Research

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps

Peter Meinicke¹ , Thomas Lingner¹ , Alexander Kaever¹ , Kirstin Feussner² , Cornelia Göbel³ , Ivo Feussner³ , Petr Karlovsky⁴ and Burkhard Morgenstern¹

¹Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany

²Department of Developmental Biochemistry, Institute for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany

³Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany

⁴Molecular Phytopathology and Mycotoxin Research Unit, University of Göttingen, Göttingen, Germany

author email corresponding author email

Algorithms for Molecular Biology 2008, 3:9doi:10.1186/1748-7188-3-9

Published:	26 June 2008

Abstract

Background

One of the goals of global metabolomic analysis is to identify metabolic markers that are hidden within a large background of data originating from high-throughput analytical measurements. Metabolite-based clustering is an unsupervised approach for marker identification based on grouping similar concentration profiles of putative metabolites. A major problem of this approach is that in general there is no prior information about an adequate number of clusters.

Results

We present an approach for data mining on metabolite intensity profiles as obtained from mass spectrometry measurements. We propose one-dimensional self-organizing maps for metabolite-based clustering and visualization of marker candidates. In a case study on the wound response of Arabidopsis thaliana, based on metabolite profile intensities from eight different experimental conditions, we show how the clustering and visualization capabilities can be used to identify relevant groups of markers.

Conclusion

Our specialized realization of self-organizing maps is well-suitable to gain insight into complex pattern variation in a large set of metabolite profiles. In comparison to other methods our visualization approach facilitates the identification of interesting groups of metabolites by means of a convenient overview on relevant intensity patterns. In particular, the visualization effectively supports researchers in analyzing many putative clusters when the true number of biologically meaningful groups is unknown.