{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:00:52Z","timestamp":1775325652909,"version":"3.50.1"},"reference-count":42,"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><jats:p>Motivation: Nuclear magnetic resonance (NMR) spectroscopy is widely used for high-throughput characterization of metabolites in complex biological mixtures. However, accurate interpretation of the spectra in terms of identities and abundances of metabolites can be challenging, in particular in crowded regions with heavy peak overlap. Although a number of computational approaches for this task have recently been proposed, they are not entirely satisfactory in either accuracy or extent of automation.<\/jats:p><jats:p>Results: We introduce a probabilistic approach Bayesian Quantification (BQuant), for fully automated database-based identification and quantification of metabolites in local regions of 1H NMR spectra. The approach represents the spectra as mixtures of reference profiles from a database, and infers the identities and the abundances of metabolites by Bayesian model selection. We show using a simulated dataset, a spike-in experiment and a metabolomic investigation of plasma samples that BQuant outperforms the available automated alternatives in accuracy for both identification and quantification.<\/jats:p><jats:p>Availability: The R package BQuant is available at: http:\/\/www.stat.purdue.edu\/~ovitek\/BQuant-Web\/.<\/jats:p><jats:p>Contact: \u00a0ovitek@stat.purdue.edu; zhengc@purdue.edu<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr118","type":"journal-article","created":{"date-parts":[[2011,3,13]],"date-time":"2011-03-13T23:38:49Z","timestamp":1300059529000},"page":"1637-1644","source":"Crossref","is-referenced-by-count":87,"title":["Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection"],"prefix":"10.1093","volume":"27","author":[{"given":"Cheng","family":"Zheng","sequence":"first","affiliation":[{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shucha","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susanne","family":"Ragg","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Raftery","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga","family":"Vitek","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"},{"name":"1 Department of Statistics, Purdue University, West Lafayette, IN 47907, 2Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 3School of Medicine, Department of Pediatrics, Indiana University, Indianapolis, IN 46202, 4Department of Chemistry, Purdue University, West Lafayette, IN 47907 and 5Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,12]]},"reference":[{"key":"2023012511151474600_B1","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1366\/0003702041655421","article-title":"Automatic generation of peak-shaped models","volume":"58","author":"Alsmeyer","year":"2004","journal-title":"Appl. Spectrosc."},{"key":"2023012511151474600_B2","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1021\/ac801982h","article-title":"Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets","volume":"81","author":"Alves","year":"2009","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B3","doi-asserted-by":"crossref","first-page":"2992","DOI":"10.1093\/bioinformatics\/btp540","article-title":"Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets","volume":"25","author":"Anderson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511151474600_B4","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/bioinformatics\/btn599","article-title":"Bag of peaks: interpretation of NMR spectrometry","volume":"25","author":"Brelstaff","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511151474600_B5","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1111\/j.1541-0420.2005.00499.x","article-title":"Bayesian covariance selection in generalized linear mixed models","volume":"62","author":"Cai","year":"2006","journal-title":"Biometrics"},{"key":"2023012511151474600_B6","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1111\/j.0006-341X.2003.00089.x","article-title":"Random effects selection in linear mixed models","volume":"59","author":"Chen","year":"2003","journal-title":"Biometrics"},{"key":"2023012511151474600_B7","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1002\/rcm.2474","article-title":"Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation","volume":"20","author":"Chen","year":"2006","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023012511151474600_B8","first-page":"67","article-title":"The practical implementation of Bayesian model selection","volume":"38","author":"Chipman","year":"2001","journal-title":"IMS Lect Notes Monogr. Ser."},{"key":"2023012511151474600_B9","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1021\/ac048630x","article-title":"Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets","volume":"77","author":"Cloarec","year":"2005","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B10","doi-asserted-by":"crossref","first-page":"2262","DOI":"10.1021\/ac0519312","article-title":"Scaling and normalization effects in NMR spectroscopic metabonomic data sets","volume":"78","author":"Craig","year":"2006","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B11","doi-asserted-by":"crossref","first-page":"4556","DOI":"10.1021\/ac0503456","article-title":"Curve-fitting method for direct quantitation of compounds in complex biological mixtures using 1H NMR: application in metabonomic toxicology studies","volume":"77","author":"Crockford","year":"2005","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B12","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1021\/ac035301g","article-title":"Molecular factor analysis applied to collections of NMR spectra","volume":"76","author":"Eads","year":"2004","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B13","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1214\/ss\/1038425655","article-title":"Flexible smoothing with b-spline and penalties","volume":"11","author":"Eilers","year":"1996","journal-title":"Stat. Sci."},{"key":"2023012511151474600_B14","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198556473.001.0001","volume-title":"Principles of Nuclear Magnetic Resonance in One and Two Dimensions","author":"Ernst","year":"1990"},{"key":"2023012511151474600_B15","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1080\/01621459.1993.10476353","article-title":"Variable selection via Gibbs sampling","volume":"88","author":"George","year":"1993","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012511151474600_B16","first-page":"339","article-title":"Approaches for Bayesian variable selection","volume":"7","author":"George","year":"1997","journal-title":"Stat. Sin."},{"key":"2023012511151474600_B17","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.jmr.2006.09.003","article-title":"Weighted least-squares deconvolution method for discovery of group differences between complex biofluid 1H NMR spectra","volume":"183","author":"Gipsona","year":"2006","journal-title":"J. Magn. Reson."},{"key":"2023012511151474600_B18","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1080\/00401706.1979.10489751","article-title":"Generalized cross-validation as a method for choosing a good ridge parameter","volume":"21","author":"Golub","year":"1979","journal-title":"Technometrics"},{"key":"2023012511151474600_B19","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1586\/14737159.8.5.617","article-title":"Metabolomics-based methods for early disease diagnostics: a review","volume":"8","author":"Gowda","year":"2008","journal-title":"Exp. Rev. Mol. Diagn."},{"key":"2023012511151474600_B20","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1214\/06-BA117B","article-title":"A default conjugate prior for variance components in generalized linear mixed models (comment on article by browne and draper)","volume":"1","author":"Kass","year":"2006","journal-title":"Bayesian Anal."},{"key":"2023012511151474600_B21","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1111\/j.1541-0420.2007.00771.x","article-title":"Fixed and random effects selection in linear and logistic models","volume":"63","author":"Kinney","year":"2007","journal-title":"Biometrics"},{"key":"2023012511151474600_B22","first-page":"1757","article-title":"Gibbs sampling approach for generation of truncated multivariate gaussian random variables","volume":"3","author":"Kotecha","year":"1999","journal-title":"Proc. Acoust. Speech Signal Process."},{"key":"2023012511151474600_B23","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1002\/mrm.1910360306","article-title":"A computational strategy for the deconvolution of NMR spectra with multiplet structures and constraints: analysis of overlapping 13c \u22122h multiplets of 13c enriched metabolites from cell suspensions incubated in deuterated media","volume":"36","author":"Laatikainen","year":"1996","journal-title":"Magn. Reson. Med."},{"key":"2023012511151474600_B24","volume-title":"NMFN: Non-Negative Matrix Factorization","author":"Liu","year":"2009"},{"key":"2023012511151474600_B25","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1080\/01621459.1994.10476894","article-title":"Model selection and accounting for model uncertainty in graphical models using occam's window","volume":"89","author":"Madigan","year":"1994","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012511151474600_B26","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/(SICI)1099-0534(2000)12:1<21::AID-CMR4>3.0.CO;2-R","article-title":"Reference deconvolution: a simple and effective method for resolution enhancement in nuclear magnetic resonance spectroscopy","volume":"12","author":"Metz","year":"2000","journal-title":"Concepts Magn. Reson."},{"key":"2023012511151474600_B27","doi-asserted-by":"crossref","first-page":"3783","DOI":"10.1021\/ac7025964","article-title":"NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm","volume":"80","author":"Meyer","year":"2008","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B28","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1080\/004982599238047","article-title":"\u2018metabonomics\u2019: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data","volume":"29","author":"Nicholson","year":"1999","journal-title":"Xenobiotica"},{"key":"2023012511151474600_B29","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1006\/jmre.1998.1639","article-title":"A new method for spectral decomposition using a bilinear Bayesian approach","volume":"137","author":"Ochs","year":"1999","journal-title":"J. Magn. Reson."},{"key":"2023012511151474600_B30","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1214\/09-BA403","article-title":"A review of Bayesian variable selection methods: what, how and which","volume":"4","author":"O'Hara","year":"2009","journal-title":"Bayesian Anal."},{"key":"2023012511151474600_B31","doi-asserted-by":"crossref","first-page":"2262","DOI":"10.1093\/bioinformatics\/btl362","article-title":"Bayesian variable selection for the analysis of microarray data with censored outcomes","volume":"22","author":"Sha","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012511151474600_B32","volume-title":"Spectrometric Identification of Organic Compounds","author":"Silverstein","year":"2005","edition":"7th edn"},{"key":"2023012511151474600_B33","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.aca.2005.03.060","article-title":"Strategies for organic impurity quantification by 1H NMR spectroscopy: constrained total-line-shape fitting","volume":"542","author":"Soininen","year":"2005","journal-title":"Anal. Chim. Acta"},{"key":"2023012511151474600_B34","doi-asserted-by":"crossref","first-page":"3666","DOI":"10.1021\/ac049849e","article-title":"Sample classification based on Bayesian spectral decomposition of metabonomic NMR data sets","volume":"76","author":"Stoyanova","year":"2004","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B35","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1111\/j.1541-0420.2007.00829.x","article-title":"A Bayesian model for sparse functional data","volume":"64","author":"Thompson","year":"2008","journal-title":"Biometrics"},{"key":"2023012511151474600_B36","doi-asserted-by":"crossref","first-page":"D402","DOI":"10.1093\/nar\/gkm957","article-title":"Biomagresbank","volume":"36","author":"Ulrich","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511151474600_B37","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1021\/ac8011544","article-title":"Recursive segment-wise peak alignment of biological 1H NMR spectra for improved metabolic biomarker recovery","volume":"81","author":"Veselkov","year":"2009","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B38","doi-asserted-by":"crossref","first-page":"4430","DOI":"10.1021\/ac060209g","article-title":"Targeted profiling: quantitative analysis of 1H-NMR metabolomics data","volume":"78","author":"Weljie","year":"2006","journal-title":"Anal. Chem."},{"key":"2023012511151474600_B39","first-page":"1181","article-title":"Quantitative metabolomics using NMR","volume":"29","author":"Wishart","year":"2008","journal-title":"Xenobiotica"},{"key":"2023012511151474600_B40","doi-asserted-by":"crossref","first-page":"D521","DOI":"10.1093\/nar\/gkl923","article-title":"HMDB: the human metabolome database","volume":"35","author":"Wishart","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012511151474600_B41","doi-asserted-by":"crossref","DOI":"10.1201\/9781420010404","volume-title":"Generalized Additive Models: an Introduction with R","author":"Wood","year":"2006"},{"key":"2023012511151474600_B42","doi-asserted-by":"crossref","first-page":"6080","DOI":"10.1021\/ac900424c","article-title":"Interdependence of signal processing and analysis of urine 1H NMR spectra for metabolic profiling","volume":"81","author":"Zhang","year":"2009","journal-title":"Anal. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1637\/48863668\/bioinformatics_27_12_1637.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1637\/48863668\/bioinformatics_27_12_1637.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T04:22:26Z","timestamp":1712290946000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/12\/1637\/255106"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,12]]},"references-count":42,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2011,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr118","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":[[2011,3,12]]}}}