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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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Books and chapters

Neumann, S., Rasche, F., Wolf, S. & Böcker, S. Metabolite Identification and Computational Mass Spectrometry.. In: The Handbook of Plant Metabolomics, Metabolite Profiling and Networking. (Weckwerth, W. & Kahl, G.). Wiley-VCH 289-303, (2013) ISBN: 978-3-527-32777-5 DOI: 10.1002/9783527669882.ch16

Previous chapters have introduced protocols and examples for high-throughput metabolomics experiments. Metabolite identification is an important step in these experiments, bridging the metabolomics experiment, metabolite profiling, and the biological interpretation of the results. The elemental composition of the individual metabolites is the most basic information that can be calculated already from the mass spectrometry (MS) profiling data. For a more thorough identification, the “interesting” peaks are subjected to MS2, or even higher-order MSn measurements. Such spectra carry rich structural hints, revealing building blocks of the unknown compound, or allowing comparison with databases of reference spectra. This chapter describes a general strategy to identify metabolites, and proceeds through the steps of the identification for two example compounds, first calculating elemental compositions, performing in silico identification without reference spectra, and finally spectral library lookup.

This page was last modified on 10.03.2014.

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