Empowering your research – get quantitative data on the building blocks of life!

Biological research in the post-genomic era has become largely dependent on technologies allowing large-scale analysis of biological systems and processes. One of these approaches, Metabolomics, aims for a comprehensive and quantitative picture of small biomolecules such as sugars, lipids, and nucleic acids in biological samples, which can then be mapped on biochemical pathways.


Research in the context of the "Shared Research Facility Metabolomics" is funded by the City of Vienna through the Vienna Business Agency - a service offered by the city of Vienna.


Targeted LC-MS/MS

We offer the analysis of user-defined compounds in extracts from biological samples by targeted liquid chromatography–tandem mass spectrometry (LC-MS/MS), including the respective methods development. In addition to relative quantification, the absolute quantification of metabolites is also offered (if the respective isotopically-labeled compounds are available). This approach can also be used to assess the quantitative changes in important biochemical pathways in biological samples by using panels of pre-defined analytes.

We also offer to develop tailor-made LC-MS/MS methods for all classes of metabolites.

Non-targeted LC-MS/MS or metabolite profiling

The facility offers non-targeted metabolite profiling, employing high-resolution mass spectrometry. This technique aims for a hypothesis-free description of metabolic differences between samples caused by different genotypes or any perturbations of the system.

Using libraries containing tandem mass spectrometry data from known substances, a subset of these compounds can also be identified.


TSQ Quantiva

The TSQ Quantiva (Thermo Fisher Scientific) is a state-of-the-art triple quadrupole mass spectrometer, optimal for targeted analysis of small molecules. The mass spectrometer is on-line coupled to an Ultimate 3000 HPLC (Dionex; Thermo Fisher Scientific). This is a bio-inert HPLC, to be operated at micro-flow conditions. A metal-free flow path ensures low binding of biomolecules to surfaces, allowing the analysis of phosphorylated compounds.




The Q-Exactive (Thermo Fisher Scientific) is a high-resolution instrument, mainly used for metabolite profiling and analysis of lipids. The mass spectrometer is on-line coupled to an inert Ultimate 3000 HPLC (Dionex; Thermo Fisher Scientific).


If you want to start a new project, please contact Thomas Köcher to discuss your project and the analytical question. The unit offers both targeted and non-targeted analysis of metabolite-containing extracts and the respective methods development in a fee-for-service model. The facility does not accept radioactively-labeled samples. Deliverables are the relative (or absolute) quantities of the metabolites as defined by the user.

For more information, please see our usage policy.

The Metabolomics Core Facility offers access to its services to all users from both academia and companies on a “first come, first served"-basis, but prioritizes users from the participating institutes of the “shared research facility metabolomics”.

In addition, the VBCF General Cooperation Conditions apply.

For further questions, please contact Thomas Köcher.



We require acknowledgement of facility use in publications. 
A simple statement is sufficient and can be placed in the Materials and Methods section or in the Acknowledgments section, depending on the journal format.

A simple statement in the acknowledgements is sufficient:

"The service xxxx was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria and funded by the City of Vienna through the Vienna Business Agency".


Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection. Colaço HG, Barros A, Neves-Costa A, Seixas E, Pedroso D, Velho T, Willmann KL, Faisca P, Grabmann G, Yi HS, Shong M, Benes V, Weis S, Köcher T, Moita LF. [2021] Immunity 54(1):53-67.e7

Anti-ferroptotic mechanism of IL4i1-mediated amino acid metabolism. Zeitler L, Fiore A, Meyer C, Russier M, Zanella G, Suppmann S, Gargaro M, Sidhu SS, Seshagiri S, Ohnmacht C, Köcher T, Fallarino F, Linkermann A, Murray PJ. [2021] Elife 10:e64806.

Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries. Rampler E, Hermann G, Grabmann G, El Abiead Y, Schoeny H, Baumgartinger C, Köcher T, Koellensperger G. [2021] Metabolites 11(3):160.

Oxidative Metabolism Drives Immortalization of Neural Stem Cells during Tumorigenesis  Bonnay F, Veloso A, Steinmann V, Köcher T, Abdusselamoglu MD, Bajaj S, Rivelles E, Landskron L, Esterbauer H, Zinzen RP, Knoblich JA. [2020] Cell 182 (6), 1490-1507

AIF-regulated oxidative phosphorylation supports lung cancer development. Rao S, Mondragón L, Pranjic B, Hanada T, Stoll G, Köcher T, Zhang P, Jais A, Lercher A, Bergthaler A, Schramek D, Haigh K, Sica V, Leduc M, Modjtahedi N, Pai TP, Onji M, Uribesalgo I, Hanada R, Kozieradzki I, Koglgruber R, Cronin SJ, She Z, Quehenberger F, Popper H, Kenner L, Haigh JJ, Kepp O, Rak M, Cai K, Kroemer G, Penninger JM. [2019] Cell Research 29, 579–591

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J. [2018] Science 360, 800–805

RIOK1 kinase activity is required for cell survival irrespective of MTAP status. Hörmann A, Hopfgartner B, Köcher T, Corcokovic M, Krammer T, Reiser C, Bader G, Shi J, Ehrenhöfer K, Wöhrle S, Schweifer N, Vakoc CR, Kraut N, Pearson M, Petronczki M, Neumüller RA. [2018] Oncotarget. 9 (47), 28625-28637