{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T21:00:51Z","timestamp":1768510851955,"version":"3.49.0"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,11,25]],"date-time":"2014-11-25T00:00:00Z","timestamp":1416873600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0376-0","type":"journal-article","created":{"date-parts":[[2014,11,24]],"date-time":"2014-11-24T20:05:26Z","timestamp":1416859526000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry"],"prefix":"10.1186","volume":"15","author":[{"given":"Ken","family":"Aoshima","sequence":"first","affiliation":[]},{"given":"Kentaro","family":"Takahashi","sequence":"additional","affiliation":[]},{"given":"Masayuki","family":"Ikawa","sequence":"additional","affiliation":[]},{"given":"Takayuki","family":"Kimura","sequence":"additional","affiliation":[]},{"given":"Mitsuru","family":"Fukuda","sequence":"additional","affiliation":[]},{"given":"Satoshi","family":"Tanaka","sequence":"additional","affiliation":[]},{"given":"Howell E","family":"Parry","sequence":"additional","affiliation":[]},{"given":"Yuichiro","family":"Fujita","sequence":"additional","affiliation":[]},{"given":"Akiyasu C","family":"Yoshizawa","sequence":"additional","affiliation":[]},{"given":"Shin-ichi","family":"Utsunomiya","sequence":"additional","affiliation":[]},{"given":"Shigeki","family":"Kajihara","sequence":"additional","affiliation":[]},{"given":"Koichi","family":"Tanaka","sequence":"additional","affiliation":[]},{"given":"Yoshiya","family":"Oda","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,11,25]]},"reference":[{"key":"376_CR1","doi-asserted-by":"publisher","first-page":"1328","DOI":"10.1074\/mcp.M500141-MCP200","volume":"4","author":"X Li","year":"2005","unstructured":"Li X, Yi EC, Kemp CJ, Zhang H, Aebersold R: A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics. 2005, 4: 1328-1340. 10.1074\/mcp.M500141-MCP200.","journal-title":"Mol Cell Proteomics"},{"key":"376_CR2","doi-asserted-by":"publisher","first-page":"1902","DOI":"10.1093\/bioinformatics\/btl276","volume":"22","author":"M Bellew","year":"2006","unstructured":"Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M: A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics. 2006, 22: 1902-1909. 10.1093\/bioinformatics\/btl276.","journal-title":"Bioinformatics"},{"key":"376_CR3","doi-asserted-by":"publisher","first-page":"4193","DOI":"10.1021\/ac0498563","volume":"76","author":"H Liu","year":"2004","unstructured":"Liu H, Sadygov RG, Yates JR: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004, 76: 4193-4201. 10.1021\/ac0498563.","journal-title":"Anal Chem"},{"key":"376_CR4","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1074\/mcp.M500061-MCP200","volume":"4","author":"Y Ishihama","year":"2005","unstructured":"Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M: Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics. 2005, 4: 1265-1272. 10.1074\/mcp.M500061-MCP200.","journal-title":"Mol Cell Proteomics"},{"key":"376_CR5","doi-asserted-by":"publisher","first-page":"6591","DOI":"10.1073\/pnas.96.12.6591","volume":"96","author":"Y Oda","year":"1999","unstructured":"Oda Y, Huang K, Cross FR, Cowburn D, Chait BT: Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A. 1999, 96: 6591-6596. 10.1073\/pnas.96.12.6591.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"376_CR6","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1074\/mcp.M200025-MCP200","volume":"1","author":"S-E Ong","year":"2002","unstructured":"Ong S-E, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M: Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002, 1: 376-386. 10.1074\/mcp.M200025-MCP200.","journal-title":"Mol Cell Proteomics"},{"key":"376_CR7","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/nmeth785","volume":"2","author":"JE Elias","year":"2005","unstructured":"Elias JE, Haas W, Faherty BK, Gygi SP: Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Meth. 2005, 2: 667-675. 10.1038\/nmeth785.","journal-title":"Nat Meth"},{"key":"376_CR8","doi-asserted-by":"publisher","first-page":"5435","DOI":"10.1002\/pmic.200600273","volume":"6","author":"PM Palagi","year":"2006","unstructured":"Palagi PM, Hernandez P, Walther D, Appel RD: Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics. 2006, 6: 5435-5444. 10.1002\/pmic.200600273.","journal-title":"Proteomics"},{"key":"376_CR9","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1021\/pr700758r","volume":"7","author":"LN Mueller","year":"2008","unstructured":"Mueller LN, Brusniak M-Y, Mani DR, Aebersold R: An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 2008, 7: 51-61. 10.1021\/pr700758r.","journal-title":"J Proteome Res"},{"issue":"840518","key":"376_CR10","first-page":"6","volume":"2010","author":"W Zhu","year":"2010","unstructured":"Zhu W, Smith JW, Huang C-M: Mass spectrometry-based label-free quantitative proteomics. BioMed Res Int. 2010, 2010 (840518): 6-","journal-title":"BioMed Res Int"},{"key":"376_CR11","doi-asserted-by":"publisher","first-page":"3846","DOI":"10.1021\/pr500155z","volume":"13","author":"S Tanaka","year":"2014","unstructured":"Tanaka S, Fujita Y, Parry HE, Yoshizawa AC, Morimoto K, Murase M, Yamada Y, Yao J, Utsunomiya S, Kajihara S, Fukuda M, Ikawa M, Tabata T, Takahashi K, Aoshima K, Nihei Y, Nishioka T, Oda Y, Tanaka K: Mass++: A Visualization and Analysis Tool for Mass Spectrometry. J Proteome Res. 2014, 13: 3846-3853. 10.1021\/pr500155z.","journal-title":"J Proteome Res"},{"key":"376_CR12","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1002\/rcm.600","volume":"16","author":"CA Hastings","year":"2002","unstructured":"Hastings CA, Norton SM, Roy S: New algorithms for processing and peak detection in liquid chromatography\/mass spectrometry data. Rapid Commun Mass Spectrom. 2002, 16: 462-467. 10.1002\/rcm.600.","journal-title":"Rapid Commun Mass Spectrom"},{"key":"376_CR13","doi-asserted-by":"publisher","first-page":"3535","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3535::AID-ELPS3535>3.0.CO;2-J","volume":"20","author":"R Gras","year":"1999","unstructured":"Gras R, M\u00fcller M, Gasteiger E, Gay S, Binz P-A, Bienvenut W, Hoogland C, Sanchez J-C, Bairoch A, Hochstrasser DF, Appel RD: Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis. 1999, 20: 3535-3550. 10.1002\/(SICI)1522-2683(19991201)20:18<3535::AID-ELPS3535>3.0.CO;2-J.","journal-title":"Electrophoresis"},{"key":"376_CR14","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1186\/1471-2105-11-395","volume":"11","author":"T Pluskal","year":"2010","unstructured":"Pluskal T, Castillo S, Villar-Briones A, Ore\u0161i\u010d M: MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics. 2010, 11: 395-10.1186\/1471-2105-11-395.","journal-title":"BMC Bioinformatics"},{"key":"376_CR15","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.1002\/pmic.200401244","volume":"5","author":"PM Palagi","year":"2005","unstructured":"Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez J-C, Binz P-A, Hochstrasser DF, Appel RD: MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics. 2005, 5: 2381-2384. 10.1002\/pmic.200401244.","journal-title":"Proteomics"},{"key":"376_CR16","doi-asserted-by":"publisher","first-page":"3470","DOI":"10.1002\/pmic.200700057","volume":"7","author":"LN Mueller","year":"2007","unstructured":"Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak M-Y, Vitek O, Aebersold R, M\u00fcller M: SuperHirn - a novel tool for high resolution LC-MS-based peptide\/protein profiling. Proteomics. 2007, 7: 3470-3480. 10.1002\/pmic.200700057.","journal-title":"Proteomics"},{"key":"376_CR17","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/1471-2105-9-163","volume":"9","author":"M Sturm","year":"2008","unstructured":"Sturm M, Bertsch A, Gr\u00f6pl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O: OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics. 2008, 9: 163-10.1186\/1471-2105-9-163.","journal-title":"BMC Bioinformatics"},{"key":"376_CR18","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: 3551-3567. 10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2.","journal-title":"Electrophoresis"},{"key":"376_CR19","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: 1466-1467. 10.1093\/bioinformatics\/bth092.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"376_CR20","doi-asserted-by":"publisher","first-page":"D736","DOI":"10.1093\/nar\/gkp964","volume":"38","author":"JA Vizca\u00edno","year":"2010","unstructured":"Vizca\u00edno JA, C\u00f4t\u00e9 R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L: The proteomics identifications database: 2010 update. Nucleic Acids Res. 2010, 38 (Database issue): D736-742. 10.1093\/nar\/gkp964.","journal-title":"Nucleic Acids Res"},{"key":"376_CR21","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1002\/pmic.201200165","volume":"13","author":"A Fabietti","year":"2013","unstructured":"Fabietti A, Gaspari M, Krishnan S, Quirino A, Liberto MC, Cuda G, Foc\u00e0 A: Shotgun proteomic analysis of two Bartonella quintana strains. Proteomics. 2013, 13: 1375-1378. 10.1002\/pmic.201200165.","journal-title":"Proteomics"},{"key":"376_CR22","doi-asserted-by":"publisher","first-page":"2534","DOI":"10.1093\/bioinformatics\/btn323","volume":"24","author":"D Kessner","year":"2008","unstructured":"Kessner D, Chambers M, Burke R, Agus D, Mallick P: ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008, 24: 2534-2536. 10.1093\/bioinformatics\/btn323.","journal-title":"Bioinformatics"},{"key":"376_CR23","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/S0140-6736(86)90837-8","volume":"1","author":"JM Bland","year":"1986","unstructured":"Bland JM, Altman DG: Statistical methods for assessing agreement between two methods of clinical measurement. Lancet. 1986, 1: 307-310. 10.1016\/S0140-6736(86)90837-8.","journal-title":"Lancet"},{"key":"376_CR24","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","volume":"26","author":"J Cox","year":"2008","unstructured":"Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotech. 2008, 26: 1367-1372. 10.1038\/nbt.1511.","journal-title":"Nat Biotech"},{"key":"376_CR25","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1021\/ac802259r","volume":"81","author":"KT Myint","year":"2009","unstructured":"Myint KT, Aoshima K, Tanaka S, Nakamura T, Oda Y: Quantitative profiling of polar cationic metabolites in human cerebrospinal fluid by reversed-phase nanoliquid chromatography\/mass spectrometry. Anal Chem. 2009, 81: 1121-1129. 10.1021\/ac802259r.","journal-title":"Anal Chem"},{"key":"376_CR26","doi-asserted-by":"publisher","first-page":"3836","DOI":"10.1021\/ac9002062","volume":"81","author":"T Uehara","year":"2009","unstructured":"Uehara T, Yokoi A, Aoshima K, Tanaka S, Kadowaki T, Tanaka M, Oda Y: Quantitative phosphorus metabolomics using nanoflow liquid chromatography-tandem mass spectrometry and culture-derived comprehensive global internal standards. Anal Chem. 2009, 81: 3836-3842. 10.1021\/ac9002062.","journal-title":"Anal Chem"},{"key":"376_CR27","doi-asserted-by":"publisher","first-page":"2770","DOI":"10.1074\/mcp.M900240-MCP200","volume":"8","author":"T Masuda","year":"2009","unstructured":"Masuda T, Saito N, Tomita M, Ishihama Y: Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics. 2009, 8: 2770-2777. 10.1074\/mcp.M900240-MCP200.","journal-title":"Mol Cell Proteomics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0376-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0376-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0376-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0376-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,2,26]],"date-time":"2019-02-26T12:42:46Z","timestamp":1551184966000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0376-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,25]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["376"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0376-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,25]]},"assertion":[{"value":"27 May 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 November 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"376"}}