title: Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides.
abstract: Cross sections for 61 palmitoylated peptides and 73 cysteine-unmodified peptides are determined and used together with a previously obtained tryptic peptide library to derive a set of intrinsic size parameters (ISPs) for the palmitoyl (Pal) group (1.26 ± 0.04), carboxyamidomethyl (Am) group (0.92 ± 0.04), and the 20 amino acid residues to assess the influence of Pal- and Am-modification on cysteine and other amino acid residues. These values highlight the influence of the intrinsic hydrophobic and hydrophilic nature of these modifications on the overall cross sections. As a part of this analysis, we find that ISPs derived from a database of a modifier on one amino acid residue (CysPal) can be applied on the same modification group on different amino acid residues (SerPaland TyrPal). Using these ISP values, we are able to calculate peptide cross sections to within ± 2% of experimental values for 83% of Pal-modified peptide ions and 63% of Am-modified peptide ions. We propose that modification groups should be treated as individual contribution factors, instead of treating the combination of the particular group and the amino acid residue they are on as a whole when considering their effects on the peptide ion mobility features.
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405.
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Dilger
authors.affiliation: Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405.
authors.forename: Vikas
authors.initials: V
authors.lastname: Pejaver
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405.
authors.forename: David
authors.initials: D
authors.lastname: Smiley
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405.
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Arnold
authors.affiliation: Buck Institute for Research on Aging, Novato, CA 94945.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Mooney
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405.
authors.forename: Suchetana
authors.initials: S
authors.lastname: Mukhopadhyay
authors.affiliation: Department of Computer Science and Informatics, Indiana University, Bloomington, IN 47405.
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, IN 47405.
authors.forename: David E
authors.initials: DE
authors.lastname: Clemmer