Metabolomics
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.
Please visit our Info Hub to learn more
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.
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.
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).
The OrbiTrap Exploris 480 (Thermo Fisher Scientific) is a state-of-the-art high-resolution instrument (480,000 at m/z 200), which we mainly employ for untargeted metabolomics. The mass spectrometer is on-line coupled to an inert Ultimate 3000 HPLC (Dionex; Thermo Fisher Scientific).
VBCF METABOLOMICS TEAM
PUBLICATIONS
Role of major cardiovascular surgery-induced metabolic reprogramming in acute kidney injury in critical care. Velho TR, Pinto F, Ferreira R, Pereira RM, Duarte A, Harada M, Willmann K, Pedroso D, Paixão T, Guerra NC, Neves-Costa A, Santos I, Gouveia E Melo R, Brito D, Almeida AG, Nobre Â, Wang-Sattler R, Köcher T, Pedro LM, Pinto F, Moita LF. Intensive Care Med. 2025 Feb;51(2):259-271. doi: 10.1007/s00134-024-07770-4. Epub 2025 Jan 27.
24-Nor-ursodeoxycholic acid improves intestinal inflammation by targeting TH17 pathogenicity and transdifferentiation. Zhu C, Boucheron N, Al-Rubaye O, Chung BK, Thorbjørnsen LW, Köcher T, Schuster M, Claudel T, Halilbasic E, Kunczer V, Muscate F, Cavanagh LL, Waltenberger D, Lercher A, Ohradanova-Repic A, Schatzlmaier P, Stojakovic T, Scharnagl H, Bergthaler A, Stockinger H, Huber S, Bock C, Kenner L, Karlsen TH, Ellmeier W, Trauner M. Gut. 2025 Jun 6;74(7):1079-1093. doi: 10.1136/gutjnl-2024-333297.
Mitochondrial Glutamine Metabolism Drives Epileptogenesis in Primary Hippocampal Neurons. Kubista H, Gentile F, Schicker K, Köcher T, Boehm S, Hotka M. J Neurosci. 2025 May 21;45(21):e0110252025. doi: 10.1523/JNEUROSCI.0110-25.2025.
Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea. Weinberger V, Darnhofer B, Thapa HB, Mertelj P, Stentz R, Jones E, Grabmann G, Mohammadzadeh R, Shinde T, Karner C, Ober J, Juodeikis R, Pernitsch D, Hingerl K, Zurabishvili T, Kumpitsch C, Kuehnast T, Rinner B, Strohmaier H, Kolb D, Gotts K, Weichhart T, Köcher T, Köfeler H, Carding SR, Schild S, Moissl-Eichinger C. Nat Commun. 2025 Jun 3;16(1):5094. doi: 10.1038/s41467-025-60271-w.
The bioarchaeology of tobacco use: An exploratory study of nicotine and cotinine detection in tooth dentine. Strang, S, Köcher, T, van der Sluis, L, Chowdhury, MP, Grabmayer, H, Douka, K, & Binder, M J Archaeol Sci. 2025 doi.org/10.1016/j.jas. 2025.106301
An unexpected tumor-resistant phenotype from floxing PAK1 in a mouse model of colitis associated cancer. Jimenez K, Lindeck-Pozza L, Frick AP, Baumgartner M, Haller F, Gmainer C, Krnjic A, Klotz A, Jambrich M, Köcher T, Khare V, Gasche C. Sci Rep. 2025 Aug 9;15(1):29174. doi: 10.1038/s41598-025-12082-8.
Mitochondrial ROS drive foam cell formation via STAT5 signaling in atherosclerosis. Boccuni L, Marka F, Salzmann M, Schirripa A, Ableitner E, Siller M, Brekalo M, Haider P, Stojkovic S, Neumayer C, Örd T, Kollmann K, Assinger A, Decker T, Köcher T, Fischer MB, Mußbacher M, Bergthaler A, Hengstenberg C, Podesser BK, Kaikkonen MU, Wojta J, Hohensinner PJ. Sci Adv. 2025 Aug 29;11(35):eadw9952. doi: 10.1126/sciadv.adw9952. Epub 2025 Aug 27.
Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus D, Ziegler C, Sandtner W, Roblek M. Proc Natl Acad Sci U S A. 2024 Mar 26;121(13):e2319686121. doi: 10.1073/pnas.2319686121. Epub 2024 Mar 20.
Epirubicin for the Treatment of Sepsis and Septic Shock (EPOS-1): study protocol for a randomised, placebo-controlled phase IIa dose-escalation trial. Thomas-Rüddel D, Bauer M, Moita LF, Helbig C, Schlattmann P, Ehler J, Rahmel T, Meybohm P, Gründling M, Schenk H, Köcher T, Brunkhorst FM, Gräler M, Heger AJ, Weis S; EPOS-1 study group; SepNetCriticalCare TrialsGroup. BMJ Open. 2024 Apr 22;14(4):e075158. doi: 10.1136/bmjopen-2023-075158.
Archaea influence composition of endoscopically visible ileocolonic biofilms. Orgler E, Baumgartner M, Duller S, Kumptisch C, Hausmann B, Moser D, Khare V, Lang M, Köcher T, Frick A, Muttenthaler M, Makristathis A, Moissl-Eichinger C, Gasche C. Gut Microbes. 2024 Jan-Dec;16(1):2359500. doi: 10.1080/19490976.2024.2359500. Epub 2024 Jun 2.
Itaconate is a metabolic regulator of bone formation in homeostasis and arthritis. Kieler M, Prammer LS, Heller G, Hofmann M, Sperger S, Hanetseder D, Niederreiter B, Komljenovic A, Klavins K, Köcher T, Brunner JS, Stanic I, Oberbichler L, Korosec A, Vogel A, Kerndl M, Hromadová D, Musiejovsky L, Hajto A, Dobrijevic A, Piwonka T, Haschemi A, Miller A, Georgel P, Marolt Presen D, Grillari J, Hayer S, Auger JP, Krönke G, Sharif O, Aletaha D, Schabbauer G, Blüml S. Ann Rheum Dis. 2024 Jul 10:ard-2023-224898. doi: 10.1136/ard-2023-224898. Online ahead of print.
Mast cell-derived BH4 and serotonin are critical mediators of postoperative pain. Starkl P, Jonsson G, Artner T, Turnes BL, Gail LM, Oliveira T, Jain A, Serhan N, Stejskal K, Lakovits K, Hladik A, An M, Channon KM, Kim H, Köcher T, Weninger W, Stary G, Knapp S, Klang V, Gaudenzio N, Woolf CJ, Tikoo S, Jain R, Penninger JM, Cronin SJF. Sci Immunol. 2024 Aug 23;9(98):eadh0545. doi: 10.1126/sciimmunol.adh0545. Epub 2024 Aug 23.
MurA-catalyzed synthesis of 5-enolpyruvylshikimate-3-phosphate confers glyphosate tolerance in bryophytes. Caygill S, Köcher T, Dolan L. Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2412997121. doi: 10.1073/pnas.2412997121. Epub 2024 Nov 11.
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.