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Palmblad M.,Biomolecular Mass Spectrometry Unit | Drijfhout J.W.,Leiden University | Deelder A.M.,Biomolecular Mass Spectrometry Unit
Journal of Combinatorial Chemistry

Combinatorial libraries can be characterized in detail by high resolving power mass spectrometry. We here demonstrate this for synthetic decapeptide libraries using a state-of-the-art 15 T Fourier transform ion cyclotron resonance mass spectrometer. Using comparison between predicted and measured spectra, a number of metrics can be derived that shed light on the library composition and degeneracy of elemental compositions. These techniques can be used to rapidly quality control combinatorial synthesis products or follow combinatorial, libraries in more detail, for instance during binding studies or chemical reactions. The methods are in principle equally applicable to the analysis of other types of combinatorial libraries. © 2010 American Chemical Society. Source

Ramautar R.,University Utrecht | Ramautar R.,Biomolecular Mass Spectrometry Unit | Nevedomskaya E.,Biomolecular Mass Spectrometry Unit | Mayboroda O.A.,Biomolecular Mass Spectrometry Unit | And 6 more authors.
Molecular BioSystems

The potential of capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS) using capillaries coated with a triple layer of polybrene-dextran sulfate-polybrene (PB-DS-PB) was evaluated for metabolic profiling of human urine. The method covers various metabolite classes and stable metabolic profiles of urine samples were obtained with favourable migration time repeatability (RSDs < 1%). The PB-DS-PB CE-TOF-MS method was used for the analysis of human urine samples from 30 males and 30 females, which had been previously analyzed by reversed-phase UPLC-TOF-MS. Multivariate data analysis of the obtained data provided clear distinction between urine samples from males and females, emphasizing gender differences in metabolic signatures. Nearly all compounds responsible for male-female classification in CE-TOF-MS were different from the classifying compounds in UPLC-TOF-MS. Almost all compounds causing classification in the CE-TOF-MS study were highly polar and did not exhibit retention in the reversed-phase UPLC system. In addition, the CE-TOF-MS classifiers had an m/z value in the range of 50-150, whereas 95% of the classifying features found with UPLC-TOF-MS had an m/z value above 150. The CE-TOF-MS method therefore appears to be highly complementary to the UPLC-TOF-MS method providing classification based on different classes of metabolites. © The Royal Society of Chemistry 2011. Source

Giera M.,VU University Amsterdam | Kloos D.-P.,VU University Amsterdam | Kloos D.-P.,Biomolecular Mass Spectrometry Unit | Raaphorst A.,VU University Amsterdam | And 4 more authors.

Malondialdehyde (MDA) has become a well-established biomarker for oxidative stress. The most commonly used way to determine urinary MDA levels is the thiobarbituric acid (TBA) assay, which suffers from several drawbacks. In this manuscript, we describe a novel derivatization strategy for the highly sensitive and selective fluorescence-based determination of MDA in urinary samples. The methodology is based on the mild labeling of MDA with 2-aminoacridone, which can be carried out in aqueous citrate buffer at 40°C, yielding a highly fluorescent substance. No further sample preparation than mixing with the necessary chemicals is necessary. The formed MDA derivative can conveniently be separated from the label itself and matrix constituents by gradient LC in less than 5 minutes on a cyano-based reversed-phase material. The method was validated with respect to matrix effects, linearity, selectivity and sensitivity (values as low as 1.8 nM for the LOD and 5.8 nM for the LOQ could be achieved). Standard addition quantitation was applied for the determination of MDA in human urine samples. Additionally, the protocol was applied to the measurement of a stability indicating analysis of MDA in urine at different storage conditions. © 2011 The Royal Society of Chemistry. Source

Garcia-Villalba R.,University of Granada | Pacchiarotta T.,Biomolecular Mass Spectrometry Unit | Carrasco-Pancorbo A.,University of Granada | Segura-Carretero A.,University of Granada | And 3 more authors.
Journal of Chromatography A

A new analytical approach based on gas chromatography coupled to atmospheric pressure chemical ionization-time of flight mass spectrometry was evaluated for its applicability for the analysis of phenolic compounds from extra-virgin olive oil. Both chromatographic and MS parameters were optimized in order to improve the sensitivity and to maximize the number of phenolic compounds detected. We performed a complete analytical validation of the method with respect to its linearity, sensitivity, precision, accuracy and possible matrix effects. The LODs ranged from 0.13 to 1.05 ppm for the different tested compounds depending on their properties. The RSDs for repeatability test did not exceed 6.07% and the accuracy ranged from 95.4% to 101.5%. To demonstrate the feasibility of our method for analysis of real samples, we analyzed the extracts of three different commercial extra-virgin olive oils. We have identified unequivocally a number of phenolic compounds and obtained quantitative information for 21 of them. In general, our results show that GC-APCI-TOF MS is a flexible platform which can be considered as an interesting tool for screening, structural assignment and quantitative determination of phenolic compounds from virgin olive oil. © 2011 Elsevier B.V. Source

Lonardi E.,Biomolecular Mass Spectrometry Unit | Balog C.I.,Biomolecular Mass Spectrometry Unit | Deelder A.M.,Biomolecular Mass Spectrometry Unit | Wuhrer M.,Biomolecular Mass Spectrometry Unit
Expert Review of Proteomics

Glycan microarrays are emerging as increasingly used screening tools with a high potential for unraveling protein-carbohydrate interactions: probing hundreds or even thousands of glycans in parallel, they provide the researcher with a vast amount of data in a short time-frame, while using relatively small amounts of analytes. Natural glycan microarrays focus on the glycans repertoire of natural sources, including both well-defined structures as well as still-unknown ones. This article compares different natural glycan microarray strategies. Glycan probes may comprise oligosaccharides from glycoproteins as well as glycolipids and polysaccharides. Oligosaccharides may be purified from scarce biological samples that are of particular relevance for the carbohydrate-binding protein to be studied. We give an overview of strategies for glycan isolation, derivatization, fractionation, immobilization and structural characterization. Detection methods such as fluorescence analysis and surface plasmon resonance are summarized. The importance of glycan density and multivalency is discussed. Furthermore, some applications of natural glycan microarrays for studying lectin and antibody binding are presented. © 2010 Expert Reviews Ltd. Source

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