Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues

Ion mobility spectrometry (IMS) has recently been established as a powerful tool to separate the protease digest mixtures and identify their peptide c omponents. As accurate calculation of mobilities is critical for this techn ique, a new rapid method based on intrinsic size parameters (ISPs) of amino acid residues has been devised. However, those parameters had to be obtain ed by tedious statistical analysis of a large body of experimental data. He re we demonstrate that they can instead be derived a priori, based on the s toichiometry of a residue. Our main finding is that the ISP of a residue is essentially determined by its density, that is, the average mass/size rati o of its constituent atoms. This is in accordance with an interpretation in which peptides assume compact conformations in the gas phase dominated by the solvation of ionic charge. (C) 2001 American Society for Mass Spectrome try.