« February 2017 »


A metabolomics study frequently involves the comparative analysis of metabolic pathways from a normal state and a perturbed state, where the perturbation can be of any nature, such as genetic knockout, administration of a drug, change in diet or general changes in the environmental conditions of a living system. The Metabolomic analysis is aimed at the comprehensive and quantitative analysis of all metabolites of a biological system, and necessarily includes novel strategies for compound identification and bioinformatic data mining.
The technology platform established at the Core Faciliy Metabolomics includes direct introduction or in-line chromatographic separation techniques, different mass spectrometric ionization modes and mass analyzers, and thereby provides powerful tools to assess molecular changes in the metabolome. The Core Facility Metabolomics focuses on analytical data generation using diverse metabolomic methodologies including fingerprinting, nontargeted, and targeted approaches, metabolic profiling and metabolic flux analysis, especially with stable isotope ratio mass spectrometry. Extensive experience has been developed by application of these methodologies to different scientific projects with collaboration partners at Freiburg University.

The Core Facility Metabolomics offers a wide range of analytical techniques for the analysis of primary and secondary metabolites. Our aim is to investigate metabolic pathways and their function within physiological networks. As central technologies, we use mass spectrometry and nuclear magnetic resonance (NMR). The technology platform available directly at the ZBSA offers all major mass spectrometric techniques, including electrospray (ESI) and electron impact (EI) ionization methods. For analysis of plant secondary metabolites, we employ gas chromatography coupled to EI mass spectrometry (GC-EI-MS). For polar, high molecular and non-volatile compounds, we mainly use liquid chromatography coupled to tandem mass spectrometry (LC-ESI-MS/MS). A focus of the Core Facility is on metabolite profiling, which is developed further towards metabolic flux analysis. In addition, it is possible to determine natural abundances of stabile isotopes (d13C, d15N, d18O, d2H) by isotope ratio mass spectrometry (IRMS).

Besides questions on endogenous metabolism, we are interested in the metabolism of xenobiotica, e.g. pharmaceuticals or toxicologically relevant contaminants.

Furthermore, individual key metabolites can be structurally elucidated by LC-ESI-QqTOF systems with enhanced mass accuracy, as well as ion trap systems with their MSn function. Several metabolomics databases are available for structure assignment to unknown metabolites.

Another mass spectrometry system belonging to the technology platform of the ZBSA is the orbitrap. Because of its high mass accuracy, it is used for determining the sum formula – and thus elemental composition - of unknown metabolites.

In close collaboration with different research groups, we develop individual analytical solutions for current research questions.







Center for Biological Systems Analysis

University of Freiburg


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    Habsburgerstr. 49
    79104 Freiburg
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