Open Access Research article

Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset

Chris Bauer1*, Frank Kleinjung1, Celia J Smith4, Mark W Towers4, Ali Tiss4, Alexandra Chadt2, Tanja Dreja2, Dieter Beule1, Hadi Al-Hasani2, Knut Reinert3, Johannes Schuchhardt1 and Rainer Cramer4

Author Affiliations

1 MicroDiscovery GmbH, Marienburger Str. 1, 10405 Berlin, Germany

2 Department of Pharmacology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany

3 Department Computer Science and Mathematics, Free University of Berlin, Berlin, Germany

4 Department of Chemistry and The BioCentre, The University of Reading, Whiteknights, Reading, RG6 6AS, UK

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BMC Bioinformatics 2011, 12:140  doi:10.1186/1471-2105-12-140

Published: 9 May 2011



Diabetes like many diseases and biological processes is not mono-causal. On the one hand multi-factorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics.


We present a comprehensive work-flow tailored for analyzing complex data including data from multi-factorial studies. The developed approach aims at revealing effects caused by a distinct combination of experimental factors, in our case genotype and diet. Applying the developed work-flow to the analysis of an established polygenic mouse model for diet-induced type 2 diabetes, we found peptides with significant fold changes exclusively for the combination of a particular strain and diet. Exploitation of redundancy enables the visualization of peptide correlation and provides a natural way of feature selection for classification and prediction. Classification based on the features selected using our approach performs similar to classifications based on more complex feature selection methods.


The combination of ANOVA and redundancy exploitation allows for identification of biomarker candidates in multi-dimensional MALDI-TOF MS profiling studies with complex experimental design. With respect to feature selection our method provides a fast and intuitive alternative to global optimization strategies with comparable performance. The method is implemented in R and the scripts are available by contacting the corresponding author.