{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:06:26Z","timestamp":1761059186944},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2011,2,15]],"date-time":"2011-02-15T00:00:00Z","timestamp":1297728000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-s1-s2","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T20:15:19Z","timestamp":1298060119000},"source":"Crossref","is-referenced-by-count":6,"title":["Score regularization for peptide identification"],"prefix":"10.1186","volume":"12","author":[{"given":"Zengyou","family":"He","sequence":"first","affiliation":[]},{"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Weichuan","family":"Yu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"issue":"18","key":"4360_CR1","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","volume":"20","author":"DN Perkins","year":"1999","unstructured":"Perkins DN, Pappin DJC, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18):3551\u20133567. 10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","journal-title":"Electrophoresis"},{"issue":"11","key":"4360_CR2","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","volume":"5","author":"JK Eng","year":"1994","unstructured":"Eng JK, Mccormack AL, Yates JR: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 1994, 5(11):976\u2013989. 10.1016\/1044-0305(94)80016-2","journal-title":"Journal of the American Society for Mass Spectrometry"},{"issue":"16","key":"4360_CR3","doi-asserted-by":"publisher","first-page":"6111","DOI":"10.1021\/ac070262k","volume":"79","author":"AA Klammer","year":"2007","unstructured":"Klammer AA, Yi X, MacCoss MJ, Noble WS: Improving Tandem Mass Spectrum Identification Using Peptide Retention Time Prediction across Diverse Chromatography Conditions. Analytical Chemistry 2007, 79(16):6111\u20136118. 10.1021\/ac070262k","journal-title":"Analytical Chemistry"},{"issue":"4","key":"4360_CR4","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1007\/s11222-007-9033-z","volume":"17","author":"U von Luxburg","year":"2007","unstructured":"von Luxburg U: A tutorial on spectral clustering. Statistics and Computing 2007, 17(4):395\u2013416. 10.1007\/s11222-007-9033-z","journal-title":"Statistics and Computing"},{"key":"4360_CR5","volume-title":"Spectral Graph Theory","author":"FRK Chung","year":"1997","unstructured":"Chung FRK: Spectral Graph Theory. American Mathematical Society; 1997."},{"key":"4360_CR6","volume-title":"Advances in Neural Information Processing Systems (NIPS03)","author":"D Zhou","year":"2003","unstructured":"Zhou D, Bousquet O, Lal TN, Weston J, Sch\u00f6lkopf B: Learning with Local and Global Consistency. In Advances in Neural Information Processing Systems (NIPS03). Edited by: Thrun S, Saul LK, Sch\u00f6lkopf B. MIT Press; 2003."},{"issue":"22","key":"4360_CR7","doi-asserted-by":"publisher","first-page":"2969","DOI":"10.1093\/bioinformatics\/btp501","volume":"25","author":"Z He","year":"2009","unstructured":"He Z, Yu W: Improving peptide identification with single-stage mass spectrum peaks. Bioinformatics 2009, 25(22):2969\u20132974. 10.1093\/bioinformatics\/btp501","journal-title":"Bioinformatics"},{"issue":"9","key":"4360_CR8","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","volume":"20","author":"R Craig","year":"2004","unstructured":"Craig R, Beavis RC: TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466\u20131467. 10.1093\/bioinformatics\/bth092","journal-title":"Bioinformatics"},{"issue":"20","key":"4360_CR9","doi-asserted-by":"publisher","first-page":"5383","DOI":"10.1021\/ac025747h","volume":"74","author":"A Keller","year":"2002","unstructured":"Keller A, Nesvizhskii AI, Kolker E, Aebersold R: Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search. Analytical Chemistry 2002, 74(20):5383\u20135392. 10.1021\/ac025747h","journal-title":"Analytical Chemistry"},{"key":"4360_CR10","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1038\/nmeth1113","volume":"4","author":"L Kall","year":"2007","unstructured":"Kall L, Canterbury JD, Weston J, Noble WS, MacCoss MJ: Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature Methods 2007, 4: 923\u2013925. 10.1038\/nmeth1113","journal-title":"Nature Methods"},{"key":"4360_CR11","first-page":"154","volume-title":"Proceedings of The 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Volume 4955 of LNBI","author":"Y Lin","year":"2008","unstructured":"Lin Y, Qiao Y, Sun S, Yu C, Dong G, Bu D: A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. In Proceedings of The 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Volume 4955 of LNBI. Edited by: Vingron M, Wong L. Springer; 2008:154\u2013166."},{"issue":"13","key":"4360_CR12","doi-asserted-by":"publisher","first-page":"i348","DOI":"10.1093\/bioinformatics\/btn189","volume":"24","author":"AA Klammer","year":"2008","unstructured":"Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS: Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics 2008, 24(13):i348-i356. 10.1093\/bioinformatics\/btn189","journal-title":"Bioinformatics"},{"issue":"11","key":"4360_CR13","doi-asserted-by":"publisher","first-page":"4878","DOI":"10.1021\/pr800484x","volume":"7","author":"Y Ding","year":"2008","unstructured":"Ding Y, Choi H, Nesvizhskii AI: Adaptive Discriminant Function Analysis and Reranking of MS\/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics. Journal of Proteome Research 2008, 7(11):4878\u20134889. 10.1021\/pr800484x","journal-title":"Journal of Proteome Research"},{"issue":"5","key":"4360_CR14","doi-asserted-by":"publisher","first-page":"2241","DOI":"10.1021\/pr800678b","volume":"8","author":"A Frank","year":"2009","unstructured":"Frank A: A Ranking-Based Scoring Function For Peptide-Spectrum Matches. Journal of Proteome Research 2009, 8(5):2241\u20132252. 10.1021\/pr800678b","journal-title":"Journal of Proteome Research"},{"issue":"6","key":"4360_CR15","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1007\/s10791-007-9034-8","volume":"10","author":"F Diaz","year":"2007","unstructured":"Diaz F: Regularizing query-based retrieval scores. Information Retrevial 2007, 10(6):531\u2013562. 10.1007\/s10791-007-9034-8","journal-title":"Information Retrevial"},{"issue":"17","key":"4360_CR16","doi-asserted-by":"publisher","first-page":"4646","DOI":"10.1021\/ac0341261","volume":"75","author":"AI Nesvizhskii","year":"2003","unstructured":"Nesvizhskii AI, Keller A, Kolker E, Aebersold R: A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry 2003, 75(17):4646\u20134658. 10.1021\/ac0341261","journal-title":"Analytical Chemistry"},{"key":"4360_CR17","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1021\/pr070244j","volume":"7","author":"J Klimek","year":"2008","unstructured":"Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB: The Standard Protein Mix Database: A Diverse Dataset to Assist in the Production of Improved Peptide and Protein Identification Software Tools. Journal of Proteome Research 2008, 7: 96\u2013103. 10.1021\/pr070244j","journal-title":"Journal of Proteome Research"},{"issue":"2","key":"4360_CR18","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1021\/pr0604920","volume":"6","author":"J Whiteaker","year":"2007","unstructured":"Whiteaker J, Zhang H, Eng J, Fang R, Piening B, Feng L, Lorentzen T, Schoenherr R, Keane J, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp D, Anderson L, Watts J, Smith R, McIntosh M, Paulovich A: Head-to-head comparison of serum fractionation techniques. Journal of Proteome Research 2007, 6(2):828\u2013836. 10.1021\/pr0604920","journal-title":"Journal of Proteome Research"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-S1-S2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:26:24Z","timestamp":1548239184000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S1-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,15]]},"references-count":18,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4360"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s1-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,15]]},"article-number":"S2"}}