Dataset Information

Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR (Calibration Standard 700 MHz samples)

ABSTRACT:

Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism.

Calibration Standard 700 MHz samples protocols and data are reported in the current study MTBLS134.

Tomato 500 MHz samples protocols and data are reported in MTBLS131.

Tomato 700 MHz samples protocols and data are reported in MTBLS132.

Calibration Standard 500 MHz samples protocols and data are reported in MTBLS133.

INSTRUMENT(S): Bruker

SUBMITTER: Daniel Jacob

PROVIDER: MTBLS134 | MetaboLights | 2015-11-11

REPOSITORIES: MetaboLights

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Project description:Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism. Tomato 700 MHz samples protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS132' rel='noopener noreferrer' target='_blank'>MTBLS132</a>.Tomato 500 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS131' rel='noopener noreferrer' target='_blank'>MTBLS131</a>.Calibration Standard 500 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS133' rel='noopener noreferrer' target='_blank'>MTBLS133</a>.Calibration Standard 700 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS134' rel='noopener noreferrer' target='_blank'>MTBLS134</a>.

Project description:Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism. Calibration Standard 500 MHz samples protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS133' rel='noopener noreferrer' target='_blank'>MTBLS133</a>.Tomato 500 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS131' rel='noopener noreferrer' target='_blank'>MTBLS131</a>.Tomato 700 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS132' rel='noopener noreferrer' target='_blank'>MTBLS132</a>.Calibration Standard 700 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS134' rel='noopener noreferrer' target='_blank'>MTBLS134</a>.

Project description:Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism. Tomato 500 MHz samples protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS131' rel='noopener noreferrer' target='_blank'>MTBLS131</a>.Tomato 700 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS132' rel='noopener noreferrer' target='_blank'>MTBLS132</a>.Calibration Standard 500 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS133' rel='noopener noreferrer' target='_blank'>MTBLS133</a>.Calibration Standard 700 MHz samples protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS134' rel='noopener noreferrer' target='_blank'>MTBLS134</a>.

Project description:Background: With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. Results: As shown in this study, suboptimal conditions can have considerable impact on biologically relevant observations. For example, deviation from the optimal temperature by one degree Celsius lead to a loss of 44% of differentially expressed genes identified. While genes from thousands of Gene Ontology categories were affected, transcription factors and other low-copy-number regulators were disproportionately lost. Calibrated protocols are thus required in order to take full advantage of the large dynamic range of microarrays. For an objective optimization of protocols we introduce an approach that maximizes the amount of information obtained per experiment. A comparison of two typical samples is sufficient for this calibration. We ensure, however, that optimization results are independent of the samples and the specific measures used for calibration. Both simulations and spike-in experiments confirm an unbiased determination of generally optimal experimental conditions. Conclusions: Well calibrated hybridization conditions are thus easily achieved and necessary for the efficient detection of differential expression. They are essential for the sensitive profiling of low-copy-number molecules. This is particularly critical for studies of transcription factor expression, or the inference and study of regulatory networks. Supporting material, including source code and data, is available at http://bioinf.boku.ac.at/pub/optMA2010/. Optimization of hybridization temperature via an assessment of differential expression between two samples (male vs female Drosophila melanogaster) in 6 technical replicates (3 regular + 3 dye-swaps) for hybridizations at different temperatures (in two batches of 50, 52, 54, and 56; and 47, 49, 50, and 51 degree Celsius, with the repeated hybridization at 50 degree Celsius serving to demonstrate batch-to-batch stability).

			Action	DRS
	MTBLS134	Other
	FILES	Other
	a_MTBLS134_uf700_cs_metabolite_profiling_NMR_spectroscopy.txt	Txt
	i_Investigation.txt	Txt
	s_MTBLS134.txt	Txt

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Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR (Calibration Standard 700 MHz samples)

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