FIMM Metabolomics/Lipidomics/Fluxomics Unit (FIMM Meta)

High-throughput tar­geted and quant­it­at­ive metabolomics

Analysis of hundreds of polar metabolites in a single method using MRM strategy. Suitable for tissues, cells, and biofluids.

Customized targeted quantitative metabolomics

Concentration analysis for ketonebodies, ketoacids, NADs, short-chain fatty acids, folate cycle intermediates or absolute quantification of TCA cycle intermediates. Suitable for tissues, cells, and biofluids.

High-throughput qual­it­at­ive metabolomics profiling and custom sets

Qualitative analysis of more than five hundred known standardized metabolites using high-resolution orbitrap Q-Exactive. Suitable also for small sample amounts (i.e. 30 000 cells or 15ul) for biofluids, tissues, cells, stem cells, organoids, spheres, and extracellular vesicles.

Metabolic flux analysis 

Isotope enrichment analysis and metabolic flux analysis of central carbon metabolism and other pathways using 13C-, 15N- and dH-tracers. Suitable also for small sample amounts (i.e. 30 000 cells or 10ul) for biofluids, tissues, cells, immune cells, stem cells, organoids, spheres, and extracellular vesicles.

High-through­put tar­geted and quant­it­at­ive lipidom­ics

Analysis of thousand lipid molecular species in a single method using the Lipidyzer platform. Suitable for biofluids (min 25ul), tissues, cells, and extracellular vesicles. More details (https://sciex.jp/content/dam/SCIEX/pdf/tech-notes/all/lipidyzer_platform_workflow.pdf)

Data analysis 

We offer via collaboration complete metabolomics/lipidomics data analysis using advanced biostatistical and chemometric methods including integrated omics data analysis, figures, tables, and metabolic pathway analysis. Reporting, data quality checks, and documentation are included in the service.

Meta­bolo­m­ics ana­lyt­ical meth­ods un­der de­vel­op­ment

New sample types taken into method development via collaboration. Contact the head of the unit.

De­mand-based meta­bolo­m­ics services and method development

We are open to develop new metabolomics analytical methods based on user demand. Contact the head of the unit.

Anni Nieminen-(Viheriäranta)

Senior Scientist, Head of the Unit
INSTITUTE FOR MOLECULAR MEDICINE FINLAND

+358 (0) 505352157
anni.nieminen@helsinki.fi

Sample types and requirements:

Shipping address:

Laboratory co-ordinator

Metabolomics Unit, 
Institute for Molecular Medicine Finland FIMM
Biomedicum Helsinki 2U, room E204b
Tukholmankatu 8
00290 Helsinki, Finland

1. Simultaneous Measurement of Tricarboxylic Acid Cycle Intermediates in Different Biological Matrices Using Liquid Chromatography–Tandem Mass Spectrometry; Quantitation and Comparison of TCA Cycle Intermediates in Human Serum, Plasma, Kasumi-1 Cell and Murine Liver Tissue. Rathod, R.; Gajera, B.; Nazir, K.; Wallenius, J.; Velagapudi, V.  Metabolites 2020, 10, 103. https://doi.org/10.3390/metabo10030103.
2. Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders. Sci Rep 9, 16054 (2019). Haruna T, Takayuki M, Vidya V, Kaori I, Moe U, Kazuto N, Anu S & Jun-Ichi H. https://doi.org/10.1038/s41598-019-52372-6.
3. Repeated Transcranial Magnetic Stimulation-Induced Motor Evoked Potentials Correlate With the Subject-Specific Serum Metabolic Profile of Creatine. J Clin Neurophysiol. 2019 [Epub ahead of print].Kallioniemi E, Kärkkäinen O, Määttä S, Könönen M, Kivimäki P, Kaarre O, Velagapudi V, Kekkonen V, Lehto SM, Laukkanen E, Tolmunen T. PMID:30720554
4. Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci. Clin Epigenetics. 2019 Jan 5;11(1):1.Gupta R, van Dongen J, Fu Y, Abdellaoui A, Tyndale RF, Velagapudi V, Boomsma DI, Korhonen T, Kaprio J, Loukola A, Ollikainen M. PMID:30611298 
5. Changes in the serum metabolite profile correlate with decreased brain grey matter volume in heavy-drinking young adults. Alcohol. 2019; 75:89-97. Heikkinen, N., Kärkkäinen, O., Laukkanen, E., Kekkonen, V., Kaarre, O., Kivimäki, P., Könönen, M., Velagapudi, V., Nandania, J., Lehto, S., Niskanen, E., Vanninen, R., Tolmunen, T. PMID:30513444
6. Metabolomes of mitochondrial diseases and inclusion body myositis: treatment targets and biomarkers. EMBO Molecular Medicine. 2018  Dec;10(12).Buzkova, J., Nikkanen, J., Ahola, S., Hakonen, A., Sevastianova, K., Hovinen, T., Yki-Järvinen, H., Pietiläinen, K., Lönnqvist, T., Velagapudi, V., Carroll, C., Suomalainen, A.  PMID:30373890
7. A Systems Approach to Study Immuno- and Neuro-Modulatory Properties of Antiviral Agents. Viruses. 2018 Aug 12;10(8).Zusinaite E, Ianevski A, Niukkanen D, Poranen MM, Bjørås M, Afset JE, Tenson T, Velagapudi V, Merits A, Kainov DE. PMID:30103549
8. Simultaneous measurement of folate cycle metabolites using liquid chromatography-tandem mass spectrometry from different biological matrices. Journal of Chromatography B. 2018; 15:1092: 168-178.Nandania, J., Kokkonen, M., Euro, L, Velagapudi, V.  PMID:29906678
9. Adipose tissue mitochondrial gene expression profile associates with long-term weight loss success. International Journal of Obesity. 2018; 42;817–825. Jokinen, R., Rinnankoski-Tuikka, R., Kaye, S., Saarinen, L., Heinonen, S., Myöhänen, M., Rappou, E., Jukarainen, S., Kaprio, J., Rissanen, A., Pessia, A., Velagapudi, V., Virtanen, K., Pirinen, E and Pietiläinen, K. PMID:29203860
10. Validation and automation of high-throughput multi-targeted method for semi-quantification of endogenous metabolites from different biological matrices using tandem mass spectrometry. Metabolites. 2018; 5:8:3. Nandania, J., Peddinti, G., Pessia, A., Kokkonen, M., Velagapudi, V. PMID:30081599
11. Pre-analytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for “Precision Medicine and Pharmacometabolomics Task Group” – The Metabolomics Society Initiative). Clinical Chemistry. 2018; 64:8:1158-1182. Kirwan, J., Brennan, L., Broadhurst, D., Fiehn, O., Cascante, M., Dunn, W., Schmidt, M., Velagapudi, V.  PMID:29921725
12. Plasma metabolites reveal distinct profiles associating with different metabolic risk factors in monozygotic twin pairs. International Journal of Obesity. 2018;Muniandy, M., Velagapudi, V., Hakkarainen, A., Lundbom, J., Lundbom, N., Rissanen, A., Kaprio, J., Pietiläinen, K., Ollikainen, M. PMID:29907843
13. Understanding the metabolic burden of recombinant antibody production in Saccharomyces cerevisiae using a quantitative metabolomics approach. Yeast. 2018; 35(4):331-341. De Ruijter, J., Koskela, E., Nandania, J., Frey, A., Velagapudi, V. PMID: 29159981
14. Global arginine bioavailability ratio is decreased in patients with major depressive disorder. Journal of Affective Disorders. 2018; 15;229:145. Ali-Sisto, T., Tolmunen, T., Toffol, E., Viinamäki, H., Mäntyselkä, P., Valkonen-Korhonen, M., Honkalampi, K., Ruusunen, A., Velagapudi, V., Lehto, S.M. PMID:29310063
15. Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C.elegans. Cell. Scott TA, Quintaneiro LM, Norvaisas P, Lui PP, Wilson MP, Leung KY, Herrera-Dominguez L, Sudiwala S, Pessia A, Clayton PT, Bryson K, Velagapudi V, Mills PB, Typas A, Greene NDE, Cabreiro F. (2017). PMID:2843124
16. Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins.  Viruses. 2017; 9, 271. Bulanova, D., Ianevski, A., Bugai, A., Akimov, Y., Kuivanen, S., Paavilainen, H., Kakkola, L., Nandania, J., Turunen, L., Ohman, T., Ala-Hongisto, H., Pesonen, H.M., Kuisma, M.S., Honkimaa, A., Walton, E.L., Oksenych, V., Lorey, M.B., Guschin, D., Shim, J., Kim, J., Than, T.T., Chang, S.Y., Hukkanen, V., Kulesskiy, E., Marjomaki, V.S., Julkunen, I., Nyman, T.A., Matikainen, S., Saarela, J.S., Sane, F., Hober, D., Gabriel, G., De Brabander, J.K., Martikainen, M., Windisch, M.P., Min, J.Y., Bruzzone, R., Aittokallio, T., Vähä-Koskela, M., Vapalahti, O., Pulk, A., Velagapudi, V., Kainov, D.E. PMID:28946654
17. mTORC1 Regulates Mitochondrial Folate Cycle and the Integrated Stress Response in Mitochondrial Disease. Cell Metabolism. 2017; 26(2):419-428. Khan, N.A., Nikkanen, J., Yatsuga, S., Wang, L., Jackson, C., Pessia, A., Riikka Kivelä, Velagapudi, V., Anu Suomalainen. PMID:28768179
18. Metabolomic profiling of extracellular vesicles and alternative normalisation methodsreveal enriched metabolites and strategies to study prostate cancer related changes. Puhka, M., Takatalo, M., Nordberg, M.E., Valkonen, S., Nandania, J., Aatonen, M., Yliperttula, M., Laitinen, S., Velgapudi, V., Mirtti, T., Kallioniemi, O., Rannikko, A., Siljander, P.R.M., af Hallstrom, T.M. Theranostics. 2017; 7(16): 3824-3841. 
19. Ketogenic diet attenuates hepatopathy in mouse model of respiratory chain complex III deficiency caused by a Bcs1l mutation. Scientific Reports. Purhonen, J., Rajendran, J., Mörgelin, M., Uusi-Rauva, K., Katayama, S., Krjutskov, K., Einarsdottir, E., Velagapudi, V., Kere, J., Jauhiainen, M., Fellman, V., Kallijärvi, J. (2017). PMID:28424480
20. Endogenous and xenobiotic metabolic stability of primary human hepatocytes in long-term 3D spheroid cultures revealed by a combination of targeted and untargeted metabolomics. The FASEB Journal. Vorrink, S..U., Ullah, S., Schmidt, S., Nandania, J., Velagapudi, V., Beck, O., Ingelman-Sundberg, M., Lauschke, V.M. (2017). ​​​​​​​PMID:28264975
21. CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs.  Journal of Cell Biology. Schatton, D., Pla-Martin, D., Marx, M.C., Hansen, H., Mourier, A., Nemazanyy, I., Pessia, A., Zentis, P., Corona, T. Kondylis, V., Barth, E., Schauss, A.C., Velagapudi, V., Rugarli, E. (2017).PMID:28188211
22. Broad AOX expression in a genetically tractable mouse model does not disturb normal physiology. Disease Models and Mechanisms. Szibor, M., Dhandapani, PK., Dufour, E., Holmström, KM., Zhuang, Y., Salwig, I., Wittig, I., Heidler, J., Gizatullina, Z., Gainutdinov, T., Consortium, GM., Fuchs, H., Gailus-Durner, V., de Angelis, MH., Nandania, J., Velagapudi, V., Wietelmann, A., Rustin, P., Gellerich, FN., Jacobs, HT., Braun, T. (2017). PMID:28067626
23. Obatoclax, saliphenylhalamide and gemcitabine inhibit Zika virus infection in vitro and differentially affect cellular signaling, transcription and metabolism. Antiviral Research. Kuivanen, S., Bespalov, MM., Nandania, J., Ianevski, A., Velagapudi, V., De Brabander, JK., Kainov, DE., Vapalahti, O. (2017). ​​​​​​​PMID:28049006.
24. Regulation of Kynurenine Biosynthesis during Influenza Virus Infection. The FEBS Journal. Gaelings, L., Söderholm, S., Bugai, A., Fu, Y., Nandania, J., Schepens, B., Lorey, M.B., Tynell, J., Ginste, L.S., Goffic, R.L., Miller, M.S., Kuisma, M., Marjomäki, V., Brabander, J.D., Matikainen, S., Nyman, T.A., Bamford, D., Saelens, X., Julkunen, I., Paavilainen, H., Hukkanen, V., Velagapudi, V., Kainov, D.E. (2017).PMID:27860276
25. The association between musculoskeletal pain and circulating ornithine – A population-based study. Pain Medicine. Mäntyselkä, P., Ali-Sisto, T., Kautiainen, H., Savolainen, J., Niskanen, L., Viinamäki, H., Velagapudi, V., Lehto, S.M. (2016).PMID:28034972
26. Combined immunodeficiency with hypoglycemia caused by mutations in hypoxia up-regulated 1. The Journal of Allergy and Clinical Immunology. Haapaniemi, E., Fogarty, C., Katayama, S., Vihinen, H., Keskitalo, S., Ilander, M., Krjutškov, K., Mustjoki, S., Lehto, M., Hautala, T., Jokitalo, E., Velagapudi, V., Varjosalo, M., Seppänen, M., Kere, J. (2016). PMID:27913302
27. Effect of high-carbohydrate diet on plasma metabolomics in mice with mitochondrial respiratory chain complex III deficiency due to a Bcs1l mutation. International Journal of Molecular Sciences. Rajendran, J., Tomašić, N., Kotarsky, H., Hansson, E., Velagapudi, V., Kallijärvi, J., Fellman, V. (2016). PMID:27809283
28. Activation of Tryptophan and Phenylalanine Catabolism in the Remission Phase of Allergic Contact Dermatitis: A Pilot Study. International Archives of Allergy and Immunology. Zinkevičienė A, Kainov D, Girkontaitė I, Lastauskienė E, Kvedarienė V, Fu Y, Anders S, Velagapudi V. (2016). PMID: 27771694
29. Fecal and serum metabolomics in pediatric inflammatory bowel disease. Journal of Crohn’s and Colitis. Kolho, K-L., Pessia, A., Jaakkola, T., de Vos, W., Velagapudi, V. (2016).  PMID: 27609529
30. Modified Atkins diet induces subacute selective ragged red fiber lysis in mitochondrial myopathy patients. EMBO Molecular Medicine. Ahola, S., Auranen, M., Isohanni, P., Niemisalo, S., Buzkova, J., Velagapudi, V., Lundbom, N., Hakkarainen, A., Piirilä, P., Pietiläinen, K., Suomalainen, A. (2016).  PMID: 27647878 Press release
31. The Pentose Phosphate Pathway Regulates the Circadian Clock. (2016). Cell Metabolsim.  Rey, G., Valekunja, U.K., Feeney, K.A., Wulund, L., Milev, N.B., Stangherlin, A., Bollepalli, L., Velagapudi, V., O’Neill, J.S., Reddy, A.B.PMID: 27546460
32. JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses. Antiviral Research.  Fu Y, Gaelings L, Söderholm S, Belanov S, Nandania J, Nyman TA, Matikainen S, Anders S, Velagapudi V, Kainov DE. (2016). PMID: 27451344
33. GATA4 regulates blood-testis barrier function and lactate metabolism in mouse Sertoli cells. Endocriniology. Schrade, A., Kyrönlahti, A., Akinrinade, O., Pihlajoki, M., Fischer, S., Martinez Rodriguez, V., Velagapudi V, Toppari, J., Wilson, DB., Heikinheimo, M. (2016). PMID: 26974005
34. Purine metabolism is dysregulated in patients with major depressive disorder. Psychoneuroendocrinology. Ali-Sisto, T., Tolmunen, T., Toffol, E., Viinamäki, H., Mäntyselkä, P., Valkonen-Korhonen, M., Honkalampi, K., Ruusunen, A., Velagapudi V, Lehto, S.M. (2016). MID: 27153521
35. Mitochondrial DNA Replication Defects Disturb Cellular dNTP Pools And Remodel One-Carbon Metabolism. Cell Metabolism. Nikkanen J, Forsström S, Euro L, Paetau I, Kohnz R.A, Wang L, Chilov D, Viinamäki J, Roivainen A, Marjamäki P, Liljenbäck H, Ahola S, Buzkova J, Terzioglu M, Khan N.A, Pirnes-Karhu S, Paetau A, Lönnqvist T, Sajantila A, Isohanni P, Tyynismaa H, Nomura D.K, Battersby B, Velagapudi V, Carroll C.J, Suomalainen A. (2016). PMID: 26924217
36. GATA4 is a key regulator of steroidogenesis and glycolysis in mouse Leydig cells. Endocrinology. Schrade A, Kyrönlahti A, Akinrinade O, Pihlajoki M, Häkkinen M, Fischer S, Alastalo T.P, Velagapudi V, Toppari J, Wilson D.B, Heikinheimo M (2015). PMID: 25668067
37. Vitamin B12–dependent taurine synthesis regulates growth and bone mass. Journal of Clinical Investigation. Roman-Garcia P, Quiros-Gonzalez I, Mottram L, Lieben L, Sharan K, Wangwiwatsin A, Tubio J, Lewis K, Wilkinson D, Santhanam B, Sarper N, Clare S, Vassiliou GS, Velagapudi V, Dougan G, Yadav V.K. (2014).PMID: 24911144
38. Effective treatment of mitochondrial myopathy by nicotinamide riboside, a vitamin B3. EMBO Molecular Medicine. Khan N.A, Auranen M, Paetau I, Pirinen E, Euro L, Forsström S, Pasila L, Velagapudi V, Carroll C.J, Auwerx J, Suomalainen A. (2014). PMID: 24711540​​​​​​​