Plant Metabolomics Facility-WPR

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).

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.