Atomistic dynamics of protonated polyglycine, gly n -H + (n = 3, 5, and 7), colliding with a fluorinated octanethiol self-assembled monolayer (F-SAM) surface has been studied by trajectory calculations. The effects of peptide size on the collision processes and energy transfer efficiencies are emphasized and discussed in detail. The simulations show that the fraction of trapping, which is related to the soft-landing process, dramatically drops with the increase in collision energy, but gently increases with the peptide size. The average energy transfer to the peptide ion's internal degrees of freedom, ΔE int , is compared with previous experiments. The limiting probability P o of energy transfer to the surface is given by fitting a function of P o exp(–b/E i ). Our results suggest that the efficiencies of energy transfer are less dependent on the masses, even the categories of the peptide ions, and are determined by the character of the surfaces.