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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\u2010isolation and thus prone to false identifications. The deconvolution approach matched complementary <jats:italic>b\u2010<\/jats:italic>, <jats:italic>y\u2010<\/jats:italic>ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co\u2010isolated 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\u201335% 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.<\/jats:p>","DOI":"10.1002\/pmic.201500549","type":"journal-article","created":{"date-parts":[[2016,6,22]],"date-time":"2016-06-22T16:24:28Z","timestamp":1466612668000},"page":"2470-2479","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Peptide de novo sequencing of mixture tandem mass spectra"],"prefix":"10.1002","volume":"16","author":[{"given":"Vladimir","family":"Gorshkov","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M, Odense  Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phanie Yuki Kolbeck","family":"Hotta","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M, Odense  Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thiago","family":"Verano\u2010Braga","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M, Odense  Denmark"},{"name":"Department of Physiology and Biophysics Federal University of Minas Gerais Belo Horizonte \u2013 MG, Belo Horizonte  Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Kjeldsen","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M, Odense  Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2016,8,5]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku989"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1195"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(94)80016-2"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr0499491"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth092"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6277"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1586\/epr.11.54"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2003.12.009"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1741-8364(04)02387-X"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2013.02.001"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1089\/106652799318300"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr060222h"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1089\/10665270152530872"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1089\/106652703763255633"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.1196"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr050070a"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac0618425"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2011.59"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1021\/ac0508853"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/1044-0305(95)00477-U"},{"key":"e_1_2_8_23_1","first-page":"19","article-title":"Derivation of Peptide Sequence from mass spectral data using the genetic algorithm","volume":"9","author":"Stranz D. 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