title: Deconvolution of mixture spectra and increased throughput of peptide identification by utilization of intensified complementary ions formed in tandem mass spectrometry.
abstract: A cornerstone of mass spectrometry based proteomics is to relate with high statistical significance experimentally obtained tandem mass spectrometry (MS/MS) data to peptide sequences from a protein database. Most sequence specific fragment ions in MS/MS spectra are represented by a subset of complementary ion pairs. Here, we investigated the reliabilities of complementary ion pairs formed in CAD and CAD/ETD MS/MS and developed a reliability-based approach of intensification of ion signals of complementary pairs prior to database searching. In a large-scale proteomics experiment using high-resolution orbitrap mass spectrometry, an increase in the number of peptide identifications was obtained relative to the original CAD MS/MS spectra when intensified golden complementary (+18.6%) and CAD complementary pairs (+17.2%) were submitted to the Mascot search engine. This also exceeded the results obtained by deisotoping/deconvolution of CAD MS/MS spectra. A novel approach for extracting sequence-specific fragment ions of co-isolated peptides was developed based on the complementarity rules. This technique demonstrated an impressive gain of 42.4% more peptide identifications as compared with the use of the initial data set.
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kryuchkov
authors.forename: Thiago
authors.initials: T
authors.lastname: Verano-Braga
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Hansen
authors.forename: Richard R
authors.initials: RR
authors.lastname: Sprenger
authors.forename: Frank
authors.initials: F
authors.lastname: Kjeldsen
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006801:Humans; D007477:Ions / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry / Q000145:classification / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D007477:Ions; D010455:Peptides