We have investigated the inelastic process for alkanethiol self-assembled monolayers by using the isotope labeling and unambiguously determine the vibrational modes active in the inelastic electron tunneling spectroscopy (IETS). By the selective deuteration of the hydrogen, we can show that (1) the vibrational modes containing substantial amount of C-C displacement are active in IETS and (2) the different parts of the molecule contribute approximately equally to the IETS. These findings are qualitatively explained by the Fermi's Golden rule of IETS and well reproduced by our calculations based on the density functional theory and nonequilibrium Green's function.