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Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and D-Ile or L-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm−1. The IRMPD spectra showed remarkably different IR spectral features for the D-Ile or L-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the D- and L-Ile complexes. DFT calculations revealed that the chiral distinction of the D- and L-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD …