Metabolomics

Nowadays, gene discovery has been made very efficient with the combination of deep sequencing and the exploitation of natural variation. Just in Arabidopsis, hundreds of genetic loci have been identified as influencing a wide variety of processes, and we aim to go from gene-of-interest to characterized protein product using approaches to “take a picture” of the comprehensive metabolome of the plant.

The IPB is currently operating a wide range of NMR and mass spectrometry instruments for metabolomics across all four departments, which are integrated into our Metabolomics Platform.

The experimental work is complemented by extensive Cheminformatics and Bioinformatics research to process and interpret the huge amounts of data. The IPB is operating the first European MassBank server, and hosts several online tools for metabolite identification.

Contact partner for all interests concerning the metabolomics platform is Dr. Steffen Neumann.

Publications by Tag: Metabolomics

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Journal / Publisher: BMC Bioinformatics Journal / Publisher: Mol Cell Proteomics

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Publications

Moreno, P.; Beisken, S.; Harsha, B.; Muthukrishnan, V.; Tudose, I.; Dekker, A.; Dornfeldt, S.; Taruttis, F.; Grosse, I.; Hastings, J.; Neumann, S.; Steinbeck, C. BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology BMC Bioinformatics 16, 56, (2015) DOI: 10.1186/s12859-015-0486-3

Background: Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein setsannotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.Results: We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.Conclusions: BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.