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BMC Bioinformatics

, 12:366

Proteomics

Abstract

BackgroundDespite wide-spread use of Nuclear Magnetic Resonance NMR in metabolomics for the analysis of biological samples there is a lack of graphically driven, publicly available software to process large one and two-dimensional NMR data sets for statistical analysis.

ResultsHere we present MetaboLab, a MATLAB based software package that facilitates NMR data processing by providing automated algorithms for processing series of spectra in a reproducible fashion. A graphical user interface provides easy access to all steps of data processing via a script builder to generate MATLAB scripts, providing an option to alter code manually. The analysis of two-dimensional spectra H,C-HSQC spectra is facilitated by the use of a spectral library derived from publicly available databases which can be extended readily. The software allows to display specific metabolites in small regions of interest where signals can be picked. To facilitate the analysis of series of two-dimensional spectra, different spectra can be overlaid and assignments can be transferred between spectra. The software includes mechanisms to account for overlapping signals by highlighting neighboring and ambiguous assignments.

ConclusionsThe MetaboLab software is an integrated software package for NMR data processing and analysis, closely linked to the previously developed NMRLab software. It includes tools for batch processing and gives access to a wealth of algorithms available in the MATLAB framework. Algorithms within MetaboLab help to optimize the flow of metabolomics data preparation for statistical analysis. The combination of an intuitive graphical user interface along with advanced data processing algorithms facilitates the use of MetaboLab in a broader metabolomics context.

List of abbreviations used1Done dimensional

2Dtwo dimensional

CHCl3Chloroform

DSSDimethylsilapentanesulfonate

FIDfree induction decay

gloggeneralised logarithm transformation

HSQCheteronuclear single quantum coherence

MeOHMethanol

NMRnuclear magnetic resonance

NOESYNuclear Overhauser spectroscopy

PCAprincipal component analysis

PLS-DApartial least squares discriminant analysis

presatpresaturation of the solvent resonance

SEMSine and exponential multiplication

TMSTetrasilylmethane

TMSPSodium Trimethylsilyl-propionate.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-12-366 contains supplementary material, which is available to authorized users.

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Autor: Christian Ludwig - Ulrich L Günther

Fuente: https://link.springer.com/







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