Sj. Valentine et al., Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions, J PHYS CH B, 103(8), 1999, pp. 1203-1207
Cross sections for mixtures of tryptic digest peptide ions formed by electr
ospray ionization have been measured by a new ion mobility/time-of-flight m
ass spectrometry technique. Analysis of a series of 113 peptides containing
5-10 residues and having a single lysine group located at the C-terminal e
nd show that cross sections are largely dependent upon the amino acid compo
sition of each peptide. Reduced cross sections (which take into account dif
ferences in mass) are found to correlate with the fractions of nonpolar or
polar aliphatic residues. Average intrinsic contributions to size for indiv
idual amino acid residues (referred to as intrinsic size parameters) have b
een obtained by solving a system of equations that relates the 113 reduced
cross sections to the occurrence frequency of each residue within the diffe
rent sequences. These parameters fall into families according to the physic
al sizes and chemical properties of the amino acids; contributions to cross
section from nonpolar residues are significantly larger than those from po
lar groups. Calculated cross sections that are obtained by combining intrin
sic size factors with peptide sequences are remarkably accurate: >90% of ca
lculated values are within 2% of experimental measurements.