Open Access Research article

MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures

Dan Tulpan14*, Serge Léger1, Luc Belliveau1, Adrian Culf23 and Miroslava Čuperlović-Culf13

Author Affiliations

1 Institute for Information Technology, National Research Council of Canada, Moncton, New Brunswick, E1A 7R1, Canada

2 Atlantic Cancer Research Institute, Moncton, New Brunswick, E1C 8X3, Canada

3 Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick, E4L 1G8, Canada

4 Department of Biology, Université de Moncton, New Brunswick, E1A 3E9, Canada

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BMC Bioinformatics 2011, 12:400  doi:10.1186/1471-2105-12-400

Published: 14 October 2011

Abstract

Background

One-dimensional 1H-NMR spectroscopy is widely used for high-throughput characterization of metabolites in complex biological mixtures. However, the accurate identification of individual compounds is still a challenging task, particularly in spectral regions with higher peak densities. The need for automatic tools to facilitate and further improve the accuracy of such tasks, while using increasingly larger reference spectral libraries becomes a priority of current metabolomics research.

Results

We introduce a web server application, called MetaboHunter, which can be used for automatic assignment of 1H-NMR spectra of metabolites. MetaboHunter provides methods for automatic metabolite identification based on spectra or peak lists with three different search methods and with possibility for peak drift in a user defined spectral range. The assignment is performed using as reference libraries manually curated data from two major publicly available databases of NMR metabolite standard measurements (HMDB and MMCD). Tests using a variety of synthetic and experimental spectra of single and multi metabolite mixtures show that MetaboHunter is able to identify, in average, more than 80% of detectable metabolites from spectra of synthetic mixtures and more than 50% from spectra corresponding to experimental mixtures. This work also suggests that better scoring functions improve by more than 30% the performance of MetaboHunter's metabolite identification methods.

Conclusions

MetaboHunter is a freely accessible, easy to use and user friendly 1H-NMR-based web server application that provides efficient data input and pre-processing, flexible parameter settings, fast and automatic metabolite fingerprinting and results visualization via intuitive plotting and compound peak hit maps. Compared to other published and freely accessible metabolomics tools, MetaboHunter implements three efficient methods to search for metabolites in manually curated data from two reference libraries.

http://www.nrcbioinformatics.ca/metabohunter/ webcite