{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T23:36:37Z","timestamp":1722728197406},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,12,1]],"date-time":"2013-12-01T00:00:00Z","timestamp":1385856000000},"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":[[2013,12]]},"DOI":"10.1186\/1471-2105-14-364","type":"journal-article","created":{"date-parts":[[2013,12,16]],"date-time":"2013-12-16T17:04:23Z","timestamp":1387213463000},"source":"Crossref","is-referenced-by-count":6,"title":["A flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information"],"prefix":"10.1186","volume":"14","author":[{"given":"Ashlee M","family":"Benjamin","sequence":"first","affiliation":[]},{"given":"J Will","family":"Thompson","sequence":"additional","affiliation":[]},{"given":"Erik J","family":"Soderblom","sequence":"additional","affiliation":[]},{"given":"Scott J","family":"Geromanos","sequence":"additional","affiliation":[]},{"given":"Ricardo","family":"Henao","sequence":"additional","affiliation":[]},{"given":"Virginia B","family":"Kraus","sequence":"additional","affiliation":[]},{"given":"M Arthur","family":"Moseley","sequence":"additional","affiliation":[]},{"given":"Joseph E","family":"Lucas","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,12,16]]},"reference":[{"issue":"6","key":"6227_CR1","doi-asserted-by":"publisher","first-page":"O111.016717","DOI":"10.1074\/mcp.O111.016717","volume":"11","author":"LC Gillet","year":"2012","unstructured":"Gillet LC, Navarro P, Tate S, R\u00f6st H, Selevsek N, Reiter L, Bonner R, Aebersold R: Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomic. 2012, 11 (6): O111.016717-","journal-title":"Mol Cell Proteomic"},{"key":"6227_CR2","doi-asserted-by":"publisher","first-page":"1683","DOI":"10.1002\/pmic.200800562","volume":"9","author":"SJ Geromanos","year":"2009","unstructured":"Geromanos SJ, Vissers JP, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI: The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependent LC-MS\/MS. Proteomics. 2009, 9: 1683-1695. 10.1002\/pmic.200800562.","journal-title":"Proteomics"},{"issue":"23","key":"6227_CR3","doi-asserted-by":"publisher","first-page":"4226","DOI":"10.1002\/pmic.200900635","volume":"10","author":"AW Dowsey","year":"2010","unstructured":"Dowsey AW, English JA, Lisacek F, Morris JS, Yang GZ, Dunn MJ: Image analysis tools and emerging algorithms for expression proteomics. Proteomics. 2010, 10 (23): 4226-4257. 10.1002\/pmic.200900635.","journal-title":"Proteomics"},{"issue":"6","key":"6227_CR4","doi-asserted-by":"publisher","first-page":"388","DOI":"10.2174\/138920209789177638","volume":"10","author":"JQ Zhang","year":"2009","unstructured":"Zhang JQ, Gonzalez E, Hestilow T, Haskins W, Huang YF: Review of peak detection algorithms in liquid-chromatography-mass spectrometry. Curr Genomics. 2009, 10 (6): 388-401. 10.2174\/138920209789177638.","journal-title":"Curr Genomics"},{"issue":"4","key":"6227_CR5","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1074\/mcp.R500005-MCP200","volume":"4","author":"J Listgarten","year":"2005","unstructured":"Listgarten J, Emili A: Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomic. 2005, 4 (4): 419-434. 10.1074\/mcp.R500005-MCP200.","journal-title":"Mol Cell Proteomic"},{"issue":"6","key":"6227_CR6","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nmeth.1333","volume":"6","author":"AW Bell","year":"2009","unstructured":"Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ: A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods. 2009, 6 (6): 423-430. 10.1038\/nmeth.1333.","journal-title":"Nat Methods"},{"issue":"14","key":"6227_CR7","doi-asserted-by":"publisher","first-page":"3066","DOI":"10.1093\/bioinformatics\/bti482","volume":"21","author":"N Jeffries","year":"2005","unstructured":"Jeffries N: Algorithms for alignment of mass spectrometry proteomic data. Bioinformatics. 2005, 21 (14): 3066-3073. 10.1093\/bioinformatics\/bti482.","journal-title":"Bioinformatics"},{"issue":"5897","key":"6227_CR8","doi-asserted-by":"publisher","first-page":"1758","DOI":"10.1126\/science.321.5897.1758","volume":"321","author":"RF Service","year":"2008","unstructured":"Service RF: Proteomics. Proteomics ponders prime time. Science. 2008, 321 (5897): 1758-1761. 10.1126\/science.321.5897.1758.","journal-title":"Science"},{"issue":"17","key":"6227_CR9","doi-asserted-by":"publisher","first-page":"6140","DOI":"10.1021\/ac0605344","volume":"78","author":"JT Prince","year":"2006","unstructured":"Prince JT, Marcotte EM: Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem. 2006, 78 (17): 6140-6152. 10.1021\/ac0605344.","journal-title":"Anal Chem"},{"issue":"5","key":"6227_CR10","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1074\/mcp.M600303-MCP200","volume":"6","author":"JPC Vissers","year":"2007","unstructured":"Vissers JPC, Langridge JI, Aerts JMFG: Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol Cell Proteomic. 2007, 6 (5): 755-766. 10.1074\/mcp.M600303-MCP200.","journal-title":"Mol Cell Proteomic"},{"issue":"4","key":"6227_CR11","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1074\/mcp.M500321-MCP200","volume":"5","author":"JC Silva","year":"2006","unstructured":"Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ: Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomic. 2006, 5 (4): 589-607.","journal-title":"Mol Cell Proteomic"},{"issue":"9","key":"6227_CR12","doi-asserted-by":"publisher","first-page":"1328","DOI":"10.1074\/mcp.M500141-MCP200","volume":"4","author":"XJ Li","year":"2005","unstructured":"Li XJ, 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 Proteomic. 2005, 4 (9): 1328-1340. 10.1074\/mcp.M500141-MCP200.","journal-title":"Mol Cell Proteomic"},{"issue":"7","key":"6227_CR13","doi-asserted-by":"publisher","first-page":"2187","DOI":"10.1021\/ac048455k","volume":"77","author":"JC Silva","year":"2005","unstructured":"Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S: Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem. 2005, 77 (7): 2187-200. 10.1021\/ac048455k.","journal-title":"Anal Chem"},{"issue":"21","key":"6227_CR14","doi-asserted-by":"publisher","first-page":"4054","DOI":"10.1093\/bioinformatics\/bti660","volume":"21","author":"XA Zhang","year":"2005","unstructured":"Zhang XA, Asara JM, Adamec J, Ouzzani M, Elmagarmid AK: Data pre-processing in liquid chromatography-mass spectrometry-based proteomics. Bioinformatics. 2005, 21 (21): 4054-4059. 10.1093\/bioinformatics\/bti660.","journal-title":"Bioinformatics"},{"issue":"5","key":"6227_CR15","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1093\/bioinformatics\/btk039","volume":"22","author":"M Katajamaa","year":"2006","unstructured":"Katajamaa M, Miettinen J, Oresic M: MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics. 2006, 22 (5): 634-636. 10.1093\/bioinformatics\/btk039.","journal-title":"Bioinformatics"},{"issue":"15","key":"6227_CR16","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, Fang RH, Lin CW, Chen JZ, 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 (15): 1902-1909. 10.1093\/bioinformatics\/btl276.","journal-title":"Bioinformatics"},{"issue":"3","key":"6227_CR17","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1021\/ac051437y","volume":"78","author":"CA Smith","year":"2006","unstructured":"Smith CA, Want EJ, O\u2019Maille G, Abagyan R, Siuzdak G: XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification. Anal Chem. 2006, 78 (3): 779-787. 10.1021\/ac051437y.","journal-title":"Anal Chem"},{"issue":"2","key":"6227_CR18","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1093\/biostatistics\/kxl015","volume":"8","author":"P Wang","year":"2007","unstructured":"Wang P, Tang H, Fitzgibbon MP, McIntosh M, Coram M, Zhang H, Yi E, Aebersold R: A statistical method for chromatographic alignment of LC-MS data. Biostatistics. 2007, 8 (2): 357-367. 10.1093\/biostatistics\/kxl015.","journal-title":"Biostatistics"},{"issue":"13","key":"6227_CR19","doi-asserted-by":"publisher","first-page":"i273","DOI":"10.1093\/bioinformatics\/btm209","volume":"23","author":"E Lange","year":"2007","unstructured":"Lange E, Gropl C, Schulz-Trieglaff O, Leinenbach A, Huber C, Reinert K: A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics. 2007, 23 (13): i273-i281. 10.1093\/bioinformatics\/btm209.","journal-title":"Bioinformatics"},{"key":"6227_CR20","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, Gropl 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"},{"issue":"15","key":"6227_CR21","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1093\/bioinformatics\/btp291","volume":"25","author":"T Yu","year":"2009","unstructured":"Yu T, Park Y, Johnson JM, Jones DP: apLCMS-adaptive processing of high-resolution LC\/MS data. Bioinformatics. 2009, 25 (15): 1930-1936. 10.1093\/bioinformatics\/btp291.","journal-title":"Bioinformatics"},{"key":"6227_CR22","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, Oresic 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"},{"issue":"10","key":"6227_CR23","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1074\/mcp.M600222-MCP200","volume":"5","author":"JD Jaffe","year":"2006","unstructured":"Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA: PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomic. 2006, 5 (10): 1927-1941. 10.1074\/mcp.M600222-MCP200.","journal-title":"Mol Cell Proteomic"},{"issue":"14","key":"6227_CR24","doi-asserted-by":"publisher","first-page":"e132","DOI":"10.1093\/bioinformatics\/btl219","volume":"22","author":"B Fischer","year":"2006","unstructured":"Fischer B, Grossmann J, Roth V, Gruissem W, Baginsky S, Buhmann JM: Semi-supervised LC\/MS alignment for differential proteomics. Bioinformatics. 2006, 22 (14): e132-e140. 10.1093\/bioinformatics\/btl219.","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"6227_CR25","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1477-5956-9-S1-S10","volume":"9","author":"Z Tang","year":"2011","unstructured":"Tang Z, Zhang L, Cheema AK, Ressom HW: A new method for alignment of LC-MALDI-TOF data. Proteome Sci. 2011, 9 (Suppl 1): S10-10.1186\/1477-5956-9-S1-S10.","journal-title":"Proteome Sci"},{"issue":"4","key":"6227_CR26","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1007\/s13361-011-0334-2","volume":"23","author":"Z Zhang","year":"2012","unstructured":"Zhang Z: Retention time alignment of LC\/MS data by a divide-and-conquer algorithm. J Am Soc Mass Spectrom. 2012, 23 (4): 764-772. 10.1007\/s13361-011-0334-2.","journal-title":"J Am Soc Mass Spectrom"},{"issue":"19","key":"6227_CR27","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 MY, Vitek O, Aebersold R, Muller M: SuperHirn - a novel tool for high resolution LC-MS-based peptide\/protein profiling. Proteomics. 2007, 7 (19): 3470-3480. 10.1002\/pmic.200700057.","journal-title":"Proteomics"},{"issue":"1-2","key":"6227_CR28","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/S0021-9673(98)00021-1","volume":"805","author":"NPV Nielsen","year":"1998","unstructured":"Nielsen NPV, Carstensen JM, Smedsgaard J: Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping. J Chromatogr A. 1998, 805 (1-2): 17-35.","journal-title":"J Chromatogr A"},{"issue":"3","key":"6227_CR29","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1074\/mcp.M500133-MCP200","volume":"5","author":"A Prakash","year":"2006","unstructured":"Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B: Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomic. 2006, 5 (3): 423-432.","journal-title":"Mol Cell Proteomic"},{"key":"6227_CR30","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1186\/1471-2105-9-375","volume":"9","author":"E Lange","year":"2008","unstructured":"Lange E, Tautenhahn R, Neumann S, Gropl C: Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics. 2008, 9: 375-10.1186\/1471-2105-9-375.","journal-title":"BMC Bioinformatics"},{"key":"6227_CR31","first-page":"325","volume":"24","author":"M West","year":"1992","unstructured":"West M: Mixture-models, Monte-Carlo, Bayesian updating and dynamic-models. Comput Sci Stat. 1992, 24: 325-333.","journal-title":"Comput Sci Stat"},{"key":"6227_CR32","first-page":"554","volume":"12","author":"CE Rasmussen","year":"2000","unstructured":"Rasmussen CE: The infinite Gaussian mixture model. Adv Neural Inf Process Syst 12. 2000, 12: 554-560.","journal-title":"Adv Neural Inf Process Syst 12"},{"issue":"5","key":"6227_CR33","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/ng0506-500","volume":"38","author":"M Reich","year":"2006","unstructured":"Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP: GenePattern 2.0. Nat Genet. 2006, 38 (5): 500-501. 10.1038\/ng0506-500.","journal-title":"Nat Genet"},{"key":"6227_CR34","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1002\/pmic.200800564","volume":"9","author":"GZ Li","year":"2009","unstructured":"Li GZ, Vissers JP, Silva JC, Golick D, Gorenstein MV, Geromanos SJ: Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics. 2009, 9: 1696-1719. 10.1002\/pmic.200800564.","journal-title":"Proteomics"},{"key":"6227_CR35","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1006\/jtbi.1996.0346","volume":"186","author":"MR Wilkins","year":"1997","unstructured":"Wilkins MR, Williams KL: Cross-species protein identification using amino acid composition, peptide mass fingerprinting, isoelectric point and molecular mass: A theoretical evaluation. J Theor Biol. 1997, 186: 7-15. 10.1006\/jtbi.1996.0346.","journal-title":"J Theor Biol"},{"issue":"23","key":"6227_CR36","doi-asserted-by":"publisher","first-page":"2926","DOI":"10.1093\/bioinformatics\/btl483","volume":"22","author":"JT Chang","year":"2006","unstructured":"Chang JT, Nevins JR: GATHER: a systems approach to interpreting genomic signatures. Bioinformatics. 2006, 22 (23): 2926-2933. 10.1093\/bioinformatics\/btl483.","journal-title":"Bioinformatics"},{"issue":"5","key":"6227_CR37","doi-asserted-by":"publisher","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","volume":"4","author":"JG Dennis","year":"2003","unstructured":"Dennis JG, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4 (5): P3-10.1186\/gb-2003-4-5-p3.","journal-title":"Genome Biol"},{"issue":"12","key":"6227_CR38","doi-asserted-by":"publisher","first-page":"R111.008565","DOI":"10.1074\/mcp.R111.008565","volume":"10","author":"H Lam","year":"2011","unstructured":"Lam H: Building and searching tandem mass spectral libraries for peptide identification. Mol Cell Proteomic. 2011, 10 (12): R111.008565-","journal-title":"Mol Cell Proteomic"},{"key":"6227_CR39","doi-asserted-by":"publisher","first-page":"4150","DOI":"10.1021\/pr2003177","volume":"10","author":"AV Nefedov","year":"2011","unstructured":"Nefedov AV, Mitra I, Brasier AR, Sadygov RG: Examining Troughs in the mass distribution of all theoretically possible tryptic peptides. J Proteome Res. 2011, 10: 4150-4157. 10.1021\/pr2003177.","journal-title":"J Proteome Res"},{"key":"6227_CR40","doi-asserted-by":"publisher","first-page":"3026","DOI":"10.1021\/ac203255e","volume":"84","author":"I Mitra","year":"2012","unstructured":"Mitra I, Nefedov AV, Brasier AR, Sadygov RG: Improved mass defect model for theoretical tryptic peptides. Anal Chem. 2012, 84: 3026-3032. 10.1021\/ac203255e.","journal-title":"Anal Chem"},{"issue":"2","key":"6227_CR41","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1053\/j.gastro.2010.10.047","volume":"140","author":"KB Schwarz","year":"2011","unstructured":"Schwarz KB, Gonzalez-Peralta RP, Murray KF, Molleston JP, Haber BA, Jonas MM, Rosenthal P, Mohan P, Balistreri WF, Narkewicz MR, Smith L, Lobritto SJ, Rossi S, Valsamakis A, Goodman Z, Robuck PR, Barton BA, Peds-C Clinical Research Network: The combination of ribavirin and peginterferon is superior to peginterferon and placebo for children and adolescents with chronic hepatitis C. Gastroenterology. 2011, 140 (2): e1-10.1053\/j.gastro.2010.03.070.","journal-title":"Gastroenterology"},{"issue":"6","key":"6227_CR42","doi-asserted-by":"publisher","first-page":"1809","DOI":"10.1002\/hep.24284","volume":"53","author":"K Patel","year":"2011","unstructured":"Patel K, Lucas JE, Thompson JW, Dubois LG, Tillmann HL, Thompson AJ, Uzarski D, Califf RM, Moseley MA, Ginsburg GS, McHutchison JG, McCarthy JJ, MURDOCK Horizon 1 Study Team: High predictive accuracy of an unbiased proteomic profile for sustained virologic response in chronic hepatitis C patients. Hepatology. 2011, 53 (6): 1809-1818. 10.1002\/hep.24284.","journal-title":"Hepatology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-364.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-364\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-364.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T06:01:26Z","timestamp":1548136886000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-364"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["6227"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-364","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12]]},"article-number":"364"}}