Methodology article
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction
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* Corresponding author: Christoph Steinbeck steinbeck@ebi.ac.uk
1 Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
2 Cologne University Bioinformatics Center (CUBIC), Zülpicher Str. 47, 50674 Köln, Germany
3 European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
BMC Bioinformatics 2008, 9:400 doi:10.1186/1471-2105-9-400
Published: 25 September 2008Abstract
Background
Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB.
Results
A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error.
Conclusion
NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.