References of "De Pauw, Edwin"
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See detailPredicting Ion Mobility-Mass Spectrometry Trends of Polymers using the Concept of Apparent Densities
Haler, Jean ULiege; Morsa, Denis ULiege; Lecomte, Philippe ULiege et al

in Methods (in press)

Ion Mobility (IM) coupled to Mass Spectrometry (MS) has been used for several decades, bringing a fast separation dimension to the MS detection. IM-MS is a convenient tool for structural elucidation. The ... [more ▼]

Ion Mobility (IM) coupled to Mass Spectrometry (MS) has been used for several decades, bringing a fast separation dimension to the MS detection. IM-MS is a convenient tool for structural elucidation. The fold- ing of macromolecules is often assessed with the support of computational chemistry. However, this strat- egy is strongly dependent on computational initial guesses. Here, we propose the analysis of the Collision Cross-Section (CCS) trends of synthetic homopolymers based on a fitting method which does not rely on computational chemistry a prioris of the three-dimensional structures. The CCS trends were evaluated as a function of the polymer chain length and the charge state. This method is also applicable to mobility trends. It leads to two parameters containing all information available through IM(-MS) measurements. One parameter can be interpreted as an apparent density. The second parameter is related to the shape of the ions and leads us to introduce the concept of trends with constant apparent density. Based on the two fitting parameters, a method for IM trend predictions is elaborated. Experimental deviations from the predictions facilitate detect- ing structural rearrangements and three-dimensional structure differences of the cationized polymer ions. This leads for instance to an easy identification and prediction of the presence of different polymer topologies in complex polymer mixtures. The classification of predicted trends could as well allow for software-assisted data processing. Finally, we suggest the link between the CCS trends of homopolymers and those obtained from (monodisperse) biomolecules to interpret potential folding differences during IM-MS studies. [less ▲]

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See detailRevisiting protomers of aniline by high-resolution ion mobility spectrometry, capillary electrophoresis-mass spectrometry, and abinitio calculations
Kune, Christopher ULiege; Delvaux, Cédric ULiege; Haler, Jean ULiege et al

Poster (2018, March 29)

Protomers are ions which displays tautomerism due to the position change of a proton. Recent papers show that two stable protomers of aniline were observed using ion mobility spectrometry. Protonation of ... [more ▼]

Protomers are ions which displays tautomerism due to the position change of a proton. Recent papers show that two stable protomers of aniline were observed using ion mobility spectrometry. Protonation of the amine functional group and the carbon in “para” position were identified [Lalli, 2012 and Attygalle, 2017]. Tautomerization was also observed for other amine functional group containing in aromatic compounds. We present here the use of capillary electrophoresis and high-resolution ion mobility spectrometry to detect other stable or metastable protomers predicted by ab-initio calculations such as protonation of the carbon in “ortho” and “meta” position of aniline. These data should allow the refinement of the energy landscape during the protomer formation and tautomerization. For this reason, it is required to characterize all the ions that can be implicated during protomers formation. High resolution ion mobility(TIMS) allowed the detection of more ions related to aniline than those presented by the stateof-the-art. In addition, benzenium (C6H7+) and phenol (C6H7O+) cations can also be formed according to the electrospray ion source settings from the mass spectrometer. All of these ions must be taken in account to refine the energy landscape during the protomer formation and tautomerization. Ab-initio computation was used to support the identification of these ions in regard of the experimental data. Preliminary calculations by Density Functional Theory show that the protonation in the carbon in “ortho” position should be almost as stable as the amine protonation and should be observed during IMS experiments using the appropriate ion mobility resolving power. Calculations using polarizable continuum model also predict that the ratio of protomers is affected in presence of solvents and especially its dielectric constant. The protonation of the amine functional group is the most predominant species when aniline is solubilized in protic solvents. To the contrary both protonations of the amine functional group and the carbon in “para” should be significantly present in aprotic solvents. Aqueous and non-aqueous capillary zone electrophoresis (CZE) coupled to mass spectrometry are then consider to confirm these hypotheses. [less ▲]

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See detailEvaluation of capillary electrophoresis separation of cyclic lipopeptides
Mc Cann, Andréa ULiege; Far, Johann ULiege; De Pauw, Edwin ULiege et al

Poster (2018, March 29)

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See detailSmall molecule analysis on FFPE-TMA samples using MALDI-mass spectrometry imaging
Massonnet, Philippe ULiege; Kriegsmann, Mark; Smargiasso, Nicolas ULiege et al

Poster (2018, March 29)

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See detailIon Mobility-Mass Spectrometry of Synthetic Polymers: Interpretation Models & Calibration Strategies
Haler, Jean ULiege; Far, Johann ULiege; de la Rosa, Victor R. et al

Conference (2018, March 11)

Detailed reference viewed: 38 (3 ULiège)
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See detailEmerging mass spectrometry techniques for lipopeptide understanding
Mc Cann, Andréa ULiege; Far, Johann ULiege; Delvaux, Cédric ULiege et al

Scientific conference (2018, March 05)

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See detailThe knotty phenotype of the frd3 Arabidopsis mutant
Scheepers, Maxime ULiege; Spielmann, Julien ULiege; Boulanger, Madeleine ULiege et al

Poster (2018, February 01)

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See detailMALDI Imaging-Guided Microproteomic Analyses of Heterogeneous Breast Tumors-A Pilot Study
Alberts, Deborah ULiege; POTTIER, Charles ULiege; Smargiasso, Nicolas ULiege et al

in Proteomics. Clinical applications (2018), 12

Matrix-assisted laser desorption/ionization (MALDI) imaging is an ideal tool to study intratumor heterogeneity (ITH) and its implication in prognostic stratification of patients. However, there are some ... [more ▼]

Matrix-assisted laser desorption/ionization (MALDI) imaging is an ideal tool to study intratumor heterogeneity (ITH) and its implication in prognostic stratification of patients. However, there are some drawbacks concerning protein identification. On the other hand, laser microdissection (LMD)-based microproteomics allows retrieving thousands of protein identifications from small tissue pieces. As a proof of concept, the authors combine these two complementary approaches to analyze heterogeneous regions in breast tumors. Invasive ductal breast cancer FFPE tissue sections from five patients are analyzed by MALDI imaging and the dataset is processed by segmentation. Heterogeneous regions within tumors are processed by LMD-based microproteomics, in duplicates. Liquid chromatography-tandem mass spectrometry data are classified by hierarchical clustering. Heterogeneous tissue regions are discriminated on the basis of their actual molecular heterogeneity. The dataset is correlated with MALDI imaging to identify m/z values discriminating heterogeneous regions. The molecular characterization of cell clones in tumors related to bad patient outcome could have great impact for pathology. A combined application of LMD-based microproteomics and MALDI imaging for ITH studies is presented. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. [less ▲]

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See detailComparison of secretome from osteoblasts derived from sclerotic versus non-sclerotic subchondral bone in OA: A pilot study.
Sanchez, Christelle ULiege; Mazzucchelli, Gabriel ULiege; Lambert, Cécile ULiege et al

in PLoS ONE (2018), 13(3), 0194591

OBJECTIVE: Osteoarthritis (OA) is characterized by cartilage degradation but also by other joint tissues modifications like subchondral bone sclerosis. In this study, we used a proteomic approach to ... [more ▼]

OBJECTIVE: Osteoarthritis (OA) is characterized by cartilage degradation but also by other joint tissues modifications like subchondral bone sclerosis. In this study, we used a proteomic approach to compare secretome of osteoblast isolated from sclerotic (SC) or non sclerotic (NSC) area of OA subchondral bone. DESIGN: Secretome was analyzed using differential quantitative and relative label free analysis on nanoUPLC G2 HDMS system. mRNA of the more differentially secreted proteins were quantified by RT-PCR in cell culture from 5 other patients. Finally, osteomodulin and fibulin-3 sequences were quantified by western blot and immunoassays in serum and culture supernatants. RESULTS: 175 proteins were identified in NSC osteoblast secretome. Data are available via ProteomeXchange with identifier PXD008494. Compared to NSC osteoblast secretome, 12 proteins were significantly less secreted (Osteomodulin, IGFBP5, VCAM-1, IGF2, 78 kDa glucose-regulated protein, versican, calumenin, IGFBP2, thrombospondin-4, periostin, reticulocalbin 1 and osteonectin), and 13 proteins were significantly more secreted by SC osteoblasts (CHI3L1, fibulin-3, SERPINE2, IGFBP6, SH3BGRL3, SERPINE1, reticulocalbin3, alpha-2-HS-glycoprotein, TIMP-2, IGFBP3, TIMP-1, SERPINF1, CSF-1). Similar changes in osteomodulin, IGF2, SERPINE1, fibulin-3 and CHI3L1 mRNA levels were observed. ELISAs assays confirm the decrease by half of osteomodulin protein in SC osteoblasts supernatant compared to NSC and in OA patients serum compared to healthy subjects. Fibulin-3 epitopes Fib3-1, Fib3-2 and Fib3-3 were also increased in SC osteoblasts supernatant compared to NSC. CONCLUSIONS: We highlighted some proteins differentially secreted by the osteoblasts coming from OA subchondral bone sclerosis. These changes contribute to explain some features observed in OA subchondral bone, like the increase of bone remodeling or abnormalities in bone matrix mineralization. Among identified proteins, osteomodulin was found decreased and fibulin-3 increased in serum of OA patients. These findings suggest that osteomodulin and fibulin-3 fragments could be biomarkers to monitor early changes in subchondral bone metabolism in OA. [less ▲]

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See detailPotential diagnostic biomarkers of Ulcerative colitis-associated colorectal dysplasia
Merli, Angela-Maria ULiege; MASSOT, Charlotte ULiege; BLETARD, Noëlla ULiege et al

in Acta Gastro-Enterologica Belgica (2018)

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See detailULg Spectra: An Interactive Software Tool To Improve Undergraduate Students’ Structural Analysis Skills
Agnello, Armélinda ULiege; Carré, Cyril ULiege; Billen, Roland ULiege et al

in Journal of Chemical Education (2018), 95

The analysis of spectroscopic data to solve chemical structures requires practical skills and drills. In this context, we have developed ULg Spectra, a computer-based tool designed to improve the ability ... [more ▼]

The analysis of spectroscopic data to solve chemical structures requires practical skills and drills. In this context, we have developed ULg Spectra, a computer-based tool designed to improve the ability of learners to perform complex reasoning. The identification of organic chemical compounds involves gathering and interpreting complementary information from mass, infrared, Raman, and nuclear magnetic resonance spectra. Here, special attention is paid to one-dimensional 1H and 13C NMR spectra and to two-dimensional NMR spectra because these techniques particularly require extensive interactive data manipulation. ULg Spectra offers tutorial-drill materials, including spectra that are “authentic” in the sense that they contain solvent and impurity traces rather than being “idealized” spectra often found in textbook examples. A public version is accessible online free of charge. The exam results for two groups of students, one having used ULg Spectra for extra home-based training and the other not, were compared. Statistical data demonstrated higher performance for the “trained” students compared with the control group. [less ▲]

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See detailPhysiological and proteomic responses to corticosteroid treatments in Eurasian perch, Perca fluviatilis: Investigation of immune-related parameters
Milla, S.; Massart, Sébastien ULiege; Mathieu, C. et al

in Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics (2018), 25

The comparative effects of cortisol and 11-deoxycorticosterone (DOC), two major corticosteroids in fish, have yet received little attention in teleosts. We evaluated the proteomic and immune responses of ... [more ▼]

The comparative effects of cortisol and 11-deoxycorticosterone (DOC), two major corticosteroids in fish, have yet received little attention in teleosts. We evaluated the proteomic and immune responses of Eurasian perch to chronic corticosteroid treatments. We implanted immature perch with cortisol (80 mg/kg) or DOC (4 mg/kg) and measured the proportions of blood leucocytes, immune indices in the plasma, spleen and liver (complement and lysozyme activity, total immunoglobulin and immune gene expression in the tissues) and differential proteome expression (corticosteroid versus control) in the liver and the spleen on days 2, 4 and 14 post-treatment. Implantation of cortisol decreased the ratio of blood leucocytes and depressed Ig levels in both organs while DOC modulated the proportion of leucocyte sub-populations (increase in lymphocytes and decrease in granulocytes). In contrast, the innate humoral immunity was not strongly influenced by any of corticosteroid implants. The only immune parameter that was significantly affected was lysozyme, after DOC treatment. A number of proteins were differentially regulated by these hormones and some were identified in the liver (21 for cortisol and 8 for DOC) and in the spleen (10 for cortisol and 10 for DOC). None of the proteins was directly linked to immunity, except the natural killer enhancing factor, which was repressed by cortisol in the spleen. Our results also confirm that the proteins involved in energetic and glucose metabolism are affected by corticosteroids. Furthermore, these corticosteroids differently regulate immune status in Eurasian perch and they primarily impact leucocytes, as opposed to innate immune function. © 2017 Elsevier Inc. [less ▲]

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See detailComparison of Different Ion Mobility Setups using Poly(ethylene oxide) PEO Polymers: Drift Tube, TIMS and T-Wave
Haler, Jean ULiege; Massonnet, Philippe ULiege; Chirot, Fabien et al

in Journal of the American Society for Mass Spectrometry (2018), 29(1), 114-120

Over the years, polymer analyses using ion mobility-mass spectrometry (IM-MS) measurements have been performed on different ion mobility spectrometry (IMS) setups. In order to be able to compare ... [more ▼]

Over the years, polymer analyses using ion mobility-mass spectrometry (IM-MS) measurements have been performed on different ion mobility spectrometry (IMS) setups. In order to be able to compare literature data taken on different IM(-MS) instruments, ion heating and ion temperature evaluations have already been explored. Nevertheless, extrapolations to other analytes are difficult and thus straightforward same-sample instrument comparisons seem to be the only reliable way to make sure that the different IM(-MS) setups do not greatly change the gas phase behavior. We used a large range of degrees of polymerization (DP) of poly(ethylene oxide) PEO homopolymers to measure IMS drift times on three different IM-MS setups: a homemade drift tube (DT), a trapped (TIMS) and a travelling wave (T-Wave) IMS setup. The drift time evolutions were followed for increasing polymer DPs (masses) and charge states and they are found to be comparable and reproducible on the three instruments. [less ▲]

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See detailThe Arabidopsis frd3 mutant phenotype: a new level of complexity
Scheepers, Maxime ULiege; Spielmann, Julien ULiege; Boulanger, Madeleine ULiege et al

Poster (2017, December 07)

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See detailIn-depth glyco-peptidomics approach reveals unexpected diversity of glycosylated peptides and atypical post-translational modifications in dendroaspis angusticeps snake venom
Degueldre, Michel ULiege; Echterbille, Julien; Smargiasso, Nicolas ULiege et al

in International Journal of Molecular Sciences (2017), 18(11), 2483

Animal venoms represent a valuable source of bioactive peptides that can be derived into useful pharmacological tools, or even innovative drugs. In this way, the venom of Dendroaspis angusticeps (DA), the ... [more ▼]

Animal venoms represent a valuable source of bioactive peptides that can be derived into useful pharmacological tools, or even innovative drugs. In this way, the venom of Dendroaspis angusticeps (DA), the Eastern Green Mamba, has been intensively studied during recent years. It mainly contains hundreds of large toxins from 6 to 9 kDa, each displaying several disulfide bridges. These toxins are the main target of venom-based studies due to their valuable activities obtained by selectively targeting membrane receptors, such as ion channels or G-protein coupled receptors. This study aims to demonstrate that the knowledge of venom composition is still limited and that animal venoms contain unexpected diversity and surprises. A previous study has shown that Dendroaspis angusticeps venom contains not only a cocktail of classical toxins, but also small glycosylated peptides. Following this work, a deep exploration of DA glycopeptidome by a dual nano liquid chromatography coupled to electrospray ionization mass spectrometry (nanoLC-ESI-MS) and Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) analyses was initiated. This study reveals unsuspected structural diversity of compounds such as 221 glycopeptides, displaying different glycan structures. Sequence alignments underline structural similarities with natriuretic peptides already characterized in Elapidae venoms. Finally, the presence of an S-cysteinylation and hydroxylation of proline on four glycopeptides, never described to date in snake venoms, is also revealed by proteomics and affined by nuclear magnetic resonance (NMR) experiments. © 2017 by the authors. Licensee MDPI, Basel, Switzerland. [less ▲]

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See detailComprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies
Haler, Jean ULiege; Kune, Christopher ULiege; Massonnet, Philippe ULiege et al

in Analytical Chemistry (2017), 89(22), 1207612086

Ion Mobility (IM) is now a well-established and fast analytical technique. The IM hardware is constantly being improved, especially in terms of the resolving power. The Drift Tube (DTIMS), the Traveling ... [more ▼]

Ion Mobility (IM) is now a well-established and fast analytical technique. The IM hardware is constantly being improved, especially in terms of the resolving power. The Drift Tube (DTIMS), the Traveling Wave (TWIMS), and the Trapped Ion Mobility Spectrometry (TIMS) coupled to mass spectrometry are used to determine the Collision Cross-Sections (CCS) of ions. In analytical chemistry, the CCS is approached as a descriptor for ion identification and it is also used in physical chemistry for 3D structure elucidation with computational chemistry support. The CCS is a physical descriptor extracted from the reduced mobility (K0) measurements obtainable only from the DTIMS. TWIMS and TIMS routinely require a calibration procedure to convert measured physical quantities (drift time for TWIMS and elution voltage for TIMS) into CCS values. This calibration is a critical step to allow inter-instrument comparisons. The previous calibrating substances lead to large prediction bands and introduced rather large uncertainties during the CCS determination. In this paper, we introduce a new IM calibrant (CCS and K0) using singly charged sodium adducts of poly(ethylene oxide) monomethyl ether (CH3O-PEO-H) for positive ionization in both helium and nitrogen as drift gas. These singly charged calibrating ions make it possible to determine the CCS/K0 of ions having higher charge states. The fitted calibration plots exhibit larger coverage with less data scattering and significantly improved prediction bands and uncertainties. The reasons for the improved CCS/K0 accuracy, advantages and limitations of the calibration procedures are also discussed. A generalized IM calibration strategy is suggested. [less ▲]

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