speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

PLoS Computational Biology
Charlie BeirnaertKris Laukens

Abstract

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated da...Continue Reading

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Citations

Apr 13, 2019·Bioinformatics·Gaëlle LefortRémi Servien
Nov 18, 2018·Electrophoresis·Biswapriya B Misra, Subhashree Mohapatra
Apr 22, 2020·Phytochemical Analysis : PCA·François N MirosPaul R Shipley
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Jan 9, 2021·Journal of Proteome Research·Matthias S Klein
Jan 27, 2021·Analytical Chemistry·Gaëlle LefortRémi Servien
Jan 29, 2021·Comprehensive Reviews in Food Science and Food Safety·Pavel A SolovyevFederica Camin
Jul 30, 2021·Nature Protocols·Benjamin J BlaiseTimothy M D Ebbels
Aug 7, 2021·Metabolites·Ulla T SchultheissHelena U Zacharias
Nov 13, 2020·Analytical Chemistry·Arthur S EdisonSicong Zhang

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Methods Mentioned

BETA
NMR
PCA

Software Mentioned

MassSpecWavelet
MassSpecWavelet R package
speaq package
Bioconductor
speaq
corrplot R package
XCMS
muma
Github
MetaboAnalyst

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