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Open Access Software

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

Xu Song12, Bo-Li Zhang13*, Hong-Min Liu2*, Bo-Yang Yu1*, Xiu-Mei Gao3 and Li-Yuan Kang3

Author Affiliations

1 Department of Chinese Medicinal Prescription, China Pharmaceutical University, Nanjing, China

2 School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China

3 State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China

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BMC Bioinformatics 2011, 12:337  doi:10.1186/1471-2105-12-337

Published: 12 August 2011

Abstract

Background

One 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.

Results

We 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.

Conclusions

IQMNMR 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/ webcite.