Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Metabolomics Society’s International Affiliations
    Roessner, U. ; Rolin, D. ; Rijswijk, M.E.C. van; Hall, R.D. ; Hankemeier, T. - \ 2015
    Metabolomics 11 (2015)3. - ISSN 1573-3882 - p. 501 - 502.
    In 2012 the Metabolomics Society established a more formal system for national and regional metabolomics initiatives, interest groups, societies and networks to become an International Affiliate of the Society. A number of groups ( tions/benefits-of-affiliation) have taken up the opportunity to sign a Memorandum of Affiliation building a bridge of collaboration with the Society. The Society is very proud to have established these relationships extending our network and bringing the Society closer to the researchers and metabolomics friends. At the 11th Annual Conference of the Metabolomics Society in San Francisco ( we will be holding a meeting of representatives of all present affiliations and will establish an Affiliates Task Group which will build the basis for affiliations to communicate better with each other and share ideas, success stories and also discuss issues of any concern. If any regional metabolomics group is interested to become an affiliate, please contact the president and you are invited to our first face-to-face meeting in June. We aim to inform our community with regular updates of existing affiliations, not only through MetaboNews, but also through our society journal Metabolomics, allowing affiliations to present their missions and activities to the wider community. In this issue three affiliations have provided an update; the French Metabolomics and Fluxomics Network, The Netherlands Metabolomics Centre and the newly established Swiss Metabolomics Society.
    Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees
    Lopez-Sanchez, P. ; Vos, R.C.H. de; Jonker, H.H. ; Mumm, R. ; Hall, R.D. ; Bialek, L. ; Leenman, R. ; Strassburg, K. ; Vreeken, R. ; Hankemeier, T. ; Schumm, S. ; Duynhoven, J.P.M. van - \ 2015
    Food Chemistry 168 (2015). - ISSN 0308-8146 - p. 348 - 355.
    mass-spectrometry - plant metabolomics - thermal treatments - vitamin-c - broccoli - tomato - fruit - antioxidant - cancer - l.
    The effects of conventional industrial processing steps on global phytochemical composition of broccoli, tomato and carrot purees were investigated by using a range of complementary targeted and untargeted metabolomics approaches including LC–PDA for vitamins, 1H NMR for polar metabolites, accurate mass LC–QTOF MS for semi-polar metabolites, LC–MRM for oxylipins, and headspace GC–MS for volatile compounds. An initial exploratory experiment indicated that the order of blending and thermal treatments had the highest impact on the phytochemicals in the purees. This blending-heating order effect was investigated in more depth by performing alternate blending-heating sequences in triplicate on the same batches of broccoli, tomato and carrot. For each vegetable and particularly in broccoli, a large proportion of the metabolites detected in the purees was significantly influenced by the blending-heating order, amongst which were potential health-related phytochemicals and flavour compounds like vitamins C and E, carotenoids, flavonoids, glucosinolates and oxylipins. Our metabolomics data indicates that during processing the activity of a series of endogenous plant enzymes, such as lipoxygenases, peroxidases and glycosidases, including myrosinase in broccoli, is key to the final metabolite composition and related quality of the purees.
    Postprandial fatty acid specific changes in circulating oxylipins in lean and obese men after high-fat challenge tests
    Strassburg, K. ; Esser, D. ; Vreeken, R.J. ; Hankemeier, T. ; Müller, M.R. ; Duynhoven, J.P.M. van; Golde, J. van; Dijk, S.J. van; Afman, L.A. ; Jacobs, D.M. - \ 2014
    Molecular Nutrition & Food Research 58 (2014)3. - ISSN 1613-4125 - p. 591 - 600.
    eicosanoid biology - markers - health
    Scope Circulating oxylipins may affect peripheral tissues and are assumed to play an important role in endothelial function. They are esterified in triglyceride-rich lipoproteins that are increased after a high-fat (HF) meal, depending on BMI and fatty acid (FA) type. Yet, it is unclear which oxylipins appear in circulation after HF meals differing in FA composition. Methods and results In a double-blind randomized crossover challenge study, we characterized the postprandial oxylipin response after different HF challenges in lean and obese men receiving HF milkshakes, either high in saturated FAs (SFA), monounsaturated FAs (MUFA), or omega 3 (n-3) polyunsaturated FAs (PUFA). Plasma oxylipin profiles were significantly altered at 2 and 4 h after shake consumption when compared to baseline. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) derived oxylipins increased after n-3 PUFA shake consumption. MUFA shake consumption increased levels of cytochrome P450 mediated oxylipins. SFA shake consumption led to strong increases in linoleic acid (LA) derived HODEs. No differences were observed between lean and obese individuals at baseline and after any shake consumption. Conclusion e are the first demonstrating acute effects on circulating oxylipins after HF meal challenges. These changes were strongly influenced by different dietary FAs and may affect endothelial function.
    Solvent exchange module for LC-NMR hyphenation using machine vision-controlled droplet evaporation
    Schoonen, J.W. ; Vulto, P. ; Roo, N. de; Duynhoven, J.P.M. van; Linden, H. van der; Hankemeier, T. - \ 2013
    Analytical Chemistry 85 (2013)12. - ISSN 0003-2700 - p. 5734 - 5739.
    solid-phase extraction - nuclear-magnetic-resonance - red wine/grape juice - ms-spe-nmr - natural-products - liquid-chromatography - flow probe - black tea - identification - system
    We report the use of pendant droplet evaporation for exchange of eluents for 1H nuclear magnetic resonance (1H NMR) purposes. Analytes are fed and retained in 500 nL droplets, which are concentrated by evaporation and subsequently redissolved in deuterated solvent. Droplet size is monitored by machine vision (MV), and heating rates are adjusted concordingly to maintain a stable droplet volume. Evaporation control is independent of solvent properties, and the setup handles feed rates up to 7 µL min–1. The interface is capable of exchanging up to 90% of solvent for deuterated solvent, with a good recovery and repeatability for tomato extracts (Solanum lycopersicum). The system was capable of handling both polar and nonpolar analytes in one run. Volatiles such as formate, acetate, and lactate and the thermosensitive compound epigallocatechin gallate were recovered without significant losses. Ethanol and propionate were recovered with significant losses due to the formation of a minimum boiling azeotrope. The current setup is ideally suited for on- and off-line hyphenation of liquid chromatography and NMR, as it is comprehensive, fully automated, and easy to operate.
    Lipidomics reveals multiple pathway effects of a multi components preparation on lipd biochemistry in ApoeE*3Leiden.CETP mice
    Wei, H. ; Hu, C. ; Wang, M. ; Hoek, A.M. van den; Reijmers, T.H. ; Wopereis, S. ; Bouwman, J. ; Ramaker, R. ; Korthout, H.A.A.J. ; Vennik, M. ; Hankemeier, T. ; Havekes, L.M. ; Witkamp, R.F. ; Verheij, E.R. ; Xu, G. ; Greef, J. de - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203
    cholesteryl ester transfer - systems biology - apoe-asterisk-3-leiden.cetp mice - aggravates atherosclerosis - overweight patients - chinese medicine - weight-reduction - transfer protein - hdl-cholesterol - transgenic mice
    Background: Causes and consequences of the complex changes in lipids occurring in the metabolic syndrome are only partly understood. Several interconnected processes are deteriorating, which implies that multi-target approaches might be more successful than strategies based on a limited number of surrogate markers. Preparations from Chinese Medicine (CM) systems have been handed down with documented clinical features similar as metabolic syndrome, which might help developing new intervention for metabolic syndrome. The progress in systems biology and specific animal models created possibilities to assess the effects of such preparations. Here we report the plasma and liver lipidomics results of the intervention effects of a preparation SUB885C in apolipoprotein E3 Leiden cholesteryl ester transfer protein (ApoE*3Leiden.CETP) mice. SUB885C was developed according to the principles of CM for treatment of metabolic syndrome. The cannabinoid receptor type 1 blocker rimonabant was included as a general control for the evaluation of weight and metabolic responses. Methodology/Principal Findings: ApoE*3Leiden.CETP mice with mild hypercholesterolemia were divided into SUB885C-, rimonabant- and non-treated control groups. SUB885C caused no weight loss, but significantly reduced plasma cholesterol (-49%, p <0.001), CETP levels (-31%, p
    Quantitative Profiling of Oxylipins through Comprehensive LC-MS/MS Analysis: Application in cardiac surgery
    Strassburg, K. ; Huijbrechts, A.M.L. ; Kortekaas, K. ; Lindeman, J. ; Pedersen, T.L. ; Newman, J.W. ; Dane, A. ; Berger, R. ; Brenkman, A. ; Hankemeier, T. ; Duynhoven, J.P.M. van; Kalkhoven, E. ; Vreeken, R. - \ 2012
    Analytical and Bioanalytical Chemistry 404 (2012)5. - ISSN 1618-2642 - p. 1413 - 1426.
    tandem mass-spectrometry - soluble epoxide hydrolase - arachidonic-acid - human plasma - lipidomic analysis - fatty-acids - in-vivo - dihydroxyeicosatrienoic acids - hydroxyeicosatetraenoic acids - simultaneous quantification
    Oxylipins, including eicosanoids, affect a broad range of biological processes, such as the initiation and resolution of inflammation. These compounds, also referred to as lipid mediators, are (non-) enzymatically generated by oxidation of polyunsaturated fatty acids such as arachidonic acid (AA). A plethora of lipid mediators exist which makes the development of generic analytical methods challenging. Here we developed a robust and sensitive targeted analysis platform for oxylipins and applied it in a biological setting, using high performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) operated in dynamic multiple reaction monitoring (dMRM). Besides the well-described AA metabolites, oxylipins derived from linoleic acid, dihomo-¿-linolenic acid, a-linolenic acid, eicosapentaenoic acid and docosahexaenoic acid were included. Our comprehensive platform allows the quantitative evaluation of approximately 100 oxylipins down to low nanomolar levels. Applicability of the analytical platform was demonstrated by analyzing plasma samples of patients undergoing cardiac surgery. Altered levels of some of the oxylipins, especially in certain monohydroxy fatty acids such as 12-HETE and 12-HEPE, were observed in samples collected before and 24 h after cardiac surgery. These findings indicate that this generic oxylipin profiling platform can be applied broadly to study these highly bioactive compounds in relation to human disease.
    Metabolite Identification Using Automated Comparison of High-Resolution Multistage Mass Spectral Trees
    Rojas-Cherto, M. ; Peironcely, J.E. ; Kasper, P.T. ; Hooft, J.J.J. van der; Vos, R.C.H. de; Vreeken, R. ; Hankemeier, T. ; Reijmers, T. - \ 2012
    Analytical Chemistry 84 (2012)13. - ISSN 0003-2700 - p. 5524 - 5534.
    development kit cdk - source java library - spectrometry data - chemical markup - fragmentation - web - optimization - instruments - algorithms - ms/ms
    Multistage mass spectrometry (MSn) generating so-called spectral trees is a powerful tool in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics to identify unknown, but biologically relevant, compounds. As a consequence, there is a growing need for computational tools specifically designed for the processing and interpretation of MSn data. Here, we present a novel approach to represent and calculate the similarity between high-resolution mass spectral fragmentation trees. This approach can be used to query multiple-stage mass spectra in MS spectral libraries. Additionally the method can be used to calculate structure-spectrum correlations and potentially deduce substructures from spectra of unknown compounds. The approach was tested using two different spectral libraries composed of either human or plant metabolites which currently contain 872 MSn spectra acquired from 549 metabolites using Orbitrap FTMSn. For validation purposes, for 282 of these 549 metabolites, 765 additional replicate MSn spectra acquired with the same instrument were used. Both the dereplication and de novo identification functionalities of the comparison approach are discussed. This novel MSn spectral processing and comparison approach increases the probability to assign the correct identity to an experimentally obtained fragmentation tree. Ultimately, this tool may pave the way for constructing and populating large MSn spectral libraries that can be used for searching and matching experimental MSn spectra for annotation and structural elucidation of unknown metabolites detected in untargeted metabolomics studies.
    The Effect of Preanalytical Factors on Stability of the Proteome and Selected Metabolites in Cerebrospinal Fluid (CSF)
    Rosenling, T. ; Slim, C.L. ; Christin, C. ; Coulier, L. ; Shi, S. ; Stoop, M.P. ; Bosman, J. ; Suits, F. ; Horvatovich, P.L. ; Stockhofe, N. ; Vreeken, R. ; Hankemeier, T. ; Gool, A.J. ; Luider, T.M. ; Bischoff, R. - \ 2009
    Journal of Proteome Research 8 (2009)12. - ISSN 1535-3893 - p. 5511 - 5522.
    chromatography-mass spectrometry - multiple-sclerosis - liquid-chromatography - biomarker discovery - cystatin-c - storage-conditions - sample collection - clinical-practice - lc-ms - serum
    To standardize the use of cerebrospinal fluid (CSF) for biomarker research, a set of stability studies have been performed on porcine samples to investigate the influence of common sample handling procedures on proteins, peptides, metabolites and free amino acids. This study focuses at the effect on proteins and peptides, analyzed by applying label-free quantitation using microfluidics nanoscale liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (chipLC-MS) as well as matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) and Orbitrap LC-MS/MS to trypsin-digested CSF samples, The factors assessed were a 30 or 120 min time delay at room temperature before storage at -80 degrees C after the collection of CSF in order to mimic potential delays in the clinic (delayed storage), storage at 4 degrees C after trypsin digestion to mimic the time that samples remain in the cooled autosampler of the analyzer, and repeated freeze-thaw cycles to mimic storage and handling procedures in the laboratory. The delayed storage factor was also analyzed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) for changes of metabolites and free amino acids, respectively. Our results show that repeated freeze/thawing introduced changes in transthyretin peptide levels. The trypsin digested samples left at 4 degrees C in the autosampler showed a time-dependent decrease of peak areas for peptides from prostaglandin D-synthase and serotransferrin. Delayed storage of CSF led to changes in prostaglandin D-synthase derived peptides as well as to increased levels of certain amino acids and metabolites. The changes of metabolites, amino acids and proteins in the delayed storage study appear to be related to remaining white blood cells. Our recommendations are to centrifuge CSF samples immediately after collection to remove white blood cells, aliquot, and then snap-freeze the supernatant in liquid nitrogen for storage at -80 degrees C. Preferably samples should not be left in the autosampler for more than 24 h and freeze/thaw cycles should be avoided if at all possible.
    Additive Diffusion from LDPE Slabs into Contacting Solvents as a Function of Solvent Absorption
    Helmroth, I.E. ; Dekker, M. ; Hankemeier, T. - \ 2003
    Journal of Applied Polymer Science 90 (2003). - ISSN 0021-8995 - p. 1609 - 1617.
    concentration-dependent diffusion - penetrant diffusion - swellable polymers - transport - temperature - polyolefins - permeation - parameters - migration - alcohols
    This article describes the simultaneous diffusion of a migrant and a solvent in low density polyethylene (LDPE). The migrant (Irganox 1076) moves out of the slab, while the solvent (isooctane, n-heptane or cyclohexane) moves inwards. Solvent absorption was measured separately by following the increase of the mass of the slab in time. It can be described by the Fick diffusion equation with a diffusivity depending on the solvent concentration, and an interface concentration depending on time. The final absorptions were 12% for isooctane, 14% for n-heptane, and 29% for cyclohexane. Additive concentrations in the slab were determined at different positions by microtoming. Experiments were done for several Contacting times. The concentration profiles were strongly affected by the solvent. A larger local solvent concentration increases the diffusivity of the migrant. The Fick equation with a migrant diffusivity depending on the solvent concentration gives a good description for the results with isooctane and n-heptane. The description is less good for the measurements with cyclohexane (when the polymer swells strongly). (C) 2003 Wiley Periodicals, Inc.
    Influence of solvent absorption on the migration of Irganox 1076 from LDPE
    Helmroth, I.E. ; Dekker, M. ; Hankemeier, T. - \ 2002
    Food Additives and Contaminants 19 (2002)2. - ISSN 0265-203X - p. 176 - 183.
    fatty food simulants - packaging interactions - diffusion - polyolefins - solubility - additives - plastics
    The effect of solvent absorption on additive migration was studied by relating the diffusion coefficient (D) of Irganox 1076 to the maximum solvent absorption of different solvents in low-density polyethylene (LDPE) film. Solvents tested were ethanol, isopropanol, isooctane, ethylacetate, cyclohexane, tributyrin, tricaprylin and olive oil. Diffusion and partition coefficients were determined by fitting the migration curves, i.e. the concentration of Irganox 1076 in solvent as a function of time, with Fick's diffusion equation. The results for the low molecular weight solvents show that with increasing maximum solvent absorption, D of Irganox 1076 is increasing as well. This trend is not observed for the two triglycerides and olive oil. In spite of absorption, no increase in D was observed. The obtained result is the basis of an extended predictive migration model that, besides migrant and polymer properties, is also based on the maximum solvent absorption in the polymer.
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