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Biomedical Metabolomics Facility Leiden

Contact Details

Leiden University

Einsteinweg 55 2333 CC Leiden

Prof. dr. T. Hankemeier

0031 (0)71 5274226

Hotel Description

Metabolomics: development and application of LC-MS, CE-MS and GC-MS metabolomics platforms with a unique biochemical coverage, including polar and non-polar lipidomics, oxylipids and eicanosoids, biogenic amines, organic and bile acids, central carbon/energy metabolism and oxidized/nitrosative stress. Determination of metabolite profiles in serum, plasma, urine, CSF and different types of tissues including muscle and plaques.

  • Biomedical & health
  • Development of innovative analytical strategies for metabolomics-driven systems biology and systems pharmacology and application thereof in answering biological questions in personalized health strategies

Expertise and Track Record

43500985020 Effects of sanitary and health status on amino acid and energy metabolism of growing-finishing pigs with A. Jansman (Wageningen University). 43500984146 A systems approach to identify metabolic vulnerabilities of triple negative breast cancer with S.E. le Dévédec (LACDR). 43500984085 Differential effects of oxylipins on occurrence of cardiovascular diseases with I. Sluijs (UMC Utrecht). 43500984074 Metabolic effects of a high level of dietary zinc in piglet diets to induce immune competence with S. kanti Kar (WUR). 43500984060 Understanding gut feelings: Metabolomics insight in the effects of probiotics on cognitive functioning and mental well-being with L. Steenbergen (University of Amsterdam). 43500984029 Towards underlying mechanisms: understanding the health benefits of wholegrain wheat products with L.A. Afman (Wageningen University). 4350098208 Oxygen-induced adaption of metabolism: effects on liver function, gene expression and metabolism with dr. E.G. Mik (Erasmus MC). 435000004 Metabolic effects of dietary proteins with prof. dr. M.A. Smits (WUR). 435000024 Metabolomic biomarkers of oxidative damage and cardiovascular disease in patients with diabetes or prediabetes with dr. M.M.J. van Greevenbroek (Maastricht UMC). 43500028 A metabolomic approach to improve personalized medicine in diabetes with dr. H.J. Lambers Heerspink (UMCG). 435000035 Lipidomic biomarkers of Cystic Fibrosis in lung lavage fluids of juvenile Cystic Fibrosis patients with dr. B.J. Scholte (Erasmus MC). 435002020 Metabolic effects of dietary proteins With Smits (WUR). 435002027 A metabolomics approach to improve personalized medicine in patients chronically infected with HIV With Boonstra (Erasmus MC).

We have created a world class metabolomics knowledge infrastructure to improve personal health and quality of life. Due to our reputation as an international leader in the field of metabolomics, we are a sought out partner for public-private scientific and academic collaborations worldwide.

We are involved in an anti-platelet study of an Amish population (HAPI) with the goal of finding biomarkers of responder/non-responders to anti-platelet therapy. We measured metabolic profiles of serum samples and combined our data with those of collaborators within the US Pharmacometabolomics Research Network (PMRN). Together we found some potential biomarkers, conducted mechanistical studies on platelets and have secured samples from a broader population to validate our findings (Ellero-Simatos S et al, CPT Pharmacometrics Syst Pharmacol. 2014 Jul 16;3:e125. doi: 10.1038/psp.2014.22).

We are partner in the BBMRI consortium and have measured lipid profiles of more than 9000 plasma samples from several biobank cohorts. We are also providing our DSP (data support platform) infrastructure to make this data available to collaborators to query with their biological questions. We discovered for example a lipid profile for healthy aging (Gonzalez-Covarrubias V et al, Aging Cell, 2013; doi: 10.1111/acel.12064)
We work with scientists from several private clients in Europe and the US to study drug effects. We have modified our existing methods to work with their non-standard matrices (plaques, xenografts, biopsies) and have developed custom platforms to target their biological questions. These new validated platforms will be available for use by other collaborators.

  • Ellero-Simatos S, Lewis JP, Georgiades A, Yerges-Armstrong LM, Beitelshees AL, Horenstein RB, Dane A, Harms AC, Ramaker R,Vreeken RJ, Perry CG, Zhu H, Sànchez CL, Kuhn C, Ortel TL, Shuldiner AR, Hankemeier T, Kaddurah-Daouk R. Pharmacometabolomics reveals that serotonin is implicated in aspirin response variability. CPT Pharmacometrics Syst Pharmacol. 2014 Jul 16;3:e125. doi: 10.1038/psp.2014.22.
  • Gonzalez-Covarrubias V, Beekman M, Uh H-W, Dane A, Paliukhovich I, van der Kloet FM, Houwing-Duistermaat J, Vreeken RJ, Hankemeier T and Slagboom EP. Lipidomics of familial longevity. Ageing Cell. 2013; 12 (3) :426–434 DOI: 10.1111/acel.12064
  • Dane AD, Hendriks MM, Reijmers TH, Harms AC, Troost J, Vreeken RJ, Boomsma DI,van Duijn CM, Slagboom EP, Hankemeier T. Integrating metabolomics profiling measurements across multiple biobanks. Anal Chem. 2014 May 6;86(9):4110-4. doi:10.1021/ac404191a.
  • Rojas-Chertó M, van Vliet M, Peironcely JE, van Doorn R, Kooyman M, te Beek T, van Driel MA, Hankemeier T, Reijmers TH. MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data. BIOINFORMATICS. 2012; 28(20):2707-9. doi: 10.1093/bioinformatics/bts486
  • Quist J, Vulto P, van der Linden HJ, Hankemeier T. Tunable Ionic Mobility Filter for Depletion Zone Isotachophoresis. ANALYTICAL CHEMISTRY. 2012; 84(21):9065-71, doi: 10.1021/ac301612n
  • Peironcely JE, Rojas-Chertó M,Tas A, Vreeken RJ, Reijmers TH, Coulier L, Hankemeier T. Automated Pipeline For De Novo Metabolite Identification Using Mass Spectrometry-Based Metabolomics. ANALYTICAL CHEMISTRY. 2012; doi: 10.1021/ac303218u
  • Lindenburg PW, Tjaden UR, van der Greef J and Hankemeier T. Feasibility of electroextraction as versatile sample preconcentration for fast and sensitive analysis of urine metabolites, demonstrated on acylcarnetines. Electrophoresis, 2012 doi: 10.1002/elps.201200276.

We are the metabolomics partner in multiple networks including NMC, CTMM, TIFN, BBMRI, VIRGO, Pharmacometabolomics Research Network (PMRN), and we participate in numerous EU, NIH and nationally-funded projects.

Hotel Characteristics

  • 1 lab manager
  • 6 dedicated technicians
  • 1 biostatician

34% external

  • Mass spectrometers: 1 LTQ-Orbitrap MS (Thermo Scientific), 2 LTQ-FT-ICR MS (Thermo Scientific), 1 Triple Tof (AB Sciex), 2 q-TOF with a triwave ion mobility (Waters Synapt G1 and G2S), 4 q-TOF-MS systems (3xAgilent, 1x Bruker), 2 TOF-MS (1xAgilent, 1x Bruker), 5 triple quadrupole MS system (1xShimadzu, 2xWaters, 2 x Agilent) , 3 ion-trap MS (Thermo Deca’s), 2 GC-qMS
  • Separations: 2 HPLC-chip systems (Agilent G4240A), 2 NanoMate direct infusion systems (Advion), 6 UPLC systems (Waters, Shimadzu), 2 high-pressure nano-LC (1 Eksigent high-pressure nano-LC), 4 CE systems (Agilent), 2 HPLC (Agilent 1200, 600 bar), 1 nanoLC (Dionex), 1 nanoLC (Agilent), 10 LC systems (various suppliers).

ISO 17025

It is possible to use our data support platform as a data repository.