Open Access Methodology article

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data

Trung N Vu14*, Dirk Valkenborg25, Koen Smets1, Kim A Verwaest3, Roger Dommisse3, Filip Lemière3, Alain Verschoren1, Bart Goethals1 and Kris Laukens14

Author Affiliations

1 Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium

2 Vlaamse Instelling voor Technologisch Onderzoek (VITO), Mol, Belgium

3 Department of Chemistry, University of Antwerp, Antwerp, Belgium

4 Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp, Antwerp, Belgium

5 Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium

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BMC Bioinformatics 2011, 12:405  doi:10.1186/1471-2105-12-405

Published: 20 October 2011

Abstract

Background

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline.

Results

We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data.

Conclusions

The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/ webcite.