{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T15:50:14Z","timestamp":1767973814142,"version":"3.49.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC\u00d7GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC\u00d7GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis.<\/jats:p><jats:p>Results: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC\u00d7GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery.<\/jats:p><jats:p>Availability: The source code of MetPP is available at http:\/\/metaopen.sourceforge.net<\/jats:p><jats:p>Contact: \u00a0xiang.zhang@louisville.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt275","type":"journal-article","created":{"date-parts":[[2013,5,12]],"date-time":"2013-05-12T00:19:28Z","timestamp":1368317968000},"page":"1786-1792","source":"Crossref","is-referenced-by-count":53,"title":["MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics"],"prefix":"10.1093","volume":"29","author":[{"given":"Xiaoli","family":"Wei","sequence":"first","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue","family":"Shi","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Imhoi","family":"Koo","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seongho","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robin H.","family":"Schmidt","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gavin E.","family":"Arteel","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter H.","family":"Watson","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig","family":"McClain","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"},{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Chemistry, 2Department of Bioinformatics and Biostatistics, 3Department of Pharmacology & Toxicology, 4Alcohol Research Center, 5Department of Medicine, University of Louisville and 6Robley Rex Louisville VAMC, Louisville, KY 40292, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,5,11]]},"reference":[{"key":"2023012810455253900_btt275-B1","doi-asserted-by":"crossref","first-page":"5731","DOI":"10.1021\/ac900528b","article-title":"Integrative normalization and comparative analysis for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight aass spectrometry","volume":"81","author":"Almstetter","year":"2009","journal-title":"Anall. Chem."},{"key":"2023012810455253900_btt275-B2","unstructured":"Astrand M Normalizing oligonucleotide arrays 2001 http:\/\/www.stat.berkeley.edu\/\u223cterry\/zarray\/Affy\/GL_Workshop\/Astrand_manuscript.pdf (7 October 2011, date last accessed)"},{"key":"2023012810455253900_btt275-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate\u2014a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. Roy. Stat. Soc. B Met."},{"key":"2023012810455253900_btt275-B4","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-0450-1","volume-title":"Pattern Recognition with Fuzzy Objective Function Algorithms","author":"Bezdek","year":"1981"},{"key":"2023012810455253900_btt275-B6","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1021\/ac103308x","article-title":"Data analysis tool for comprehensive two-dimensional gas chromatography\/time-of-flight mass spectrometry","volume":"83","author":"Castillo","year":"2011","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B7","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1152\/ajpregu.2000.279.1.R1","article-title":"Multiple comparisons: philosophies and illustrations","volume":"279","author":"Curran-Everett","year":"2000","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"2023012810455253900_btt275-B8","first-page":"29","article-title":"Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments","volume":"12","author":"Dudoit","year":"2002","journal-title":"Stat. Sinica"},{"key":"2023012810455253900_btt275-B9","doi-asserted-by":"crossref","first-page":"5833","DOI":"10.1021\/ac010656q","article-title":"Objective data alignment and chemometric analysis of comprehensive two-dimensional separations with run-to-run peak shifting on both dimensions","volume":"73","author":"Fraga","year":"2001","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B10","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1002\/cem.1239","article-title":"Toward automated peak resolution in complete GC x GC-TOFMS chromatograms by PARAFAC","volume":"23","author":"Hoggard","year":"2009","journal-title":"J. Chemometr."},{"key":"2023012810455253900_btt275-B11","volume-title":"Principal Component Analysis","author":"Jolliffe","year":"2002"},{"key":"2023012810455253900_btt275-B12","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1093\/bioinformatics\/btr188","article-title":"An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure","volume":"27","author":"Kim","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810455253900_btt275-B13","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1093\/bioinformatics\/bts083","article-title":"A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry","volume":"28","author":"Kim","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810455253900_btt275-B14","doi-asserted-by":"crossref","first-page":"5631","DOI":"10.1021\/ac200740w","article-title":"Wavelet- and Fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography\/mass spectrometry","volume":"83","author":"Koo","year":"2011","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B15","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1002\/hlca.19580410703","article-title":"Gas-chromatographische charakterisierung organischer verbindungen. Teil 1: retentionsindices aliphatischer halogenide, alkohole, aldehyde und ketone","volume":"41","author":"Kovats","year":"1958","journal-title":"Helv. Chim. Acta."},{"key":"2023012810455253900_btt275-B16","doi-asserted-by":"crossref","first-page":"7735","DOI":"10.1021\/ac0511142","article-title":"A comprehensive two-dimensional retention time alignment algorithm to enhance chemometric analysis of comprehensive two-dimensional separation data","volume":"77","author":"Pierce","year":"2005","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B17","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.chroma.2004.08.125","article-title":"Computer language for identifying chemicals with comprehensive two-dimensional gas chromatography and mass spectrometry","volume":"1071","author":"Reichenbach","year":"2005","journal-title":"J. Chromatogr. A"},{"key":"2023012810455253900_btt275-B18","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.chroma.2011.07.046","article-title":"Features for non-targeted cross-sample analysis with comprehensive two-dimensional chromatography","volume":"1226","author":"Reichenbach","year":"2012","journal-title":"J. Chromatogr. A"},{"key":"2023012810455253900_btt275-B19","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1007\/11752790_2","article-title":"Overiew and recent advances in partial least squares","volume-title":"Subspace, Latent Structure and Feature Selection: Statistical and Optimization Perspectives Workshop (SLSFS 2005)","author":"Rosipal","year":"2006"},{"key":"2023012810455253900_btt275-B20","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.chroma.2003.08.081","article-title":"Trilinear chemometric analysis of two-dimensional comprehensive gas chromatography-time-of-flight mass spectrometry data","volume":"1027","author":"Sinha","year":"2004","journal-title":"J. Chromatogr. A"},{"key":"2023012810455253900_btt275-B21","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/1467-9868.00346","article-title":"A direct approach to false discovery rates","volume":"64","author":"Storey","year":"2002","journal-title":"J. R. Stat. Soc. Series B Stat. Methodol."},{"key":"2023012810455253900_btt275-B22","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.taap.2011.09.019","article-title":"Chronic subhepatotoxic exposure to arsenic enhances hepatic injury caused by high fat diet in mice","volume":"257","author":"Tan","year":"2011","journal-title":"Toxicol Appl. Pharmacol."},{"key":"2023012810455253900_btt275-B23","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1093\/bioinformatics\/17.6.520","article-title":"Missing value estimation methods for DNA microarrays","volume":"17","author":"Troyanskaya","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012810455253900_btt275-B24","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.chroma.2003.08.101","article-title":"Quantitative analysis of target components by comprehensive two-dimensional gas chromatography","volume":"1019","author":"van Mispelaar","year":"2003","journal-title":"J. Chromatogr. A"},{"key":"2023012810455253900_btt275-B25","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1021\/ac202124t","article-title":"Bayesian approach for peak detection in two-dimensional chromatography","volume":"84","author":"Vivo-Truyols","year":"2012","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B26","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1021\/ac100064b","article-title":"DISCO: distance and spectrum correlation optimization alignment for two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics","volume":"82","author":"Wang","year":"2010","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B27","doi-asserted-by":"crossref","first-page":"7668","DOI":"10.1021\/ac2017025","article-title":"MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics","volume":"83","author":"Wei","year":"2011","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B28","doi-asserted-by":"crossref","first-page":"2664","DOI":"10.1021\/ac7024317","article-title":"Two-dimensional correlation optimized warping algorithm for aligning GCxGC-MS data","volume":"80","author":"Zhang","year":"2008","journal-title":"Anal. Chem."},{"key":"2023012810455253900_btt275-B29","doi-asserted-by":"crossref","first-page":"6522","DOI":"10.1016\/j.chroma.2011.07.039","article-title":"iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data","volume":"1218","author":"Zhang","year":"2011","journal-title":"J. Chromatogr. A"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1786\/48891855\/bioinformatics_29_14_1786.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1786\/48891855\/bioinformatics_29_14_1786.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T15:48:46Z","timestamp":1715356126000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/14\/1786\/231276"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,11]]},"references-count":28,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2013,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt275","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,15]]},"published":{"date-parts":[[2013,5,11]]}}}