A database of 660 peptide ion cross sections: Use of intrinsic size parameters for bona fide predictions of cross sections

An ion trap/ion mobility/time-of-flight mass spectrometry technique has bee n used to measure collision cross sections for 660 peptide ions generated b y tryptic digestion of 34 common proteins. Measured cross sections have bee n compiled into a database that contains peptide molecular weight and seque nce information. The database is used to generate average intrinsic contrib utions to cross section (size parameters) for different amino acid residues by solving systems of equations that relate the unknown contributions of i ndividual residues to the sequences and cross sections of database peptides . Size parameters are combined with information about amino acid compositio n to calculate cross sections for database peptides. Bona fide cross sectio n predictions (made prior to measurement) for peptides observed in tryptic digests of sperm whale myoglobin and yeast enolase are made. Eight of 10 pr edicted cross sections are within 2% of the experimental values and all 10 are within 32%. The utility of size parameters for cross section prediction is explored and discussed. (J Am Soc Mass Spectrom 1999, 10, 1188-1211) (C ) 1999 American Society for Mass Spectrometry.