title: Peptide de novo sequencing of mixture tandem mass spectra.
abstract: The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20-35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark. vgor@bmb.sdu.dk.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Gorshkov
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark.
authors.forename: Stéphanie Yuki Kolbeck
authors.initials: SY
authors.lastname: Hotta
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark.|Department of Physiology and Biophysics, Federal University of Minas Gerais Belo Horizonte - MG, Belo Horizonte, Brazil.
authors.forename: Thiago
authors.initials: T
authors.lastname: Verano-Braga
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense M, Odense, Denmark.
authors.forename: Frank
authors.initials: F
authors.lastname: Kjeldsen
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006367:HeLa Cells; D006801:Humans; D010455:Peptides / Q000032:analysis; D012604:Scorpion Venoms / Q000032:analysis / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D012604:Scorpion Venoms
keywords: Bioinformatics; Complementary ions; De novo sequencing; Mass spectral interference; Mixture fragmentation spectra