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van Duijn, E. (author), Sandman, H. (author), Grossouw, D. (author), Mocking, J.A.J. (author), Coulier, L. (author), Vaes, W.H.J. (author)The increasing role of accelerator mass spectrometry (AMS) in biomedical research necessitates modernization of the traditional sample handling process. AMS was originally developed and used for carbon dating, therefore focusing on a very high precision but with a comparably low sample throughput. Here, we describe the combination of automated...article 2014
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Zha, Y. (author), Westerhuis, J.A. (author), Muilwijk, B. (author), Overkamp, K.M. (author), Nijmeijer, B.M. (author), Coulier, L. (author), Smilde, A.K. (author), Punt, P.J. (author)Background: Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates.Results: We studied the composition and fermentability of 24 different...article 2014
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Krishnan, S. (author), Verheij, E.E.R. (author), Bas, R.C. (author), Hendriks, M.W.B. (author), Hankemeier, T. (author), Thissen, U. (author), Coulier, L. (author)RATIONALE Mass spectra obtained by deconvolution of liquid chromatography/high-resolution mass spectrometry (LC/HRMS) data can be impaired by non-informative mass-over-charge (m/z) channels. This impairment of mass spectra can have significant negative influence on further post-processing, like quantification and identification. METHODS A metric...article 2013
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Karaffa, L. (author), Coulier, L. (author), Fekete, E. (author), Overkamp, K.M. (author), Druzhinina, I.S. (author), Mikus, M. (author), Seiboth, B. (author), Novák, L. (author), Punt, P.J. (author), Kubicek, C.P. (author)Lactose (1,4-0-β-d-galactopyranosyl-d-glucose) is used as a soluble carbon source for the production of cellulases and hemicellulases for - among other purposes - use in biofuel and biorefinery industries. The mechanism how lactose induces cellulase formation in T. reesei is enigmatic, however. Previous results from our laboratory raised the...article 2013
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Coulier, L. (author), Muilwijk, B. (author), Bijlsma, S. (author), Noga, M. (author), Tienstra, M. (author), Attali, A. (author), van Aken, H. (author), Suidgeest, E. (author), Tuinstra, T. (author), Luider, T.M. (author), Hankemeier, T. (author), Bobeldijk, I. (author)Analysis of metabolites in biofluids by gas chromatography-mass spectrometry (GC-MS) after oximation and silylation is a key method in metabolomics. The GC-MS method was modified by a modified vial design and sample work-up procedure in order to make the method applicable to small volumes of cerebrospinal fluid (CSF), i. e. 10 μL, with similar...article 2013
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Peironcely, J.E. (author), Rojas-Chertó, M. (author), Tas, A. (author), Vreeken, R. (author), Reijmers, T. (author), Coulier, L. (author), Hankemeier, T. (author)Metabolite identification is one of the biggest bottlenecks in metabolomics. Identifying human metabolites poses experimental, analytical, and computational challenges. Here we present a pipeline of previously developed cheminformatic tools and demonstrate how it facilitates metabolite identification using solely LC/MSn data. These tools process...article 2013
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Noga, M.J. (author), Dane, A. (author), Shi, S. (author), Attali, A. (author), van Aken, H. (author), Suidgeest, E. (author), Tuinstra, T. (author), Muilwijk, B. (author), Coulier, L. (author), Luider, T. (author), Reijmers, T.H. (author), Vreeken, R.J. (author), Hankemeier, T. (author)Experimental Autoimmune Encephalomyelitis (EAE) is the most commonly used animal model for Multiple Sclerosis (MScl). CSF metabolomics in an acute EAE rat model was investigated using targetted LC-MS and GC-MS. Acute EAE in Lewis rats was induced by co-injection of Myelin Basic Protein with Complete Freund's Adjuvant. CSF samples were collected...article 2012
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Peironcely, J.E. (author), Rojas-Chertó, M. (author), Fichera, D. (author), Reijmers, T. (author), Coulier, L. (author), Faulon, J.-L. (author), Hankemeier, T. (author)Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental...article 2012
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Coulier, L. (author), Muilwijk, B. (author), Bijlsma, S. (author), Noga, M. (author), Tienstra, M. (author), Attali, A. (author), van Aken, H. (author), Suidgeest, E. (author), Tuinstra, T. (author), Hankemeier, T. (author), Bobeldijk, I. (author)Analysis of metabolites in biofluids by gas chromatography–mass spectrometry (GC–MS) after oximation and silylation is a key method in metabolomics. The GC–MS method was modified by a modified vial design and sample work-up procedure in order to make the method applicable to small volumes of cerebrospinal fluid (CSF), i.e. 10 μL, with similar...article 2012
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Smolinska, A. (author), Blanchet, L. (author), Coulier, L. (author), Ampt, K.A.M. (author), Luider, T. (author), Hintzen, R.Q. (author), Wijmenga, S.S. (author), Buydens, L.M.C. (author)Background: In the last decade data fusion has become widespread in the field of metabolomics. Linear data fusion is performed most commonly. However, many data display non-linear parameter dependences. The linear methods are bound to fail in such situations. We used proton Nuclear Magnetic Resonance and Gas Chromatography-Mass Spectrometry, two...article 2012
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Krishnan, S. (author), Vogels, J.T.W.E. (author), Coulier, L. (author), Bas, R.C. (author), Hendriks, M.W.B. (author), Hankemeier, T. (author), Thissen, U. (author)Setting appropriate bin sizes to aggregate hyphenated high-resolution mass spectrometry data, belonging to similar mass over charge (m/. z) channels, is vital to metabolite quantification and further identification. In a high-resolution mass spectrometer when mass accuracy (ppm) varies as a function of molecular mass, which usually is the case...article 2012
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Coulier, L. (author), Tas, A. (author), Thissen, U. (author)Comprehensive analysis of both volatile and non-volatile metabolites in food combined with information on sensory properties and multivariate statistics can be a valuable tool in understanding and improving the taste of food. Performing food metabolomics studies is, however, challenging and requires the analytical measurements to be of a very...article 2011
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Thissen, U. (author), Coulier, L. (author), Overkamp, K.M. (author), Jetten, J. (author), van de Werff, B.J.C. (author), van de Ven, T. (author), van der Werf, M.J. (author)In agricultural and food products, typical quality parameters are sensory properties, shelf-life, safety, health, nutritional value, crop yield per area and disease resistance. It is known that these parameters are importantly determined by the metabolites in the crops and food products. Metabolomics is the state-of-the-art routine technique...article 2011
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Coulier, L. (author), Gerritsen, H. (author), van Kampen, J.J.A. (author), Reedijk, M.L. (author), Luider, T.M. (author), Osterhaus, A.D.M.E. (author), Gruters, R.A. (author), Brüll, L. (author)Nucleoside reverse transcriptase inhibitors (NRTIs) are a key class of drugs for the treatment of HIV infection. NRTIs are intracellularly phosphorylated to their active triphosphate metabolites and compete with endogenous deoxynucleotides (dNTP) for substrate binding. It is therefore important to analyze the intracellular concentrations of...article 2011
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Braaksma, M. (author), Bijlsma, S. (author), Coulier, L. (author), Punt, P.J. (author), van der Werf, M.J. (author)For the optimization of microbial production processes, the choice of the quantitative phenotype to be optimized is crucial. For instance, for the optimization of product formation, either product concentration or productivity can be pursued, potentially resulting in different targets for strain improvement. The choice of a quantitative...article 2011
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Mateo Anson, N. (author), Havenaar, R. (author), Vaes, W. (author), Coulier, L. (author), Venema, K. (author), Selinheimo, E. (author), Bast, A. (author), Haenen, G.R.M.M. (author)The health benefits of whole grain consumption can be partly attributed to the inclusion of the bran or outer-layers of the grain rich in dietary fibre. Fibre is fermented in the colon, leading to the production of beneficial metabolites, such as short-chain fatty acids (SCFA). The effect of five different types of bread on the SCFA production...article 2011
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van Batenburg, M.F. (author), Coulier, L. (author), van Eeuwijk, F. (author), Smilde, A.K. (author), Westerhuis, J.A. (author)In the field of metabolomics, hundreds of metabolites are measured simultaneously by analytical platforms such as gas chromatography/mass spectrometry (GC/MS), liquid chromatography/mass spectrometry (LC/MS) and NMR to obtain their concentration levels in a reliable way. Analytical repeatability (intrabatch precision) is a common figure of merit...article 2011
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Coulier, L. (author), Bas, R. (author), Hekman, M. (author), van der Werff, B.J.C. (author), Burgering, M. (author), Thissen, U. (author)An ion-pair LC-ESI-MS method was developed capable of analyzing various reported umami or umami-enhancing compounds, including glutamic acid and 5'-ribonucleotides. The method was validated using tomato and potato samples and showed overall good analytical performance with respect to selectivity, detection limit, linearity, and repeatability....article 2011
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Rosenling, T. (author), Stoop, M.P. (author), Smolinska, A. (author), Muilwijk, B. (author), Coulier, L. (author), Shi, S. (author), Dane, A. (author), Christin, C. (author), Suits, F. (author), Horvatovich, P.L. (author), Wijmenga, S.S. (author), Buydens, L.M.C. (author), Vreeken, R. (author), Hankemeier, T. (author), van Gool, A.J. (author), Luider, T.M. (author), Bischoff, R. (author)BACKGROUND: Because cerebrospinal fluid (CSF) is in close contact with diseased areas in neurological disorders, it is an important source of material in the search for molecular biomarkers. However, sample handling for CSF collected from patients in a clinical setting might not always be adequate for use in proteomics and metabolomics studies....article 2011
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Peironcely, J.E. (author), Reijmers, T. (author), Coulier, L. (author), Bender, A. (author), Hankemeier, T. (author)While the entirety of 'Chemical Space' is huge (and assumed to contain between 1063 and 10200 'small molecules'), distinct subsets of this space can nonetheless be defined according to certain structural parameters. An example of such a subspace is the chemical space spanned by endogenous metabolites, defined as 'naturally occurring' products of...article 2011
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