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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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Displaying results 1 to 2 of 2.

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.
Publications

Brack, W.; Altenburger, R.; Schüürmann, G.; Krauss, M.; López Herráez, D.; van Gils, J.; Slobodnik, J.; Munthe, J.; Gawlik, B. M.; van Wezel, A.; Schriks, M.; Hollender, J.; Tollefsen, K. E.; Mekenyan, O.; Dimitrov, S.; Bunke, D.; Cousins, I.; Posthuma, L.; van den Brink, P. J.; López de Alda, M.; Barceló, D.; Faust, M.; Kortenkamp, A.; Scrimshaw, M.; Ignatova, S.; Engelen, G.; Massmann, G.; Lemkine, G.; Teodorovic, I.; Walz, K.-H.; Dulio, V.; Jonker, M. T.O.; Jäger, F.; Chipman, K.; Falciani, F.; Liska, I.; Rooke, D.; Zhang, X.; Hollert, H.; Vrana, B.; Hilscherova, K.; Kramer, K.; Neumann, S.; Hammerbacher, R.; Backhaus, T.; Mack, J.; Segner, H.; Escher, B.; de Aragão Umbuzeiro, G. The SOLUTIONS project: Challenges and responses for present and future emerging pollutants in land and water resources management Science total Environ 503-504, 22-31, (2015) DOI: 10.1016/j.scitotenv.2014.05.143

SOLUTIONS (2013 to 2018) is a European Union Seventh Framework Programme Project (EU-FP7). The project aims to deliver a conceptual framework to support the evidence-based development of environmental policies with regard to water quality. SOLUTIONS will develop the tools for the identification, prioritisation and assessment of those water contaminants that may pose a risk to ecosystems and human health. To this end, a new generation of chemical and effect-based monitoring tools is developed and integrated with a full set of exposure, effect and risk assessment models. SOLUTIONS attempts to address legacy, present and future contamination by integrating monitoring and modelling based approaches with scenarios on future developments in society, economy and technology and thus in contamination. The project follows a solutions-oriented approach by addressing major problems of water and chemicals management and by assessing abatement options. SOLUTIONS takes advantage of the access to the infrastructure necessary to investigate the large basins of the Danube and Rhine as well as relevant Mediterranean basins as case studies, and puts major efforts on stakeholder dialogue and support. Particularly, the EU Water Framework Directive (WFD) Common Implementation Strategy (CIS) working groups, International River Commissions, and water works associations are directly supported with consistent guidance for the early detection, identification, prioritisation, and abatement of chemicals in the water cycle. SOLUTIONS will give a specific emphasis on concepts and tools for the impact and risk assessment of complex mixtures of emerging pollutants, their metabolites and transformation products. Analytical and effect-based screening tools will be applied together with ecological assessment tools for the identification of toxicants and their impacts. The SOLUTIONS approach is expected to provide transparent and evidence-based candidates or River Basin Specific Pollutants in the case study basins and to assist future review of priority pollutants under the WFD as well as potential abatement options.

This page was last modified on 24.10.2018.

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