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Plant Metabolomics Facility-WPR

Contact Details

Wageningen Plant Research, Wageningen-UR

Droevendaalsesteeg 1 (building 107), 6708 PB Wageningen, The Netherlands

Dr. R.C.H. de Vos, Dr. R. Mumm, Prof. Dr. R.D. Hall

0031 (0)317 480841 dr. R. de Vos; 0031 (0)317 481982 dr. R. Mumm; 0031 (0)317 480441 Prof. dr. R. Hall

Hotel Description

Within the business unit Bioscience of Wageningen Plant Research, WPR (formerly Plant Research International) we have established a state-of-the-art metabolomics facility for large-scale analyses of compounds present in plants and their products, as well as in other organisms related to plant phytonutrient production and intake. Our facility comprises a range of instruments dedicated to and fully available for metabolomics research, including UPLC / HPLC instruments coupled to both photodiode array detection (DAD) and high resolution Q Exactive FTMS or LTQ- Orbitrap FTMS, and GC instruments coupled to TOF MS, single or triple quadrupole MS, as well as an entire in-house workflow for data preprocessing. Our platforms enable both targeted and untargeted metabolomics approaches for the analysis of only a few target compounds up to a few thousand volatile and non-volatile compounds detectable by mass spectrometry in the headspace and polar, semi-polar and/or a-polar extracts of plant materials. Our special expertise is untargeted metabolomics, aiming to get an unbiased and comprehensive overview of the metabolic differences between samples in relation to the underlying research question, such as defining genetic variation, plant physiology and pathology topics, food processing effects, compounds key to sensory characteristics, product storage, seed quality etcetera. To cope with the large datasets inherent to untargeted metabolomics, we have developed a dedicated, partly automated data processing workflow, metabolite databases and statistical tools, which we are constantly improving and expanding.
We have more than 15 years of experience and know-how in LCMS and GCMS based metabolomics approaches in numerous plant species including important crops and model plants, such as Arabidopsis, tomato, potato, cabbages, coffee, cocoa, apple, berries, lettuce, peppers, etcetera, but also algae, micro-organisms and human fluids. We are world-wide recognized as one of the leading groups in the plant metabolomics field and have built up an excellent track record.

  • Biomedical & health
  • Agri & Food
  • Industrial biotech
  • Mass spectrometry
  • Bioinfomatics
  • Biostatistics
  • Developing new metabolomics platforms and methods
  • LAESI-MS imaging
  • Plant breeding research; Biodiversity screening
  • Plant physiology
  • Plant insect / pathogen interactions
  • Biomarker research related to plant and product quality characteristics, including taste
  • Food processing and fermentation effects on metabolite compositions

Expertise and Track Record

43500985042 Coupling metabolomics to de novo Brassica oleracea crop genomes to explore and control crop phytochemical composition with C. Bachem (Wageningen University). 43500985037 Scent of foodborne pathogens – Detection of volatile biomarkers associated with Campylobacter infection in broiler chickens with E. Pacholewicz (Wageningen Bioveterinary Research). 43500985036 Metabolic profiling of strawberry fruit to identify volatile and non-volatile components involved in botrytis resistance and postharvest longevity with R. Schouten (Wageningen University). 43500985026 Rhodobacter metabolomics for producing different plant flavours with D. Bosch (Wageningen University). 4350098234 Metabolomics in space: quality of crops grown on Mars and Moon with prof.dr.ir. L.F.M. Marcelis (WUR). 4350098202 Healthier lettuces for healthier food wit dr. R. van Treuren (Centrum voor Genetische Bronnen Nederland). 4350098242 Metabolomic profiling of Brassica fruticulosa to identify plant compounds causing resistance to the cabbage root fly with prof.dr.ir. J.J.A. van Loon (WUR). 435000003 Natural variation in drought response and adaptation in Arabidopsis thaliana with Dr. ing. J.J.B. Keurentjes (WUR). 435000012 Metabolome of chemically primed tomatoes with Dr. B. Vosman (WUR). 435000014 Metabolic changes during dormancy release in tulips with mr.dr.ir. R.G.H. Immink (WUR). 435002018 Healthy tomato fruits by localised LED light With Marcelis (WUR). 435002019 Climate ready crops; The metabolic basis of adaptive growth responses to high ambient temparatures in plants With Van Zanten (Utrecht University). 435002026 Feasibility of 13C-labelled plant extracts as internal standards in metabolomics studies in Life Sciences and Health With Wevers (RadboudUMC).

We offer a unique combination of both biological and technological expertise and knowhow of applying single or multiple MS-based metabolomics approaches in research dealing with plants and their products, starting with experimental set up and sample handling up to targeted and untargeted MS data processing and biostatistical analyses.

1. Lopez-Sanchez, Patricia.*, Ric C.H. de Vos*, Roland Mumm, Robert D. Hall, L. Bialek, R. Leenman, K. Strassburg, R. Vreeken, T. Hankemeier, S. Schumm, and J. van Duynhoven. 2015. Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees. Food Chem. 168, 348-355. A range of analytical platforms havs ben used to determine differential effects of industrial processing methods. The WPR-metabolomics facility played a key role in the untargeted metabolomics analyses and data processing / interpretation.

2. Van Duynhoven, John*, J.J.J. van der Hooft*, F. van Dorsten, S. Peters, M. Foltz, M.V Gomez-Roldan, J. Vervoort, Ric C.H. de Vos*, D.M. Jacobs*. 2014. Rapid and sustained systemic circulation of conjugated gut microbial metabolites after single-dose black tea consumption. J. of Proteome Research 13, 2668-2678. Untargeted UPLC-LTQ-Orbitrap FTMS to plasma samples of volunteers after black tea intake, to identify and quantify metabolites from tea polyphenols during circulation. The WPR-metabolomics facility played a key role in the untargeted metabolomics analyses, data processing and metabolite identifications.

3. Tikunov, Yury M, Jos Molthoff, Ric C.H. de Vos, Jules Beekwilder, Adele van Houwelingen, Justin J. J. van der Hooft, Mariska Nijenhuis-de Vries, Caroline W. Labrie, Wouter Verkerke, Henri van de Geest, Marcela Viquez Zamora, Silvia Presa, Jose Luis Rambla Nebot, Antonio Granell, Robert D. Hall and Arnaud G. Bovy. 2013. NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit. Plant Cell 25, 3067-3078. Integrating data from untargeted metabolomics of non-volatile (by LCMS) and natural volatile compounds (by headspace GCMS) resulted in the identification of a novel gene responsible for the smoky flavour trait within consumption tomatoes.

4. Gomez-Roldan M.V., Bas Engel, Ric C.H. de Vos, Pieter Vereijken, Laura Astola, Marian Groenenboom, Henri van de Geest, Arnaud Bovy, Jaap Molenaar, Fred van Eeuwijk, Robert D. Hall. 2014. Metabolomics reveals organ-specific metabolic rearrangements during early tomato seedling development. Metabolomics DOI 10.1007/s11306-014-0625-2. Untargeted LCMS-based metabolomics and statistical analyses to determine biochemical pathways activated upon tomato plant growth. A combined effort of the PRI-metabolomici (RdV, MVG-R, AB, HvdG, RDH) and WUR-Biometris group.

The Metabolomics Hotel facility at the WPR department Bioscience is actively and strongly interacting and collaborating with genetici, biostatisticians and bioinformaticians, some of which are part of the same department Bioscience, in order to integrate metabolomics data to other -omics data or plant quality trait data. The hotel managers also collaborates with other relevant analytical groups within Wageningen-UR, including RIKILT (Lommen, Nielen) and Biochemistry (Vervoort, Ridder).

  • Keurentjes JJ*, Fu J*, De Vos RCH*, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M. 2006. The genetics of plant metabolism. Nature Genetics 3, 842-849. This study combines, for the first time in plants, genome-wide untargeted LCMS metabolomics with genetic variation in a recombinant inbred line population of Arabidopsis, in order to identify novel loci regulating metabolite composition. De Vos (* shared first author) was responsible for the metabolomics part and both De Vos and Hall were involved in setting up the experiments and writing the manuscript.
  • De Vos R.C.H.*, Moco S*, Lommen A*, Keurentjes JJ, Bino RJ, Hall RD. 2007. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nature Protocols 2, 778-791. This technology development paper provides a detailed protocol for large-scale untargeted metabolomics in plants using accurate mass LCMS, mainly focused on secondary metabolites. The protocol includes sample harvest, extract preparation, LCMS set-up and strategy for sample analysis, untargeted data processing and quality control, and strategies for identifying selected compounds. De Vos (*shared first author) was responsible for the experiments and wrote a large part of the paper; Hall was managing the research and responsible for the final quality of the paper.
  • Moing, A., A. Aharoni, B. Biais, I. Rogachev, S. Meir, L. Brodsky, J.W. Allwood, A. Erban, W.B. Dunn, L. Kay, S. de Koning, R.C.H. de Vos, H. Jonker, R. Mumm, C. Deborde, M. Maucourt, S. Bernillon, Y. Gibon, T.H. Hansen, S. Husted, R. Goodacre, J. Kopka, J.K. Schjoerring, D. Rolin & R.D. Hall. 2011. Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. New Phytologist 190, 683-696 . This paper deals with integration of comprehensive metabolomics data from various complementary analytical platforms as technology innovation, to get the most comprehensive insight into the metabolome of ripening melon fruit. De Vos and Mumm were responsible for setting up and carrying out GCMS-volatile, LCMS and carotenoid profiling techniques; Hall was coordinator of this EU-granted project and the final responsible person for setting up the experiments and quality of the paper.
  • Moco S, Bino RJ, Vorst O, Verhoeven HA, de Groot J, van Beek TA, Vervoort J, De Vos CH. 2006. A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiology 141(4):1205-18. This paper introduces accurate mass LCMS as untargeted metabolomics research tool in tomato and provides, for the first time, a publicly accessible database for annotation of tomato fruit metabolites in LCMS data sets. De Vos was co-supervisor of this PhD study and was mainly responsible for the ideas, management of this study and for the quality of the final manuscript.
  • Tikunov Y. M., S. Laptenok, R. D. Hall , A. Bovy, R. C. H. de Vos. 2012. MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data. Metabolomics 8, 714-718. This paper describes a novel software tool in the processing of untargeted metabolomics data, in order to cluster all mass features originating from a single metabolite into mass spectra, that can be used for searching in metabolite libraries. Both De Vos and Hall have been involved in discussing the research and developing the software, and helped in writing the paper.
  • Ridder L.. Justin J. J. van der Hooft, Stefan Verhoeven, Ric C. H. de Vos, Raoul J. Bino, and Jacques Vervoort. 2013 Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea. Analytical Chemistry 2013 85 (12), 6033-6040. This paper describes a novel tool, MAGMa, that can automatically match LCMSn data with metabolite libraries
  • Ishita Ahuja, Ric C. H. de Vos. Jens Rohloff, Geert M. Stoopen, Kari K. Halle, Samina Jam Nazeer Ahmad, Linh Hoang, Robert D. Hall & Atle M. Bones 2016. Arabidopsis myrosinases link the glucosinolate-myrosinase system and the cuticle. Scientific Reports 6, 38990; DOI: 10.1038/srep38990. Comprehensive metabolomics of myrosinase mutants in Arabidopsis reveals novel functions of the glucosinolate pathway
  • Mumm, R, J. A. Hageman, M. N. Calingacion, R.C.H. de Vos, H. H. Jonker, A. Erban, J. Kopka, T. H. Hansen, K. H. Laursen, J. K. Schjoerring, J. L. Ward, M. H. Beale, S. Jongee, A. Rauf, F. Habibi, S. D. Indrasari, S. Sakhan, A. Ramli, M. Romero, R. F. Reinke, K. Ohtsubo, C. Boualaphanh, M. A. Fitzgerald, R. D. Hall. 2016 Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics. Metabolomics 12:38. DOI 10.1007/s11306-015-0925-1.
  • Etalo D., De Vos R.C.H., Joosten M.H.A.J., Hall R.D. (2015) Spatially-resolved plant metabolomics: some potentials and limitations of Laser-Ablation Electrospray Ionization (LAESI) Mass Spectrometry metabolite imaging. Plant Physiology 169, 1424-1435.
  • Lopez-Sanchez, P., R.C.H. de Vos., R. Mumm, R.D. Hall, L. Bialeka, R. Leenman, K. Strassburg, R. Vreeken, T. Hankemeier, S. Schumma and J. van Duynhoven (2015). Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees. Food Chemistry 168, 348-355

The metabolomics facility at Bioscience-WPR has been / still is part of the Centre of Biosystems Genomics (CBSG; ended December 2012), the Netherlands Centre for Biosystems Genomics (NCSB; ended December 2012), the Netherlands Metabolomics Centre (NMC) and the Consortium for Improving Plant Yield (CIPY), which are all large collaborative programs of the Netherlands Genomics Initiative. The head of our metabolomics group, Prof. Dr. Robert Hall, has been managing director of CBSG, while both Dr. Hall and Dr. De Vos were part of the management team of the NMC. Within these consortia our metabolomics group has been / still is dealing with technology innovation, developing new tools to improve and expand the applications of metabolomics techniques in plant research. With regard to international collaborations, Dr. Robert Hall has been coordinator of the EU-project Meta-PHOR (Metabolomics for Outreach and Health), which aimed to set up new metabolomics technologies and protocols for major food crops, including broccoli, melon and rice. Next to this dedicated technology development project, our metabolomics group has been and still is involved in various other EU-projects further developing and applying metabolomics technologies, like EU-Flavo, EU-Flora, EU-Athena, EU-Sol, EU-TerpMed and EU-Fuel4Me.

Hotel Characteristics

  • visiting scientists / postdocs: 1-2 fte
  • MS and lab technicians: 3 fte
  • hotel managers: 2.0 fte
  • biostatisticians: 0.2 fte
  • bioinformaticians: 0.3 fte


  • Dionex (U)HPLC with Thermo PDA-Q Exactive FTMS
  • Waters Acquity (U)HPLC with Thermo PDA- LTQ-Orbitrap FTMS
  • Waters UPLC-triple Q MS
  • Agilent GCMS
  • Thermo GCMS
  • Da Vinci-Agilent GCMS
  • Interscience tripleQ MS

own quality standards and MSI

Internal server and, if desired, the Metabolight repository (http://www.ebi.ac.uk/metabolights)