Chemometrics in Metabolomics — An Introduction

Trygg, Johan; Gullberg, Jonas; Johansson, Ann-Sofi; Jonsson, Pär; Moritz, Thomas

doi:10.1007/3-540-29782-0_9

Cited by 42 publications

(32 citation statements)

References 19 publications

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“…Chemometric strategies, such as PCA, help to circumvent the overwhelming size and complexity of metabolomic information (Eriksson et al, 2004). Multivariate techniques are routinely used to identify groupings, trends, and outliers within NMR data sets (Trygg et al, 2007). Our results show that variations in alkaloid profile were generally associated with relatively few detectable, but potentially important, differences in the steady-state levels of primary metabolites.…”

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confidence: 83%

Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy

et al. 2008

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Opium poppy (Papaver somniferum) produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a versatile model system to study plant alkaloid metabolism. The plant is widely cultivated as the only commercial source of the narcotic analgesics morphine and codeine. Variations in plant secondary metabolism as a result of genetic diversity are often associated with perturbations in other metabolic pathways. As part of a functional genomics platform, we used 1 H nuclear magnetic resonance (NMR) metabolite profiling for the analysis of primary and secondary metabolism in opium poppy. Aqueous and chloroform extracts of six different opium poppy cultivars were subjected to chemometric analysis. Principle component analysis of the 1 H NMR spectra for latex extracts clearly distinguished two varieties, including a low-alkaloid variety and a high-thebaine, low-morphine cultivar. Distinction was also made between pharmaceutical-grade opium poppy cultivars and a condiment variety. Such phenotypic differences were not observed in root extracts. Loading plots confirmed that morphinan alkaloids contributed predominantly to the variance in latex extracts. Quantification of 34 root and 21 latex metabolites, performed using Chenomx NMR Suite version 4.6, showed major differences in the accumulation of specific alkaloids in the latex of the low-alkaloid and high-thebaine, low-morphine varieties. Relatively few differences were found in the levels of other metabolites, indicating that the variation was specific for alkaloid metabolism. Exceptions in the lowalkaloid cultivar included an increased accumulation of the alkaloid precursor tyramine and reduced levels of sucrose, some amino acids, and malate. Real-time polymerase chain reaction analysis of 42 genes involved in primary and secondary metabolism showed differential gene expression mainly associated with alkaloid biosynthesis. Reduced alkaloid levels in the condiment variety were associated with the reduced abundance of transcripts encoding several alkaloid biosynthetic enzymes.

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confidence: 83%

Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy

et al. 2008

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“…These are exploratory/informative, classification/discrimination and regression/prediction [16,38,41]. While informative analyses are focused on identification and quantification to obtain sample intrinsic information (such as the development of metabolite databases and the discovery of biomarkers), discriminative analyses are majorly aimed at finding differences between samples/treatments [16,42].…”

Section: Data Analysis and Treatmentmentioning

confidence: 99%

Food Metabolomics: A New Frontier in Food Analysis and its Application to Understanding Fermented Foods

Adebo¹,

Njobeh²,

AdeyinkaAdebiyi³

et al. 2017

Functional Food - Improve Health Through Adequate Food

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The emergence of food metabolomics, otherwise known as foodomics, has opened new frontiers and possibilities for scientists to characterize and simultaneously determine and obtain the comprehensive profile of the food metabolome. Qualitative and quantitative determinations of this metabolome offer insights into the underlying processes involved and details about the content of the food analytes. This had seemed technically challenging and impossible over time, but can now be done due to the advent of sophisticated analytical equipment and chemometric tools. The application of this technique offers enormous opportunities to obtain detailed information that can be correlated to various properties, functionalities and potentials in fermented foods. This chapter thus evaluated and documented studies presented in the literature on the food metabolomics study of fermented foods, with a view of appraising its prospects, applications and subsequent utilization in the study of fermented foods.

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“…Fingerprinting circumvents problems associated with peak assignment and instead relies on multivariate analysis to discriminate between sample sets. The most common approach involves subdividing one-dimensional (1D) 1 H NMR spectra for different samples into multiple regions or 'bins' (Trygg et al 2007). This method of data reduction assumes that minor peak shifts and line width differences for the same compound can be accounted for across samples by considering spectral regions, as opposed to individual data points.…”

Section: Nmrmentioning

confidence: 99%

“…Chemometrics and pattern recognition methods have been extensively reviewed (Trygg et al 2007;Eriksson et al 2004;Lavine and Workman 2004;Holmes and Antii 2002). The most common multivariate technique is principle component analysis (PCA), which is used to extract and display systematic variation within a dataset.…”

Section: Metabolomics Workflow and Data Analysismentioning

confidence: 99%

Plant metabolomics: analytical platforms and integration with functional genomics

Hagel

Facchini

2007

Phytochem Rev

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As the final downstream product of the genome, the plant metabolome is a highly complex, dynamic assortment of primary and secondary compounds. Although technological platforms to study genomes, transcriptomes and even proteomes are presently available, methods to pursue genuine metabolomics have not yet been developed due to the extensive chemical diversity of plant primary and secondary metabolites. No single analytical method can accurately survey the entire metabolome. However, recent technical, chemometric and bioinformatic advances promise to enhance our global understanding of plant metabolism. Separation-based mass spectrometry (MS) approaches, such as gas (GC) or liquid chromatography (LC)-MS, are relatively inexpensive, highly sensitive and provide excellent identifying capacity. However, Fourier transform-ion cyclotron resonance (FT-ICR)-MS is better suited for rapid, high-throughput applications and is currently the most sensitive method available. Unlike MS-based analyses, nuclear magnetic resonance (NMR) spectroscopy provides a large amount of information regarding molecular structure, and novel software innovations have facilitated the unequivocal identification and absolute quantification of compounds within composite samples. Due to the size and complexity of metabolomics datasets, numerous chemometric methods are used to extract and display systematic variation. Coupled with pattern recognition techniques and plant-specific metabolite databases, broad-scope metabolite analyses have emerged as functional genomics tools for novel gene discovery and functional characterization. In this review, key metabolomics technologies are compared and the applications of FT-ICR-MS and NMR to the study of benzylisoquinoline alkaloid metabolism in opium poppy are discussed. AbbreviationsAPCI Atmospheric pressure chemical ionization BL Batch-learning CE Capillary electrophoresis CAS Chemical Abstract Service CID Collision induced dissociation DIMS Direct injection mass spectrometry ESI Electrospray ionization EST Expressed sequence tag FID Free induction decay J. M. Hagel is the recipient of an Alberta Ingenuity Graduate Student Scholarship. P. J. Facchini holds the Canada Research Chair in Plant Metabolic Processes Biotechnology.

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Chemometrics in Metabolomics — An Introduction

Cited by 42 publications

References 19 publications

Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy

Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy

Food Metabolomics: A New Frontier in Food Analysis and its Application to Understanding Fermented Foods

Plant metabolomics: analytical platforms and integration with functional genomics

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