Dataset Information

PJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.

ABSTRACT:

Motivation

Data processing is a key bottleneck for 1H NMR-based metabolic profiling of complex biological mixtures, such as biofluids. These spectra typically contain several thousands of signals, corresponding to possibly few hundreds of metabolites. A number of binning-based methods have been proposed to reduce the dimensionality of 1 D 1H NMR datasets, including statistical recoupling of variables (SRV). Here, we introduce a new binning method, named JBA ("pJRES Binning Algorithm"), which aims to extend the applicability of SRV to pJRES spectra.

Results

The performance of JBA is comprehensively evaluated using 617 plasma 1H NMR spectra from the FGENTCARD cohort. The results presented here show that JBA exhibits higher sensitivity than SRV to detect peaks from low-abundance metabolites. In addition, JBA allows a more efficient removal of spectral variables corresponding to pure electronic noise, and this has a positive impact on multivariate model building.

Availability and implementation

The algorithm is implemented using the MWASTools R/Bioconductor package.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Rodriguez-Martinez A

PROVIDER: S-EPMC6546129 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Publications

pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.

Rodriguez-Martinez Andrea A Ayala Rafael R Posma Joram M JM Harvey Nikita N Jiménez Beatriz B Sonomura Kazuhiro K Sato Taka-Aki TA Matsuda Fumihiko F Zalloua Pierre P Gauguier Dominique D Nicholson Jeremy K JK Dumas Marc-Emmanuel ME

Bioinformatics (Oxford, England) 20190601 11

<h4>Motivation</h4>Data processing is a key bottleneck for 1H NMR-based metabolic profiling of complex biological mixtures, such as biofluids. These spectra typically contain several thousands of signals, corresponding to possibly few hundreds of metabolites. A number of binning-based methods have been proposed to reduce the dimensionality of 1 D 1H NMR datasets, including statistical recoupling of variables (SRV). Here, we introduce a new binning method, named JBA ("pJRES Binning Algorithm"), w ...[more]

PMID: 30351417

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