-SAM surface give P(ΔEint) distributions in good agreement with previous experiments and an average transfer to ΔEint of 15% as compared with the experimental value of 21%. The UA F-SAM model gives energy transfer efficiencies in qualitative agreement with those of the EA model, but there are important quantitative differences.