Metabolomics is an important component of life science multi-omics. Metabolomics investigates small molecules — lipids and hydrophilic compounds — from animal, plant, and microbial sources at the systems level. Targeted and untargeted metabolomics reveal cellular responses to illnesses, nutrition, environmental changes, gene function, medication metabolism, and interactions with other organisms. Mass spectrometry (MS) and NMR-based services from Biocenter Finland Metabolomics Technology Platform encompass all sectors of life science from medicine to plant and environmental science, serving a wide national and international customer base with proven performance. The five nodes hosted by UH/HiLIFE, UEF, and UTU provide complementing analytical services with skilled staff and outstanding publication records. The platform has a clear strategy for its line up and continuously improves the resolution of the analyses in terms of molecular structure, time (flux analyses) and space (spatial imaging).


Contact details


Platform chair:
Teemu Teeri (UH), teemu.teeri@helsinki.fi
Viikki Metabolomics Unit, HiLIFE, University of Helsinki

Platform chair (2025-2028):
Anni Nieminen (UH), anni.nieminen@helsinki.fi


Nodes


Node/Host UniversityNode PI
Viikki Metabolomics Unit (ViMU) UH
Teemu Teeri, UH 2021-2024
(Nina Sipari, UH 2025-2028)
teemu.teeri@helsinki.fi
nina.sipari@helsinki.fi
FIMM Metabolomics (FIMM-META) UH
Anni Nieminen, UH
anni.nieminen@helsinki.fi
Biocenter Kuopio Metabolomics Center (BCK) UEF
Seppo Auriola, UEF 2021-2024
(Marko Lehtonen, UEF, platform vice-chair 2025-2026)
seppo.auriola@uef.fi
marko.lehtonen@uef.fi
Helsinki University Lipidomics Unit (HiLIPID) UH
Reijo Käkelä UH
reijo.kakela@helsinki.fi
Turku Metabolomics Centre (TMC) UTU
Matej Orešič UTU
(Alex Dickens UTU, platform vice-chair 2027-2028)
matej.oresic@utu.fi
alex.dickens@utu.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University
of Oulu; UTU: University of Turku; TAU: Tampere University; ÅAU: Åbo
Akademi University.



Services


Researchers, universities, healthcare facilities, institutes and businesses from different fields can easily access the nodes from their webpages (where contact information is available). Each of the platform nodes has extensive knowledge and experience in a specific area of the life sciences. Please get in touch with us if you would like further details about the current and future goals of each node.

Platform service workflow


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The Metabolomics Platform offers a range of complementary analytical services.

Recent user publications


Xing L, Gkini V, Nieminen AI, Zhou HC, Aquilino M, Naumann R, Reppe K, Tanaka K, Carmeliet P, Heikinheimo O, Pääbo S, Huttner WB, Namba T. Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development. Nat Commun. 2024 Apr 24;15(1):3468. doi: 10.1038/s41467-024-47437-8.


Comparative steroid profiling of newborn hair and umbilical cord serum highlights the role of fetal adrenals, placenta, and pregnancy outcomes in fetal steroid metabolism. Koskivuori J, Voutilainen R, Storvik M, Häkkinen MR, Uusitalo L, Keski-Nisula L, Backman K, Auriola S, Lehtonen M. .J Steroid Biochem Mol Biol. 2023 Sep;232:106357. (doi: 10.1016/j.jsbmb.2023.106357)

Liu L, Pan D, Chen S, Martikainen MV, Kårlund A, Ke J, Pulkkinen H, Ruhanen H, Roponen M, Käkelä R, Xu W, Wang J, Lehto VP. Systematic design of cell membrane coating to improve tumor targeting of nanoparticles. Nat Commun. 2022 Oct 19;13(1):6181. doi: 10.1038/s41467-022-33889-3

Lamichhane S, Sen P, Dickens AM, Alves MA, Härkönen T, Honkanen J, Vatanen T,Xavier RJ, Hyötyläinen T, Knip M, Orešič M. Dysregulation of secondary bile acidmetabolism precedes islet autoimmunity and type 1 diabetes. Cell Rep Med. 2022 Oct 18;3(10):100762. doi: 10.1016/j.xcrm.2022.100762. Epub 2022 Oct 3. PMID:36195095; PMCID: PMC9589006.

Purhonen, J. P., Banerjee, R., Wanne, V., Sipari, N., Morgelin, M., Fellman, V. & Kallijärvi J. Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria. Nat Commun 14, 2356 (2023). https://doi.org/10.1038/s41467-023-38027-1.



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Available instrumentation


Node 1 FIMM-METADescription
UPLC-MS/MS (Orbitrap)High-resolution Thermo QExactive Orbitrap mass spectrometer for fluxomics and high-throughput profiling
UPLC-MS/MS (QqQ)Exion LC with AB/SCIEX 6500+ QTRAP mass spectrometer high sensitivity to detect low abundance metabolites
UPLC-MS/MS (QqQ) with SelexION® DMSLipidyzer platform with Nexera Shimadzu UPLC with AB/SCIEX 5500 QTRAP mass spectrometer, high-throughput quantitative lipidomics
UPLC-MS/MS (QqQ)ACQUITY ultra pressure liquid chromatography (UPLC) coupled to WATERS Xevo-TQ-S triple quadrupole mass spectrometer)
Node 2 BCKDescription
Thermo Q Exactive Classic UPLC-high resolution Orbitrap instrument for lipidomics and extra high-resolution analysis
Thermo Q Exactive Focus UPLC-high resolution Orbitrap instrument for untargeted metabolomics, steroidomics and drug metabolism analysis
Agilent QQQ 6495 UPLC-triple stage quadrupole for targeted metabolomics and drug analysis
MALDI ion source MALDI imaging ion source
Agilent Q-tof 6540 UPLC-high resolution Q-tof instrument for untargeted metabolomics
Bruker AVANCE III HD 600 MHz NMR NMR with cryogenically cooled probehead and sample changer for 5x96 tubes for measurement of a variety of 1D and 2D NMR spectra and to observe several NMR active nuclei.
Bruker AVANCE III HD 600 MHz NMRNMR with cryogenically cooled Prodigy TCI proton-optimized triple resonance inverse probehead and sample changer for 5x96 tubes for high-throughput 1H NMR metabolomics
Node 3 HiLPIDDescription
UPLC-QTRAPAB Sciex QTRAP 6500+ LC-MS/MS with Agilent 1290 Infinity UPLC for targeted analysis of lipid mediators
UPLC-3QMSAgilent 6490 Triple Quad LC/MS with 1290 Infinity UPLC for dynamic and global analysis of lipid composition
GC-MSDShimadzu GCMS-QP2010 Ultra for analysis of fatty acid structures
GC-FIDShimadzu GC-2010 Plus system for quantitative analysis of fatty acid composition
3QMS (syringe infusion)Agilent 6410 Triple Quad LC/MS with syringe infusion for shot gun lipidomics
Node 4 TMCDescription
GC-MSD Agilent 5890B GC system coupled to an Agilent 5977A MSD. For targeted analysis of polar metabolites
UPLC-QTRAP AB Sciex QTRAP 5500 LC-MS/MS with a Shimadzu AD40 LC system for targeted analysis of metabolites
GC-TOFLECO Pegasus BT mass spectrometer with an Agilent 5890B GC system for untargeted analysis of polar metabolites
UPLC-QTOF AB Sciex TripleQ 6600 mass spectrometer with a Sciex AD30 LC system for untargeted metabolomics and lipidomics
MALDI2 timsTOF flex Bruker instrument for MS imaging and ion mobility as it has a standard ESI source.
UPLC-QTRAPSciex 7500 QTRAP instrument with Sciex LC30 UPLC set up for 2D chromatography. Most sensitive MS on the market.
Bruker AVANCE III HD 600 MHz NMR NMR with cryogenically cooled Prodigy TCI proton-optimized triple resonance inverse probehead and sample changer for 5x96 tubes for high throughput 1H NMR metabolomics
Bruker AVANCE III HD 400 MHz NMRNMR with a CP-MAS and HR-MAS probes for solid and semi solid samples
UPLC-QTRAPAB Sciex QTRAP 65500+ LC-MS/MS with a Shimadzu AD3040 LC system for targeted GLP assays
UPLC-QqQAB Sciex QqQ4000 LC-MS/MS with a Shimadzu AD240 LC system backup of the 6500+ in GLP assays.
Andrew pipetting robotSample preparation robot
Waters RDa detectorUsed for quickly screening how compounds are detectable in ESI as a prescreening tool to assess new projects
UPLC-QqQAgilent 6460 QqQ with and Agilent 1290 LC system for routine analysis of targeted metabolites.
Node 5 ViMUDescription
UPLC-PDA-QTOF/MS Waters Synapt G2 UPLC-HD/MS for untargeted metabolomics and for exact mass measurements
UPLC-QTRAP/MS Sciex UPLC-6500+ QTRAP/MS for quantitative analysis and targeted metabolomics
GC-QQQ/MS Agilent GC-QQQ/MS for primary metabolite analysis, volatiles & untargeted analysis