title: Improved peptide sequencing using isotope information inherent in tandem mass spectra.
abstract: We demonstrate here the use of natural isotopic 'labels' in peptides to aid in the identification of peptides with a de novo algorithm. Using data from ion trap tandem mass spectrometric (MS/MS) analysis of 102 tryptic peptides, we have analyzed multiple series of peaks within LCQ MS/MS spectra that 'spell' peptide sequences. Isotopic peaks from naturally abundant isotopes are particularly prominent even after peak centroiding on y- and b-series ions and lead to increased confidence in the identification of the precursor peptides. Sequence analysis of the MS/MS data is accomplished by finding sequences and subsequences in a hierarchical manner within the spectra.
authors.affiliation: Computational Biosciences, Pacific Northwest National Laboratory, Richland, WA 99352, USA. William.Cannon@pnl.gov
authors.forename: William R
authors.initials: WR
authors.lastname: Cannon
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Jarman
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D034301:Deinococcus / Q000737:chemistry; D007553:Isotope Labeling; D007554:Isotopes / Q000737:chemistry; D010455:Peptides / Q000032:analysis*; D020539:Sequence Analysis, Protein / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D007554:Isotopes; D010455:Peptides