Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions

Cross sections for mixtures of tryptic digest peptide ions formed by electrospray ionization have been measured by a new ion mobility/time-of-flight mass spectrometry technique. Analysis of a series of 113 peptides containing 5-10 residues and having a single lysine group located at the C-terminal end show that cross sections are largely dependent upon the amino acid composition of each peptide. Reduced cross sections (which take into account differences in mass) are found to correlate with the fractions of nonpolar or polar aliphatic residues. Average intrinsic contributions to size for individual amino acid residues (referred to as intrinsic size parameters) have been obtained by solving a system of equations that relates the 113 reduced cross sections to the occurrence frequency of each residue within the different sequences. These parameters fall into families according to the physical sizes and chemical properties of the amino acids; contributions to cross section from nonpolar residues are significantly larger than those from polar groups. Calculated cross sections that are obtained by combining intrinsic size factors with peptide sequences are remarkably accurate: >90% of calculated values are within 2% of experimental measurements.