Bioanalytic Core Facility

Mass Spectrometry Laboratory

The Mass Spectrometry Laboratory at the Bioanalytical Core Facility of the CBBM supports research groups by providing metabolomic and lipidomics analyses.

Services | Instruments | Publications

Metobolomics and Lipidomics Services

The Mass Spectrometry Laboratory offers metabolomics and lipidomics research services including

  • LC/MS method development
  • Qualitative and quantitative analysis of small molecules or drugs in biological samples
  • Sample preparation (e.g. homogenization, extraction)
  • Omics data analysis and help with the experimental design for omics studies.

Range of metabolites covered (by established methods or methods in development)

  • Targeted analysis:
    Advanced glycation end-products
    Sphingoid bases and sphingosine 1 phosphate
  • Untargeted and semi-targeted anaylsis
    Metabolomics: metabolites covering glycolysis, TCA cycle, pentose phosphate pathway, amino acids, nucleotides and vitamin and cofactor metabolism
    Lipidomics: metabolites covering sphingolipid, phospholipid, cholesterol and triglyceride metabolism

For new method development projects, the mass spectrometry committee has to approve the project funding and secure that number of sample that will cover the cost of method development. Standard prices as stated in the user guidelines are € 40,-/sample for targeted analyses and € 80,-/sample for untargeted analyses, e.g. Lipidomics and Metabolomics screens. 


The lab is equipped with two state-of-the art liquid chromatography–mass spectrometry (LC/MS) systems to cover both the targeted and untargeted metabolomics research questions

  • Triple Quad: Thermo TSQ Endura
  • LC system 1: Dionex Ultimate 3000 RS with a Dionex degasser, auto-sampler and column oven
  • Q-Orbitrap: Thermo Q-Exactive
  • LC system 2: Dionex Ultimate 3000 SD with a Dionex degasser, auto-sampler and column oven
  • Liquid handling devices, ultrasonic bath, heating oven, sample concentrator with gas chamber, lyophilisator and medium-throughput tissue homogenization device.


  • Aherrahrou R, Kulle AE, Alenina N, Werner R, Vens-Cappell S, Bader M, Schunkert H, Erdmann J, Aherrahrou Z (2020) CYP17A1 deficient XY mice display susceptibility to atherosclerosis, altered lipidomic profile and atypical sex development. Sci Rep 10:8792.
  • Dogbevia G, Grasshoff H, Othman A, Penno A, Schwaninger M (2020) Brain endothelial specific gene therapy improves experimental Sandhoff disease. J Cereb Blood Flow Metab 40:1338-1350.
  • Folberth J, Begemann K, Jöhren O, Schwaninger M, Othman A (2020) MS(2) and LC libraries for untargeted metabolomics: Enhancing method development and identification confidence. J Chromatogr B Analyt Technol Biomed Life Sci 1145:122105.
  • Hirose M, Schilf P, Gupta Y, Zarse K, Künstner A, Fähnrich A, Busch H, Yin J, Wright MN, Ziegler A, Vallier M, Belheouane M, Baines JF, Tautz D, Johann K, Oelkrug R, Mittag J, Lehnert H, Othman A, Jöhren O, Schwaninger M, Prehn C, Adamski J, Shima K, Rupp J, Häsler R, Fuellen G, Köhling R, Ristow M, Ibrahim SM (2018) Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice. Sci Rep 8:5872.
  • Khan MA, Schultz S, Othman A, Fleming T, Lebrón-Galán R, Rades D, Clemente D, Nawroth PP, Schwaninger M (2016) Hyperglycemia in Stroke Impairs Polarization of Monocytes/Macrophages to a Protective Noninflammatory Cell Type. J Neurosci 36:9313-9325.
  • Rawish E, Nickel L, Schuster F, Stölting I, Frydrychowicz A, Saar K, Hübner N, Othman A, Kuerschner L, Raasch W (2020) Telmisartan prevents development of obesity and normalizes hypothalamic lipid droplets. J Endocrinol 244:95-110.