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Metabolites. 2016 Dec 15;6(4). pii: E46.

Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems.

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School of Health and Biomedical Sciences, RMIT University, 3083 Melbourne, Australia.
Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, 3001 Melbourne, Australia.
Commonwealth Scientific and Industrial Research Organisation (CSIRO), Land and Water, EcoSciences Precinct, 4001 Brisbane, Australia.
Metabolomics Australia, School of Biosciences, The University of Melbourne, 3010 Parkville, Australia.
Department of Physiology, Anatomy and Microbiology, Latrobe University, 3086 Melbourne, Australia.
Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3010 Parkville, Australia.
Phytochemistry and Bioactive Natural Products, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU Rue Michel Servet 1, 1211 Geneva 11, Switzerland.
Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, T6G 2E8 AB, Canada.


Although significant advances have been made in recent years, the structural elucidation of small molecules continues to remain a challenging issue for metabolite profiling. Many metabolomic studies feature unknown compounds; sometimes even in the list of features identified as "statistically significant" in the study. Such metabolic "dark matter" means that much of the potential information collected by metabolomics studies is lost. Accurate structure elucidation allows researchers to identify these compounds. This in turn, facilitates downstream metabolite pathway analysis, and a better understanding of the underlying biology of the system under investigation. This review covers a range of methods for the structural elucidation of individual compounds, including those based on gas and liquid chromatography hyphenated to mass spectrometry, single and multi-dimensional nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry and includes discussion of data standardization. Future perspectives in structure elucidation are also discussed; with a focus on the potential development of instruments and techniques, in both nuclear magnetic resonance spectroscopy and mass spectrometry that, may help solve some of the current issues that are hampering the complete identification of metabolite structure and function.


Fourier transform-infrared spectroscopy; mass spectrometry; metabolite profiling; metabolomics; nuclear magnetic resonance spectroscopy; structure elucidation

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