Bioanalytic Core Facility


Mass Spectrometry Laboratory

Services | Instruments | Publications

The Mass Spectrometry Laboratory at the Bioanalytical Core Facility of the CBBM supports research groups by providing LC-MS/MS analysis for targeted or untargeted approaches.


LC-MS/MS (Liquid chromatography coupled to tandem mass spectrometry) is a versatile, state-of-the-art technique to identify and quantify a variety of different compounds. High-confidence identification is based on the exact molecular mass and a specific fragmentation pattern determined by MS/MS. Prior separation via LC adds the retention time as additional factor for identification and reduces sample complexity. LC-MS/MS is not only the method of choice for untargeted analysis, but also for the targeted analysis of specific metabolites or drugs.


Metobolomics and Lipidomics Services (untargeted analysis)

The Mass Spectrometry Laboratory offers metabolomics and lipidomics research services including

  • Sample preparation (e.g. homogenization, extraction)
  • Qualitative and semi-quantitative analysis of small molecules or lipids in biological samples
  • Omics data analysis and help with the experimental design for omics studies.

Range of metabolites covered (by established methods):

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


Targeted Analysis Services

The Mass Spectrometry Laboratory offers targeted analysis of specific compounds including

  • LC-MS/MS method development for compound(s) of interest
  • Samples preparation (e.g. homogenization, extraction)
  • Qualitative and quantitative analysis of biological samples
  • Data analysis and help with the experimental design

Range of metabolites covered (by established methods or methods in development):
α-Dicarbonyls, Advanced glycation end-products, Monomethylfumarate, D-/L-2-Hydroxyglutarate



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 Quadrupole: Thermo TSQ Endura
  • LC system 1: Dionex Ultimate 3000 RS with a Dionex degasser, auto-sampler and column oven
  • Quadrupole-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


  • Begemann K, Heyde I, Witt P, Inderhees J, Leinweber B, Koch CE, Jöhren O, Oelkrug R, Liskiewicz A, Muller TD, Oster H (2023) Rest phase snacking increases energy resorption and weight gain in male mice. Mol Metab:101691.
  • Filipovic D, Inderhees J, Korda A, Tadic P, Schwaninger M, Inta D, Borgwardt S (2023) Metabolic Fingerprints of Effective Fluoxetine Treatment in the Prefrontal Cortex of Chronically Socially Isolated Rats: Marker Candidates and Predictive Metabolites. Int J Mol Sci 24.
  • Oelkrug R, Harder L, Pedaran M, Hoffmann A, Kolms B, Inderhees J, Gachkar S, Resch J, Johann K, Jöhren O, Krause K, Mittag J (2023) Maternal thyroid hormone receptor beta activation in mice sparks brown fat thermogenesis in the offspring. Nat Commun 14:6742.
  • Rhein S, Inderhees J, Herrmann O, Othman A, Begemann K, Fleming T, Nawroth PP, Klika KD, Isa R, Konig IR, Royl G, Schwaninger M (2023) Glyoxal in hyperglycaemic ischemic stroke - a cohort study. Cardiovasc Diabetol 22:173.
  • Boch K, Sharma A, Folberth J, Zillikens D, Schmidt E, Bieber K, Schwaninger M, Ludwig RJ, Dempfle A (2022) Distinct Metabolite Profile in Pemphigus Vulgaris. J Invest Dermatol 142:3327-3331 e3321.
  • Nickel L, Sunderhauf A, Rawish E, Stölting I, Derer S, Thorns C, Matschl U, Othman A, Sina C, Raasch W (2022) The AT1 Receptor Blocker Telmisartan Reduces Intestinal Mucus Thickness in Obese Mice. Front Pharmacol 13:815353.
  • Stephan D, Taege N, Dore R, Folberth J, Jöhren O, Schwaninger M, Lehnert H, Schulz C (2022) Knockdown of Endogenous Nucb2/Nesfatin-1 in the PVN Leads to Obese-Like Phenotype and Abolishes the Metformin- and Stress-Induced Thermogenic Response in Rats. Horm Metab Res 54:768-779.
  • Matlac DM, Hadrava Vanova K, Bechmann N, Richter S, Folberth J, Ghayee HK, Ge GB, Abunimer L, Wesley R, Aherrahrou R, Dona M, Martinez-Montes AM, Calsina B, Merino MJ, Schwaninger M, Deen PMT, Zhuang Z, Neuzil J, Pacak K, Lehnert H, Fliedner SMJ (2021) Succinate Mediates Tumorigenic Effects via Succinate Receptor 1: Potential for New Targeted Treatment Strategies in Succinate Dehydrogenase Deficient Paragangliomas. Front Endocrinol (Lausanne) 12:589451.
  • Wenzel J, Lampe J, Müller-Fielitz H, Schuster R, Zille M, Müller K, Krohn M, Körbelin J, Zhang L, Ozorhan U, Neve V, Wagner JUG, Bojkova D, Shumliakivska M, Jiang Y, Fähnrich A, Ott F, Sencio V, Robil C, Pfefferle S, Sauve F, Coelho CFF, Franz J, Spiecker F, Lembrich B, Binder S, Feller N, König P, Busch H, Collin L, Villasenor R, Jöhren O, Altmeppen HC, Pasparakis M, Dimmeler S, Cinatl J, Puschel K, Zelic M, Ofengeim D, Stadelmann C, Trottein F, Nogueiras R, Hilgenfeld R, Glatzel M, Prevot V, Schwaninger M (2021) The SARS-CoV-2 main protease M(pro) causes microvascular brain pathology by cleaving NEMO in brain endothelial cells. Nat Neurosci 24:1522-1533.
  • 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.
  • Rawish E, Nickel L, Schuster F, Stölting I, Frydrychowicz A, Saar K, Hubner N, Othman A, Kuerschner L, Raasch W (2020) Telmisartan prevents development of obesity and normalizes hypothalamic lipid droplets. J Endocrinol 244:95-110.
  • 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, Lebron-Galan 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.