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For efficient analysis, an ideal peak alignment method to deal with such variations is in great need.<\/jats:p><\/jats:sec>Results<\/jats:title>Using experimental data of a mixture of metabolite standards, we demonstrated that our method has better performance than other existing method which is not model-based. We then applied our method to the data generated from the plasma of a rat, which also demonstrates good performance of our model.<\/jats:p><\/jats:sec>Conclusions<\/jats:title>We developed a model-based peak alignment method to process both homogeneous and heterogeneous experimental data. The unique feature of our method is the only model-based peak alignment method coupled with metabolite identification in an unified framework. Through the comparison with other existing method, we demonstrated that our method has better performance. Data are available athttp:\/\/stage.louisville.edu\/faculty\/x0zhan17\/software\/software-development\/mspa<\/jats:ext-link>. The R source codes are available athttp:\/\/www.biostat.iupui.edu\/~ChangyuShen\/CodesPeakAlignment.zip<\/jats:ext-link>.<\/jats:p><\/jats:sec>Trial Registration<\/jats:title>2136949528613691<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-13-27","type":"journal-article","created":{"date-parts":[[2012,2,8]],"date-time":"2012-02-08T17:14:10Z","timestamp":1328721250000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry"],"prefix":"10.1186","volume":"13","author":[{"given":"Jaesik","family":"Jeong","sequence":"first","affiliation":[]},{"given":"Xue","family":"Shi","sequence":"additional","affiliation":[]},{"given":"Xiang","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Seongho","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Changyu","family":"Shen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,2,8]]},"reference":[{"key":"5123_CR1","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.ab.2007.01.028","volume":"363","author":"T Kind","year":"2007","unstructured":"Kind T, Tolstikov V, Fiehn O, Weiss RH: A comprehensive urinary metabolomic approach for identifying kidney cancer. 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