title: Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry.
abstract: Tandem mass spectrometry (MS/MS) is a powerful tool for characterization of post-translationally modified proteins, including epsilon-N-acetyllysine-containing species. Previous reports indicate that epsilon-N-acetyllysine immonium ions are useful marker ions for peptides containing epsilon-N-acetyllysine, but the specificity and sensitivity of these ions for assignment of lysine acetylation by MS/MS have not been studied in detail. We investigated MS/MS data sets of 172 epsilon-N-acetyllysine tryptic peptides and 268 nonacetylated tryptic peptides to establish the utility and reliability of epsilon-N-acetyllysine immonium ions for identification and validation of acetylated peptides. Our analysis shows that the immonium ion at m/z 143 lacks specificity for lysine-acetylated peptides, whereas the derivative at m/z 126 is highly specific (98.1%). We also studied the positional effect of the epsilon-N-acetyllysine on the intensity of observed acetyllysine immonium ions. We observed an increase in acetyllysine immonium ion intensities when the acetylated lysine was N-terminally positioned in the peptide as compared to internal positions. Based on these observations we propose a validation scheme for unambiguous assignment of acetyllysine-containing peptides by MS/MS. Our analysis of epsilon-N-acetyllysine immonium ions provide a framework for investigation of MS/MS marker ion specificity and sensitivity that can be applied in studies of other types of post-translational modifications.
authors.affiliation: Department of Biochemistry and Molecular Biology and Centre for Epigenetics, University of Southern Denmark, DK-5230 Odense M, Denmark.
authors.forename: Morten B
authors.initials: MB
authors.lastname: Trelle
authors.forename: Ole N
authors.initials: ON
authors.lastname: Jensen
mesh_terms: D000465:Algorithms; D008239:Lysine / Q000031:analogs & derivatives* / Q000032:analysis / Q000737:chemistry; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D012680:Sensitivity and Specificity; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; C016949:N-epsilon-acetyllysine; D008239:Lysine