Omics platforms - Metabolomic Profiler

Short description:

Omics platforms - Metabolomic Profiling The platform has been designed to perform qualitative and quantitave metabolome analysis based on mass spectrometry. The platform allows global metabolic profiling based on LC and GC preseparation and detection and identification of metabolites by subsequent mass spectrometry. The high resolution instruments support verified identification of endogenous and exogenous chemicals in connection with existing and in-house spectra databases. These global analyses provide relative quantification and in targeted approaches also absolute quantification can be obtained in highly specified assays (prostaglandins or CoA-esters) and also in broader applications (serum metabolome profiling). The preprocessing for metabolite extraction is established for passive sampling of VOCs, eukaryotic body fluids, tissue, cellular models, and bacterials samples.

Major research issues/sites:

In respect to human health we focus on deciphering the effects of contaminants on the liver, immune, and respiratory system and model organisms. Of specific interest are the consequences of contaminants on the endogenous metabolome of very young children and the correlation of atopic diseases to the endogenous metabolism. The platform allows the global analysis of tissues and cellular models after exposition in terms of the transformation of the contaminants and the endogenous metabolome. Selected metabolites e.g. of the central carbon and nitrogen metabolism can be absolutely quantified by targeted analysis.

In respect to microbial ecology and biodegradation a focus lies on the targeted analysis of key transformation products of contaminants or key endogenous metabolites. Furthermore the functional analysis is supported by detecting the carbon and nitrogen flux in tissue and cellular eukaryotic and prokaryotic models.

5 exemplary references:

Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013 Mar 1;339(6123):1084-8.

Herberth G, Bauer M, Gasch M, Hinz D, Röder S, Olek S, Kohajda T, Rolle-Kampczyk U, von Bergen M, Sack U, Borte M, Lehmann I; Lifestyle and Environmental Factors and Their Influence on Newborns Allergy Risk study group. Maternal and cord blood miR-223 expression associates with prenatal tobacco smoke Exposure and low regulatory T-cell numbers. J Allergy Clin Immunol. 2014 Feb;133(2):543-50.

Oberbach A, Blüher M, Wirth H, Till H, Kovacs P, Kullnick Y, Schlichting N, Tomm JM, Rolle-Kampczyk U, Murugaiyan J, Binder H, Dietrich A, von Bergen M. Combined proteomic and metabolomic profiling of serum reveals association of the  complement system with obesity and identifies novel markers of body fat mass changes. J Proteome Res. 2011 Oct 7;10(10):4769-88.

Kung JW, Baumann S, von Bergen M, Müller M, Hagedoorn PL, Hagen WR, Boll M. Reversible biological Birch reduction at an extremely low redox potential. J Am Chem Soc. 2010 Jul 21;132(28):9850-6.

Kuntze K, Kiefer P, Baumann S, Seifert J, von Bergen M, Vorholt JA, Boll M. Enzymes involved in the anaerobic degradation of meta-substituted halobenzoates. Mol Microbiol. 2011 Nov;82(3):758-69.

Short technical description:


  • LTQ-Orbitrap Velos: Mass accuracy <1ppm, mass range m/z 50-2000, m/z 200-4000, Max. Resolution >100.000; 60,000 at m/z 400 at a scan rate of 1 Hz, Multiple fragmentation techniques: CID, HCD, ETD
  • Orbitrap XL
  • GC/LC-QToF-MS: Mass accuracy <3ppm, mass range m/z 50-2000, m/z 200-4000, Max. Resolution >60.000, comprehensive metabolite databases for metabolite identification
  • 4xQTrap-MS: Fast polarity switching (50ms), Scan speeds up to 20,000 Da/sec, MS/MS and MS³ applications possible, 100 x gain in sensitivity in ion trap scan modes (LINAC collision cell)
  • GCxGC-ToF-MS: Spectral collection rates up to 500spectra/second (500 Hz), Comprehensive Two-Dimensional GC (GCxGC), True Signal Deconvolution
  • GC-MS/MS: MRM speed at 500 transitions per second with a minimum dwell time of 1 msec, hyperbolic quadrupole enhances performance up to 1050 amu
  • 3xGC-MS

Specific features/uniqueness:

Coverage of state-of-the-art metabolomics platform for untargeted as well as targeted metabolite screening and quantification.

Options and conditions for visiting scientists:

Need to be discussed, depending on joint research interest or projects.

Unit Cost of use and principles of costing:

No general cost calculation possible. Cost are depending on several aspects and have to be calculated specifically considering e.g.:

  • Complexity of sample preparation / use or necessity of consumables, e.g. spin- or SPE-columns, detergents, reagents
  • Costs for analyses, e.g. chemicals, kits, solvents, internal standards
  • Method dependent run times range from few minutes to several hours per sample

centre running the infrastructure:

UFZ - Helmholtz Centre for Environmental Research

type of facility:

Laboratory / high-end instrument


  • UFZ - Helmholtz Centre for Environmental Research
  • Phone: +49 341 235-0