Analysis of time course ¹H NMR metabolomics data by multivariate curve resolution

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Journal titleMagnetic Resonance in Chemistry
Subjecttime course metabolomics; multivariate curve resolution; embryogenesis; nephrotoxicity
AbstractModeling NMR-based metabolomics data often involves linear methods such as principal component analysis (PCA) and partial least squares (PLS). These methods have the objective of describing the main variance in the data and maximum covariance between the predictor variables and some response variable respectively. If the experiment is designed to investigate temporal biological fluctuations, however, the factors obtained become difficult to interpret in a biological context. Moreover, when these methods are applied to analyze data, an implicit assumption is made that the measurement errors exhibit an iid-normal distribution, often limiting the extent of the information recovered. A method for the linear decomposition of NMR-based metabolomics data by multivariate curve resolution (MCR), which has been used elsewhere for time course transcriptomics applications, is introduced and implemented via a weighted alternating least squares (ALS) approach. Measurement of error information is incorporated in the modeling process, allowing the least squares projections to be performed in a maximum likelihood fashion. As a result, noise heteroscedasticity resulting from pH-induced peak shifts can be modeled, eliminating the need for binning/bucketing. The utility of the method is demonstrated using two sets of temporal NMR metabolomics data, HgCl2-induced nephrotoxicity in rat, and fish (Japanese medaka, Oryzias latipes) embryogenesis. Profiles extracted for the nephrotoxicity data exhibit strong correlations with metabolites consistent with temporal fluctuations in glucosuria. The concentration of metabolites such as acetate, glucose, and alanine exhibit a steady increase, which peaks at Day 3 post dose and returns to basal levels at Day 8. Other metabolites including citrate and 2-oxoglutarate exhibit the opposite characteristics. Although the fish embryogenesis data are more complex, the profiles extracted by the algorithm display characteristics that depict temporal variation consistent with processes associated with embryogenesis.
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AffiliationNational Research Council Canada; NRC Institute for Marine Biosciences
Peer reviewedYes
NRC number42811
NPARC number21268310
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Record identifierc727ebee-0760-4514-907f-f4f1a33072a3
Record created2013-06-19
Record modified2016-05-09
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