Dataset Information

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

ABSTRACT:

Introduction

Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.

Objectives

The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.

Methods

NMRProcFlow was developed to be a graphical and interactive 1D NMR (¹H & ¹³C) spectra processing tool.

Results

NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.

Conclusion

Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.

SUBMITTER: Jacob D

PROVIDER: S-EPMC5313591 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Publications

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

Jacob D D Deborde C C Lefebvre M M Maucourt M M Moing A A

Metabolomics : Official journal of the Metabolomic Society 20170217 4

<h4>Introduction</h4>Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.<h4>Objectives</h4>The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.<h4>Methods</h4>NMRProcFlow was developed to be a graphical and interactive 1D NMR (<sup>1</sup>H & <sup>13</sup>C) spectra processing tool.<h4>Results</h4>NMRProcFlow (http://nmrprocflow.org), dedicated to met ...[more]

PMID: 28261014

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Project description:INTRODUCTION:Proton nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomic profiling has a range of applications in plant sciences. OBJECTIVES:The aim of the present work is to provide advice for minimizing uncontrolled variability in plant sample preparation before and during NMR metabolomic profiling, taking into account sample composition, including its specificity in terms of pH and paramagnetic ion concentrations, and NMR spectrometer performances. METHODS:An automation of spectrometer preparation routine standardization before NMR acquisition campaign was implemented and tested on three plant sample sets (extracts of durum wheat spikelet, Arabidopsis leaf and root, and flax leaf, root and stem). We performed 1H-NMR spectroscopy in three different sites on the wheat sample set utilizing instruments from two manufacturers with different probes and magnetic field strengths. The three collections of spectra were processed separately with the NMRProcFlow web tool using intelligent bucketing, and the resulting buckets were subjected to multivariate analysis. RESULTS:Comparability of large- (Arabidopsis) and medium-size (flax) datasets measured at 600 MHz and from the wheat sample set recorded at the three sites (400, 500 and 600 MHz) was exceptionally good in terms of spectral quality. The coefficient of variation of the full width at half maximum (FWHM) and the signal-to-noise ratio (S/N) of two selected peaks was comprised between 5 and 10% depending on the size of sample set and the spectrometer field. EDTA addition improved citrate and malate resonance patterns for wheat sample sets. A collection of 22 samples of wheat spikelet extracts was used as a proof of concept and showed that the data collected at the three sites on instruments of different field strengths and manufacturers yielded the same discrimination pattern of the biological groups. CONCLUSION:Standardization or automation of several steps from extract preparation to data reduction improves data quality for small to large collections of plant samples of different origins.

Dataset Information

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

Introduction

Objectives

Methods

Results

Conclusion

Publications

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

Similar Datasets

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