Abstract
Metabolomics datasets are commonly acquired by either mass spectrometry (MS) or nuclear magnetic resonance spectroscopy (NMR), despite their fundamental complementarity. In fact, combining MS and NMR datasets greatly improves the coverage of the metabolome and enhances the accuracy of metabolite identification, providing a detailed and high-throughput analysis of metabolic changes due to disease, drug treatment, or a variety of other environmental stimuli. Ideally, a single metabolomics sample would be simultaneously used for both MS and NMR analyses, minimizing the potential for variability between the two datasets. This necessitates the optimization of sample preparation, data collection and data handling protocols to effectively integrate direct-infusion MS data with one-dimensional (1D) 1H NMR spectra. To achieve this goal, we report for the first time the optimization of (i) metabolomics sample preparation for dual analysis by NMR and MS, (ii) high throughput, positive-ion direct infusion electrospray ionization mass spectrometry (DI-ESI–MS) for the analysis of complex metabolite mixtures, and (iii) data handling protocols to simultaneously analyze DI-ESI–MS and 1D 1H NMR spectral data using multiblock bilinear factorizations, namely multiblock principal component analysis (MB-PCA) and multiblock partial least squares (MB-PLS). Finally, we demonstrate the combined use of backscaled loadings, accurate mass measurements and tandem MS experiments to identify metabolites significantly contributing to class separation in MB-PLS-DA scores. We show that integration of NMR and DI-ESI–MS datasets yields a substantial improvement in the analysis of metabolome alterations induced by neurotoxin treatment.
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Acknowledgments
We would like to thank Dr. Jiantao Guo for providing us with the Escherichia coli Mach1 cell line. This manuscript was supported in part by funds from the National Institute of Health (R01 AI087668, R21 AI087561, R01 CA163649, P20 RR-17675, P30 GM103335), the University of Nebraska, the Nebraska Tobacco Settlement Biomedical Research Development Fund, and the Nebraska Research Council. The research was performed in facilities renovated with support from the National Institutes of Health (RR015468-01).
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Darrell D. Marshall, Shulei Lei and Bradley Worley have equally contributed to this study.
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Marshall, D.D., Lei, S., Worley, B. et al. Combining DI-ESI–MS and NMR datasets for metabolic profiling. Metabolomics 11, 391–402 (2015). https://doi.org/10.1007/s11306-014-0704-4
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DOI: https://doi.org/10.1007/s11306-014-0704-4