IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches

BMC Bioinformatics

Software

Bo-Yang Yu¹  Xu Song²  Bo-Li Zhang³  Hong-Min Liu⁴  Xiu-Mei Gao⁵  Li-Yuan Kang⁵ 

[1] Department of Chinese Medicinal Prescription, China Pharmaceutical University, Nanjing, China;Department of Chinese Medicinal Prescription, China Pharmaceutical University, Nanjing, China;School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China;Department of Chinese Medicinal Prescription, China Pharmaceutical University, Nanjing, China;State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China;School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China;State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China;

关键词: Cloud Computing;    Digital Filter;    Metabolic Modeling;    Relaxation Time Constant;    Relax Algorithm;   

DOI  :  10.1186/1471-2105-12-337

 received in 2011-04-20, accepted in 2011-08-12,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundOne of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches.ResultsWe created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites.ConclusionsIQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation.IQMNMR is available at http://cran.r-project.org/web/packages/IQMNMR/.

【 授权许可】

Unknown   
© Song et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.