{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T07:50:26Z","timestamp":1778053826265,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Comprehensive two-dimensional gas chromatography mass spectrometry (GC \u00d7 GC\u2013MS) brings much increased separation capacity, chemical selectivity and sensitivity for metabolomics and provides more accurate information about metabolite retention times and mass spectra. However, there is always a shift of retention times in the two columns that makes it difficult to compare metabolic profiles obtained from multiple samples exposed to different experimental conditions.<\/jats:p>\n               <jats:p>Results: The existing peak alignment algorithms for GC \u00d7 GC\u2013MS data use the peak distance and the spectra similarity sequentially and require predefined either distance-based window and\/or spectral similarity-based window. To overcome the limitations of the current alignment methods, we developed an optimal peak alignment using a novel mixture similarity by employing the peak distance and the spectral similarity measures simultaneously without any variation windows. In addition, we examined the effect of the four different distance measures such as Euclidean, Maximum, Manhattan and Canberra distances on the peak alignment. The performance of our proposed peak alignment algorithm was compared with the existing alignment methods on the two sets of GC \u00d7 GC\u2013MS data. Our analysis showed that Canberra distance performed better than other distances and the proposed mixture similarity peak alignment algorithm prevailed against all literature reported methods.<\/jats:p>\n               <jats:p>Availability: The data and software mSPA are available at http:\/\/stage.louisville.edu\/faculty\/x0zhan17\/software\/software-development.<\/jats:p>\n               <jats:p>Contact: \u00a0s0kim023@louisville.edu; xiang.zhang@louisville.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr188","type":"journal-article","created":{"date-parts":[[2011,4,15]],"date-time":"2011-04-15T00:50:25Z","timestamp":1302828625000},"page":"1660-1666","source":"Crossref","is-referenced-by-count":42,"title":["An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure"],"prefix":"10.1093","volume":"27","author":[{"given":"Seongho","family":"Kim","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and Biostatistics, 2Department of Chemistry, University of Louisville, Louisville, KY 40292 and 3Division of Biostatistics, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aiqin","family":"Fang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Biostatistics, 2Department of Chemistry, University of Louisville, Louisville, KY 40292 and 3Division of Biostatistics, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bing","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Biostatistics, 2Department of Chemistry, University of Louisville, Louisville, KY 40292 and 3Division of Biostatistics, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaesik","family":"Jeong","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Biostatistics, 2Department of Chemistry, University of Louisville, Louisville, KY 40292 and 3Division of Biostatistics, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Biostatistics, 2Department of Chemistry, University of Louisville, Louisville, KY 40292 and 3Division of Biostatistics, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,4,14]]},"reference":[{"key":"2023012511151501200_B1","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/mas.20108","article-title":"Mass spectrometry-based metabolomics","volume":"26","author":"Dettmer","year":"2007","journal-title":"Mass Spectrom. Rev."},{"key":"2023012511151501200_B2","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":"2023012511151501200_B3","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.aca.2008.11.058","article-title":"Comprehensive two-dimensional gas chromatography\/time-of-flight mass spectrometry for metabonomics: biomarker discovery for diabetes mellitus","volume":"633","author":"Li","year":"2009","journal-title":"Anal. Chim. Acta"},{"key":"2023012511151501200_B4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1477-5956-5-3","article-title":"Methods for peptide identification by spectral comparison","volume":"5","author":"Liu","year":"2007","journal-title":"Prot. Sci."},{"key":"2023012511151501200_B5","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":"Mispelaar","year":"2003","journal-title":"J. Chromatograph."},{"key":"2023012511151501200_B6","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1002\/mas.20158","article-title":"Comprehensive two-dimensional gas chromatography-mass spectrometry: a review","volume":"27","author":"Mondello","year":"2008","journal-title":"Mass Spectro. Rev."},{"key":"2023012511151501200_B7","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.chroma.2007.11.101","article-title":"Comprehensive two-dimensional gas chromatography\/time-of-flight mass spectrometry peak sorting algorithm","volume":"1179","author":"Oh","year":"2008","journal-title":"J. Chromatography A"},{"key":"2023012511151501200_B8","article-title":"Comprehensive two dimensional gas chromatography","volume-title":"Comprehensive Analytical Chemistry","author":"Ramos","year":"2009"},{"key":"2023012511151501200_B9","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":"2023012511151501200_B10","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/1044-0305(94)87009-8","article-title":"Optimization and testing of mass spectral library search algorithms for Compound Identification","volume":"5","author":"Stein","year":"1994","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023012511151501200_B11","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":"2023012511151501200_B12","doi-asserted-by":"crossref","first-page":"2664","DOI":"10.1021\/ac7024317","article-title":"Two-dimensional correlation optimized warping algorithm for aligning GC \u00d7 GC\u2013MS data","volume":"80","author":"Zhang","year":"2008","journal-title":"Anal. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1660\/48863545\/bioinformatics_27_12_1660.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1660\/48863545\/bioinformatics_27_12_1660.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:21:07Z","timestamp":1674645667000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/12\/1660\/255685"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,4,14]]},"references-count":12,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2011,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr188","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,6,15]]},"published":{"date-parts":[[2011,4,14]]}}}