Metabolite Profiling and Small Molecule Mass Spectrometry

The Metabolomics Service and Research Facility provides services for the quantitative analysis of small molecules and metabolites.

Biological research in the post-genomic era has become largely dependent on advanced technologies and high-end instrumentation, allowing large-scale analysis of biological systems and processes. The most recent approach in -omics technologies, metabolomics, aims for a comprehensive and quantitative picture of small biomolecules in biological samples. The analysis of metabolomes allows the direct read-out of molecular phenotypes, representing the nexus of interactions between the genome and the environment. The beauty of the approach is that the metabolome directly represents the biochemical condition of cells, tissues, and organisms, thus allowing insights into perturbed biochemical pathways.

Our LC-MS/MS platforms provide both targeted and nontargeted metabolomics analysis of biological samples, revealing changes in metabolic pathways, consequences of various perturbations or simply quantifying small molecules of any origin. The facility has established methods for more than 1000 metabolites and additionally offers methods development on demand.

We offer:

  • Targeted metabolomics.
  • Stable isotope tracer analysis.
  • Global (nontargeted) metabolite profiling.
  • Small molecule analysis: identification & quantification.

We thank the Vienna Business Agency - a service offered by the city of Vienna for generous funding of the implementation of this Core Facility. To learn more about our research, please check our publications.


Targeted LC-MS/MS

We provide analysis of user-defined compounds in extracts from biological samples by targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our services are not limited to biomolecules but include other small molecules such as drugs.

The facility has a growing portfolio of LC-MS/MS methods for almost 1000 small molecules spanning over a wide variety of metabolites from different substance classes such as amino acids, bile acids, carboxylic acids (e.g. citric acid, stearic acid), coenzymes (NAD+/H, Acetyl-CoA/CoA, etc.), ketone bodies, lipids, mono amines (dopamine etc.), nucleoside tri-, di-, mono-phosphates, coenzymes (NAD+/H, Acetyl-CoA/CoA, etc.). We also offer methods development for small molecule analysis on demand.

We offer the analysis of panels consisting of metabolites of biochemical pathways such as the TCA cycle, glycolysis, purine and pyrimidine metabolism, urea cycle, amino acid metabolism or the pentose phosphate pathway but also tailor-made panels.

Additionally, we offer methods development on demand and more sophisticated assays such as stable isotope tracer analysis (e.g. 13C, 15N). In addition to relative quantification, the absolute quantification of metabolites is also offered.

Non-targeted LC-MS/MS or metabolite profiling

The facility offers global metabolite profiling employing liquid chromatography on-line coupled to high-resolution tandem mass spectrometry. Each sample is measured twice, with two different separation techniques hydrophilic interaction liquid chromatography (HILIC) and reversed phase chromatography, maximizing coverage of the metabolome.

The technique provides a hypothesis-free description of metabolic differences between samples caused by different genotypes or any perturbations of the system, usually detecting more than 1,000 distinct small molecules. Many of them will be identified with high confidence by our steadily growing in-house library containing more than 500 compounds. Another subset of the detected compounds will be identified by searching public databases.


TSQ Altis

We currently operate two HPLC-coupled TSQ Altis (Thermo Fisher Scientific). The TSQ Altis is a state-of-the-art triple quadrupole mass spectrometer, optimal for the targeted analysis of small molecules. Metabolites are separated on a bioinert Vanquish (Thermo Fisher Scientific) HPLC system, on-line coupled via electrospray ionization to the mass spectrometer.

TSQ Quantiva

We also operate one TSQ Quantiva (Thermo Fisher Scientific) MS system, which is a robust triple quadrupole mass spectrometer used for LC-MS/MS-based targeted analysis. This system is connected to a bioinert Ultimate 3000 HPLC system (Dionex; Thermo Fisher Scientific).




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).


In general, we offer four types of access to our shared research infrastructure:

  1. Research projects
  2. Full research services
  3. Trained user access | user labs
  4. Shared technology platform

Typically, these are set but not limited by the offered technology or instrument, and differ in the required user expertise, the usability of a technology, the user’s pre- and postprocessing input, and the underlying operational models.

Research project

Research projects are the equivalent of contract research organizations (CRO). The customer submits the starting material/sample and receives the ready-to-use data for publication. Hence, core facility members are often co-authoring and involved in the entire publication process.

Full research service

The user submits the sample, we perform a pre-defined workflow (incl. QC) and process the raw data. Data interpretation or contributions to publications cannot be offered in this service mode.

Trained user access | User labs

VBCF experts maintain an instrument park and train users to operate it. This requires a certain level of expertise, maturity of the offered technology, a hands-on attitude and reliability from the user.

Shared technology platform | Instrument park

These technologies require expert knowledge to run the offered instruments. Experts are hired by one of the research institutes on the Vienna BioCenter Campus. The experts maintain an instrument park, run the experiments and train other trainers. Machines can only be operated by experts.


The VBCF Metabolomics facility can be accessed via research projects and provides full research service.

In general, the VBCF General Cooperation Conditions apply. To get started, please contact Thomas Köcher to discuss your project and the analytical question you have, especially if you want to start a new project. Please label samples properly and send a sample information sheet via Email along with the samples. Samples can be submitted as extracts, preferentially shipped on dry ice.

Shipping Address:

Thomas Köcher

Vienna BioCenter Core Facilities GmbH

Metabolomics Facility


Campus Vienna Biocenter 1

1030 Vienna

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.

Suggested format:

The XXXXXX was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

In case of (co-)authorship:

The Vienna BioCenter Core Facilities (VBCF) Metabolomics Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna.



Reduced coenzyme Q synthesis confers non-target site resistance to the herbicide thaxtomin A. Casey C, Köcher T, Champion C, Jandrasits K, Mosiolek M, Bonnot C, et al. (2023) PLoS Genet 19(1): e1010423.

Mast cell-derived BH4 is a critical mediator of postoperative pain. Starkl P, Jonsson G, Artner T, Turnes BL, Serhan N, Oliveira T, Gail LM, Stejskal K, Channon KM, Köcher T, Stary G, Klang V, Gaudenzio N, Knapp S, Woolf CJ, Penninger JM, Cronin SJF. bioRxiv. 2023 Jan 24:2023.01.24.525378. doi: 10.1101/2023.01.24.525378. Preprint. 

Transcriptome changes in chlorsulfuron-treated plants are caused by acetolactate synthase inhibition and not induction of a herbicide detoxification system in Marchantia polymorpha. Casey A, Köcher T, Caygill S, Champion C, Bonnot C, Dolan L. Pestic Biochem Physiol. 2023 Apr;191:105370. doi: 10.1016/j.pestbp.2023.105370.  

ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia. Ebner J, Schmoellerl J, Piontek M, Manhart G, Troester S, Carter BZ, Neubauer H, Moriggl R, Szakács G, Zuber J, Köcher T, Andreeff M, Sperr WR, Valent P, Grebien F. Nat Commun. 2023 Sep 19;14(1):5709. doi: 10.1038/s41467-023-41229-2. 

Adult neural stem cells and neurogenesis are resilient to intermittent fasting. Gabarró-Solanas R, Davaatseren A, Kleifeld J, Kepčija T, Köcher T, Giralt A, Crespo-Enríquez I, Urbán N. EMBO Rep. 2023 Nov 21:e57268. doi: 10.15252/embr.202357268. Online ahead of print. 


Role of Omega-6 Fatty Acid Metabolism in Cardiac Surgery Postoperative Bleeding Risk. Velho TR, Ferreira R, Willmann K, Pedroso D, Paixão T, Pereira RM, Junqueira N, Guerra NC, Brito D, Almeida AG, Nobre Â, Köcher T, Pinto F, Moita LF. Crit Care Explor. 2022 4(10):e0763

Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Mitter M, Takacs Z, Köcher T, Micura R, Langer CCH, Gerlich DW. Nat Protoc. 2022 17(6):1486-1517.

Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. Emtenani S, Martin ET, Gyoergy A, Bicher J, Genger JW, Köcher T, Akhmanova M, Guarda M, Roblek M, Bergthaler A, Hurd TR, Rangan P, Siekhaus DE. EMBO J. 2022 41(12):e109049.

Kynurenine importation by SLC7A11 propagates anti-ferroptotic signaling. Fiore A, Zeitler L, Russier M, Groß A, Hiller MK, Parker JL, Stier L, Köcher T, Newstead S, Murray PJ. Mol Cell. 2022 82(5):920-932

Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity. Sasaki E, Köcher T, Filiault DL, Nordborg M. Heredity (Edinb). 2021, Epub ahead of print.

Mucosal biofilms are an endoscopic feature of irritable bowel syndrome and ulcerative colitis. Baumgartner M, Lang M, Holley H, Crepaz D, Hausmann B, Pjevac P, Moser D, Haller F, Hof F, Beer A, Orgler E, Frick A, Khare V, Evstatiev R, Strohmaier S, Primas C, Dolak W, Köcher T, Kristaps K, Rath T, Neurath MF, Berry D, Makristathis A, Muttenthaler M, Gasche C. Gastroenterology. 2021, Epub ahead of print.

The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Asanović I, Strandback E, Kroupova A, Pasajlic D, Meinhart A, Tsung-Pin P, Djokovic N, Anrather D, Schuetz T, Suskiewicz MJ, Sillamaa S, Köcher T, Beveridge R, Nikolic K, Schleiffer A, Jinek M, Hartl M, Clausen T, Penninger J, Macheroux P, Weitzer S, Martinez J. Mol Cell. 2021 Apr 23:S1097-2765(21)00312-9. doi: 10.1016/j.molcel.2021.04.007. Online ahead of print.

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