122 results on '"Pauw, A."'
Search Results
2. FT-ICR Mass Spectrometry Imaging at Extreme Mass Resolving Power Using a Dynamically Harmonized ICR Cell with 1ω or 2ω Detection
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Mathieu Tiquet, Raphaël La Rocca, Stefan Kirnbauer, Samuele Zoratto, Daan Van Kruining, Loïc Quinton, Gauthier Eppe, Pilar Martinez-Martinez, Martina Marchetti-Deschmann, Edwin De Pauw, Johann Far, RS: MHeNs - R3 - Neuroscience, and Basic Neuroscience 3
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CALIBRATION ,Diagnostic Imaging ,Ions ,SPACE-CHARGE ,MOTION ,Fourier Analysis ,ACCURACY ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,SAMPLE PREPARATION ,Cyclotrons ,ELECTRIC-FIELD ,Analytical Chemistry - Abstract
MALDI mass spectrometry imaging (MALDI MSI) is a powerful analytical method for achieving 2D localization of compounds from thin sections of typically but not exclusively biological samples. The dynamically harmonized ICR cell (ParaCell) was recently introduced to achieve extreme spectral resolution capable of providing the isotopic fine structure of ions detected in complex samples. The latest improvement in the ICR technology also includes 2 omega detection, which significantly reduces the transient time while preserving the nominal mass resolving power of the ICR cell. High-resolution MS images acquired on FT-ICR instruments equipped with 7T and 9.4T superconducting magnets and the dynamically harmonized ICR cell operating at suboptimal parameters suffered severely from the pixel-to-pixel shifting of m/z peaks due to space-charge effects. The resulting profile average mass spectra have depreciated mass measurement accuracy and mass resolving power under the instrument specifications that affect the confidence level of the identified ions. Here, we propose an analytical workflow based on the monitoring of the total ion current to restrain the pixel-to-pixel m/z shift. Adjustment of the laser parameters is proposed to maintain high spectral resolution and mass accuracy measurement within the instrument specifications during MSI analyses. The optimized method has been successfully employed in replicates to perform high-quality MALDI MS images at resolving power (FWHM) above 1,000,000 in the lipid mass range across the whole image for superconducting magnets of 7T and 9.4T using 1 and 2 omega detection. Our data also compare favorably with MALDI MSI experiments performed on higher-magnetic-field superconducting magnets, including the 21T MALDI FT-ICR prototype instrument of the NHMFL group at Tallahassee, Florida.
- Published
- 2022
3. FT-ICR Mass Spectrometry Imaging at Extreme Mass Resolving Power Using a Dynamically Harmonized ICR Cell with 1ω or 2ω Detection
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Tiquet, Mathieu, primary, La Rocca, Raphaël, additional, Kirnbauer, Stefan, additional, Zoratto, Samuele, additional, Van Kruining, Daan, additional, Quinton, Loïc, additional, Eppe, Gauthier, additional, Martinez-Martinez, Pilar, additional, Marchetti-Deschmann, Martina, additional, De Pauw, Edwin, additional, and Far, Johann, additional
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- 2022
- Full Text
- View/download PDF
4. Use of Capillary Zone Electrophoresis Coupled to Electrospray Mass Spectrometry for the Detection and Absolute Quantitation of Peptidoglycan-Derived Peptides in Bacterial Cytoplasmic Extracts
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Madeleine Boulanger, Cédric Delvaux, Johann Far, Bernard Joris, Marjorie Dauvin, Loïc Quinton, Edwin De Pauw, Dominique Mengin-Lecreulx, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Enveloppes Bactériennes et Antibiotiques (ENVBAC), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
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Cytoplasm ,Spectrometry, Mass, Electrospray Ionization ,[SDV]Life Sciences [q-bio] ,Peptide ,Peptidoglycan ,Tripeptide ,Bacterial growth ,010402 general chemistry ,01 natural sciences ,Bacterial cell structure ,Analytical Chemistry ,chemistry.chemical_compound ,Capillary electrophoresis ,chemistry.chemical_classification ,biology ,Chemistry ,010401 analytical chemistry ,Electrophoresis, Capillary ,biology.organism_classification ,Cephalosporins ,0104 chemical sciences ,Biochemistry ,Peptides ,Bacteria ,Bacillus subtilis - Abstract
Peptidoglycan (PGN) is an essential structure found in the bacterial cell wall. During the bacterial life cycle, PGN continuously undergoes biosynthesis and degradation to ensure bacterial growth and division. The resulting PGN fragments (muropeptides and peptides), which are generated by the bacterial autolytic system, are usually transported into the cytoplasm to be recycled. On the other hand, PGN fragments can act as messenger molecules involved in the bacterial cell wall stress response as in the case of β-lactamase induction in the presence of β-lactam antibiotic or in triggering mammalian innate immune response. During their cellular life, bacteria modulate their PGN degradation by their autolytic system or their recognition by the mammalian innate immune system by chemically modifying their PGN. Among these modifications, the amidation of the ε-carboxyl group of meso-diaminopimelic acid present in the PGN peptide chain is frequently observed. Currently, the detection and quantitation of PGN-derived peptides is still challenging because of the difficulty in separating these highly hydrophilic molecules by RP-HPLC as these compounds are eluted closely after the column void volume or coeluted in many cases. Here, we report the use of capillary zone electrophoresis coupled via an electrospray-based CE-MS interface to high-resolution mass spectrometry for the quantitation of three PGN peptides of interest and their amidated derivatives in bacterial cytoplasmic extracts. The absolute quantitation of the tripeptide based on the [13C,15N] isotopically labeled standard was also performed in crude cytoplasmic extracts of bacteria grown in the presence or absence of a β-lactam antibiotic (cephalosporin C). Despite the high complexity of the samples, the repeatability of the CZE-MS quantitation results was excellent, with relative standard deviations close to 1%. The global reproducibility of the method including biological handling was better than 20%.
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- 2021
5. Response to Comment on Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry
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Denis Morsa, Edwin De Pauw, Valérie Gabelica, and Emeline Hanozin
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Chemistry ,Ion-mobility spectrometry ,Analytical chemistry ,Effective temperature ,Analytical Chemistry - Published
- 2020
6. Identification of the Calcium, Aluminum, and Magnesium Distribution within Millimeter-Sized Extraterrestrial Materials Using Nonresonant X-ray Raman Spectroscopy in Preparation for the Hayabusa2 Sample Return Mission
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Laszlo Vincze, Beverley J. Tkalcec, Christoph J. Sahle, Pieter Tack, Frank E. Brenker, Ella De Pauw, and Alessandro Longo
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Scattering ,business.industry ,Chemistry ,Extraterrestrial materials ,Inelastic scattering ,Analytical Chemistry ,symbols.namesake ,Optics ,Beamline ,Core electron ,Sample return mission ,symbols ,business ,Absorption (electromagnetic radiation) ,Raman spectroscopy - Abstract
The nondestructive investigation of millimeter-sized meteoritic materials is often hindered by self-absorption effects. Using X-ray-based analytical methods, the information depth for many elements (Z < 30) is in the range of up to only a few hundred micrometers, and for low-Z elements (Z < 20), this is reduced even further to only a few tens of micrometers. However, the investigation of these low-Z elements, in particular calcium, aluminum, and magnesium, is of great importance to planetary geologists and cosmochemists, as these elements are regularly used to characterize and identify specific features of interest in extraterrestrial materials, especially primitive chondritic material. In this work, nonresonant inelastic X-ray scattering from core electrons was performed at beamline ID20 of the ESRF in a direct tomography approach in order to visualize these low-Z elements within the millimeter-sized meteoritic samples. The obtained 3D elemental distribution volumes were compared to results from X-ray fluorescence-CT and absorption CT experiments and were found to be in good agreement. Additionally, several regions of interest could be identified within the inelastic scattering volumes, containing information that is not available through the other presented means. As such, the proposed approach presents a valuable tool for the nondestructive investigation of low-Z elemental distributions within millimeter-sized extraterrestrial materials, such as the samples of the Hayabusa2 sample return mission.
- Published
- 2021
7. MALDI-in source decay applied to mass spectrometry imaging: a new tool for protein identification
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Debois, Delphine, Bertrand, Virginie, Quinton, Loic, De Pauw-Gillet, Marie-Claire, and De Pauw, Edwin
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Mass spectrometry -- Methods ,Proteins -- Chemical properties ,Proteins -- Identification and classification ,Imaging systems -- Methods ,Imaging systems -- Technology application ,Technology application ,Chemistry - Abstract
Matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) imaging is a powerful technique giving access to the distribution of a large range of biomolecules directly from a tissue section, allowing, for example, the discovery of new pathological biomarkers. Nevertheless, one main difficulty lies in the identification of the detected species, especially proteins. MALDI-in source decay (ISD) is used to fragment ions directly in the mass spectrometer ion source. This technique does not require any special sample treatment but only the use of a specific MALDI matrix such as 2,5-dihydroxybenzoic acid or 1,5-diaminonaphthalene. MALDI-ISD is generally employed on classical, purified samples, but here we demonstrate that ISD can also be performed directly on mixtures and on a tissue slice leading to fragment ions, allowing the identification of major proteins without any further treatment. On a porcine eye lens slice, de novo sequencing was even performed. Crystallins not yet referenced in databases were identified by sequence homology with other mammalian species. On a mouse brain slice, we demonstrate that results obtained with ISD are comparable and even better than those obtained with a classical in situ digestion. 10.1021/ac902875q
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- 2010
8. Identification of the Calcium, Aluminum, and Magnesium Distribution within Millimeter-Sized Extraterrestrial Materials Using Nonresonant X-ray Raman Spectroscopy in Preparation for the Hayabusa2 Sample Return Mission
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Tack, Pieter, primary, De Pauw, Ella, additional, Tkalcec, Beverley, additional, Longo, Alessandro, additional, Sahle, Christoph J., additional, Brenker, Frank, additional, and Vincze, Laszlo, additional
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- 2021
- Full Text
- View/download PDF
9. Rapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect As a Filter in Mass Spectrometry Imaging
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Daan van Kruining, Mathieu Tiquet, La Rocca Raphaël, Edwin De Pauw, Christopher Kune, Marc Ongena, Anthony Arguelles Arias, Gauthier Eppe, Pilar Martinez Martinez, Loïc Quinton, Johann Far, Andréa McCann, Promovendi PHPC, Psychiatrie & Neuropsychologie, and RS: MHeNs - R3 - Neuroscience
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Bacillus ,010402 general chemistry ,Mass spectrometry ,Proof of Concept Study ,01 natural sciences ,LIPIDOMICS ,Mass spectrometry imaging ,Analytical Chemistry ,Mice ,Data filtering ,Pseudomonas ,Animals ,SPECTRA ,TOOL ,Organic Chemicals ,BRAIN SECTIONS ,Chromatography ,Kendrick mass ,Chemistry ,010401 analytical chemistry ,Brain ,0104 chemical sciences ,Molecular Weight ,PHOSPHOLIPIDS ,Mass ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Algorithms ,Software - Abstract
Kendrick mass defect (KMD) analysis is widely used for helping the detection and identification of chemically related compounds based on exact mass measurements. We report here the use of KMD as a criterion for filtering complex mass spectrometry dataset. The method enables an automated, easy and efficient data processing, enabling the reconstruction of 2D distributions of family of homologous compounds from MSI images. We show that the KMD filtering, based on an in-house software, is suitable and robust for high resolution (full width at half-maximum, FWHM, at m/z 410 of 20 000) and very high-resolution (FWHM, at m/z 410 of 160 000) MSI data. This method has been successfully applied to two different types of samples, bacteria co-cultures and brain tissue section
- Published
- 2019
10. Optimization of matrix conditions for the control of MALDI in-source decay of permethylated glycans
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Smargiasso, Nicolas and De Pauw, Edwin
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Mathematical optimization -- Research ,Ionization -- Methods ,Mass spectrometry -- Methods ,Polysaccharides -- Chemical properties ,Chemistry - Abstract
Due to its fastness and its easiness to use, MALDI-MS is currently an analytical tool widely used in glycomic applications. However, the MALDI ionization process could result in the so-called 'in-source decay', or ISD, of analytes, leading to complex spectra. On the other hand, ISD opens the possibility to perform pseudo-[MS.sup.3] experiments. This phenomenon must therefore be controlled in order to be used on demand as a supplementary tool for the analysis of permethylated glycans by MALDI mass spectrometry. For this purpose, several matrices were tested and MALDI imaging was used to determine optimal conditions promoting or, inversely, avoiding ISD of permethylated glycans. 2,5-DHB was shown to be a versatile matrix allowing one to induce or prevent ISD according to the location of laser shots. Inversely, it was shown that 9-aminoacridine forms homogeneous spots and avoids completely ISD. This matrix would therefore be suitable for automatic analysis. 10.1021/ac1017452
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- 2010
11. A simple method to determine electrospray response factors of noncovalent complexes
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Gabelica, Valerie, Rosu, Frederic, and De Pauw, Edwin
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Coordination compounds -- Electric properties ,Coordination compounds -- Chemical properties ,Mass spectrometry -- Research ,Chemistry - Abstract
The quantitative study of noncovalent complexes by electrospray mass spectrometry requires the determination of the relative response of each species. The method proposed here to determine the electrospray response factors is based on the use of (1) an internal standard and (2) the mass balance equation applied to one binding partner M, for which different complexes [M.sub.x][L.sub.y] are detected in the electrospray mass spectra. A set of experiments providing various ratios between the complexes (e.g., different ligand concentrations in a titration experiment or different time points in a kinetics experiment) is used to generate a set of independent linear equations that can be solved using simple matrix algebra to find the response factors of each MxLy complex relative to that of the internal standard. The response factors can then be used to determine equilibrium dissociation constants or for the quantitative monitoring of reaction kinetics. The first is illustrated with a study of DNA-ligand complexes, where we show that neither minor groove binding nor intercalation dramatically affects the DNA response factor. The second is illustrated with a study of the association kinetics of the telomeric G-quadruplex d~AGGG)3 with its complementary strand, where the response factors allow correcting for the relative response of the quadrnplex and the long duplex and obtaining reproducible association rate constants independently of the source tuning potentials.
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- 2009
12. Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals
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La Rocca, Raphaël, primary, Kune, Christopher, additional, Tiquet, Mathieu, additional, Stuart, Lachlan, additional, Eppe, Gauthier, additional, Alexandrov, Theodore, additional, De Pauw, Edwin, additional, and Quinton, Loïc, additional
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- 2021
- Full Text
- View/download PDF
13. Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay
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Demeure, Kevin, Quinton, Loic, Gabelica, Valerie, and De Pauw, Edwin
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Structural optimization -- Methods ,Ionization -- Innovations ,Mass spectrometry -- Methods ,Mass spectrometry -- Equipment and supplies ,Laser beams -- Properties ,Composite materials -- Properties ,Chemistry - Abstract
In-source decay (ISD) in MALDI leads to c- and z-fragment ion series enhanced by hydrogen radical donors and is a useful method for sequencing purified peptides and proteins. Until now, most efforts to improve methods using ISD concerned instrumental optimization. The most widely used ISD matrix is 2,5-dihydroxybenzoic acid (DHB). We present here a rational way to select MALDI matrixes likely to enhance ISD for top-down proteomic approaches. Starting from Takayama's model (Takayama, M. J. Am. Soc. Mass Spectrom. 2001, 12, 1044-9), according to which formation of ISD fragments (c and z) would be due to a transfer of hydrogen radical from the matrix to the analyte, we evaluated the hydrogen-donating capacities of matrixes, and thus their ISD abilities, with spirooxazines (hydrogen scavengers). The determined hydrogen-donating abilities of the matrixes are ranked as follows: picolinic acid (PA) [less than] 1,5-diaminonaphtalene (1,5-DAN) [less than] DHB [less than] sinapinic acid [less than] [alpha]-cyano-4-hydroxy-cinnamic acid. The ISD enhancement obtained by using 1,5-DAN compared to DHB was confirmed with peptides and proteins. On that basis, a matrix-enhanced ISD approach was successfully applied to sequence peptides and proteins up to ~8 kDa. Although PA alone is not suitable for peptide and protein ionization, ISD signals could be further enhanced when PA was used as an additive to 1,5-DAN. The optimized matrix preparation was successfully applied to identify larger proteins by large ISD tag researches in protein databases (BLASTp). Coupled with an adequate separation method, ISD is a promising tool to include in a top-down proteomic strategy.
- Published
- 2007
14. Electron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer
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Gabelica, Valerie, Tabarin, Thibault, Antoine, Rodolphe, Rosu, Frederic, Compagnon, Isabelle, Broyer, Michel, De Pauw, Edwin, and Dugourd, Philippe
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Anions -- Optical properties ,Anions -- Research ,Dissociation -- Analysis ,Ion bombardment -- Analysis ,DNA -- Research ,Chemistry - Abstract
We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer single strands and 12-base pair double strands. In all cases, laser irradiation causes electron detachment from the multiply charged DNA anions. Electron photodetachment efficiency directly depends on the number of guanines in the strand, and maximum efficiency is observed between 260 and 275 nm. Subsequent collision-induced dissociation (CID) of the radical anions produced by electron photodetachment results in extensive fragmentation. In addition to neutral losses, a large number of fragments from the w, d, a *, and z *. ion series are obtained, contrasting with the w and (a-base) ion series observed in regular CID. The major advantage of this technique, coined electron photodetachment dissociation (EPD) is the absence of internal fragments, combined with good sequence coverage. EPD is therefore a highly promising approach for de novo sequencing of oligonucleotides. EPD of nucleic acids is also expected to give specific radical-induced strand cleavages, with conservation of other fragile bonds, including noncovalent bonds. In effect, preliminary results on a DNA hairpin and on double strands suggest that EPD could also be used to probe intra- and intermolecular interactions in nucleic acids.
- Published
- 2006
15. Use of Capillary Zone Electrophoresis Coupled to Electrospray Mass Spectrometry for the Detection and Absolute Quantitation of Peptidoglycan-Derived Peptides in Bacterial Cytoplasmic Extracts
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Delvaux, Cédric, primary, Dauvin, Marjorie, additional, Boulanger, Madeleine, additional, Quinton, Loïc, additional, Mengin-Lecreulx, Dominique, additional, Joris, Bernard, additional, Pauw, Edwin De, additional, and Far, Johann, additional
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- 2021
- Full Text
- View/download PDF
16. Multilabel Per-Pixel Quantitation in Mass Spectrometry Imaging
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Dewez, Frédéric, primary, De Pauw, Edwin, additional, Heeren, Ron M. A., additional, and Balluff, Benjamin, additional
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- 2020
- Full Text
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17. Response to Comment on Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry
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Morsa, Denis, primary, Hanozin, Emeline, additional, Gabelica, Valérie, additional, and De Pauw, Edwin, additional
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- 2020
- Full Text
- View/download PDF
18. Calibration of ion effective temperatures achieved by resonant activation in a quadrupole ion trap
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Gabelica, Valerie, Karas, Michael, and De Pauw, Edwin
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Chemical reaction, Rate of -- Research ,Mass spectrometry -- Usage ,Metal ions ,Leucine ,Chemical compounds ,Chemistry, Analytic -- Research ,Chemistry - Abstract
The present paper describes a calibration of the ion effective temperatures as a function of the resonant activation amplitude in a quadrupole ion trap mass spectrometer. MS/MS experiments are performed on leucine enkephalin [(M + H).sup.+], bradykinin [(M + H).sup.+], [(M + 2H).sup.2+], and [(M + 3H).sup.3+], and [(M + 11H).sup.11+]. For each amplitude, the effective temperature is calculated as the temperature that would give the same dissociation rate constant as the one observed and is calculated using published Arrhenius parameters. The effective temperature is found to be linearly dependent on the activation amplitude on the range investigated. The dependence of the slope and of the intercept of the [T.sub.eff] = f (amplitude) functions on the parent ion m/z is examined and an equation is derived to calibrate the ion effective temperature between 365 and 600 K. Below 365 K, a deviation from linearity is expected. Above 600 K, the validity of the equation will depend on whether the rapid energy exchange limit is still reached. Calculating backward, the Arrhenius parameters from the measured dissociation rates using this calibration show excellent agreement with the published values. The calibration can therefore be used to determine Arrhenius activation parameters from dissociation kinetics under resonant activation in quadrupole ion trap mass spectrometers.
- Published
- 2003
19. Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry
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Morsa, Denis, primary, Hanozin, Emeline, additional, Eppe, Gauthier, additional, Quinton, Loïc, additional, Gabelica, Valérie, additional, and Pauw, Edwin De, additional
- Published
- 2020
- Full Text
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20. Supercritical Fluid Extraction and Accelerated Solvent Extraction of Dioxins from High- and Low-Carbon Fly Ash
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Windal, I., Miller, D.J., Pauw, E. De, and Hawthorne, S.B.
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Extraction (Chemistry) -- Research ,Supercritical fluid extraction -- Methods ,Dioxin -- Analysis ,Fly ash -- Analysis ,Toluene -- Usage ,Chemistry - Abstract
This study investigates the replacement of Soxhlet extraction by supercritical fluid extraction (SFE) or accelerated solvent extraction (ASE) for the removal of dioxins from municipal waste incinerator fly ash. SFE is very matrix dependent; higher percent recoveries versus Soxhlet extraction can be obtained for low-carbon-level fly ash, but only a few percent of dioxins can be extracted from high-carbon-level fly ash. The addition of large quantifies of toluene in the extraction cell prior to extraction of high-carbon fly ash improves the recovery of the lowest chlorinated dioxins (approximately 90%), but a maximum of 20% of the octachlorodibenzo-p-dioxins can be extracted. Since large quantifies of toluene are needed to improve the recoveries, ASE with toluene was tested. Recoveries similar to Soxhlet extraction can be obtained in 2 h at 80 degrees C. Increasing the temperature to 150 degrees C increases the extraction rate and yields recoveries of approximately 110-160% compared to 48-h Soxhlet extraction for all congeners for both low- and high-carbon fly ashes. These results question the choice of Soxhlet extraction as a reference method for dioxin determination.
- Published
- 2000
21. Combination of Capillary Zone Electrophoresis-Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Theoretical Calculations for Cysteine Connectivity Identification in Peptides Bearing Two Intramolecular Disulfide Bonds
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Delvaux, Cédric, primary, Massonnet, Philippe, additional, Kune, Christopher, additional, Haler, Jean R. N., additional, Upert, Gregory, additional, Mourier, Gilles, additional, Gilles, Nicolas, additional, Quinton, Loïc, additional, De Pauw, Edwin, additional, and Far, Johann, additional
- Published
- 2019
- Full Text
- View/download PDF
22. Highly Sensitive Nondestructive Rare Earth Element Detection by Means of Wavelength-Dispersive X-ray Fluorescence Spectroscopy Enabled by an Energy Dispersive pn-Charge-Coupled-Device Detector
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De Pauw, Ella, primary, Tack, Pieter, additional, Lindner, Miles, additional, Ashauer, Antonia, additional, Garrevoet, Jan, additional, Vekemans, Bart, additional, Falkenberg, Gerald, additional, Brenker, Frank E., additional, and Vincze, Laszlo, additional
- Published
- 2019
- Full Text
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23. Covalent Cross-Linking as an Enabler for Structural Mass Spectrometry
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Hugo Gattuso, Elodie Grifnée, Emeline Hanozin, Edwin De Pauw, Denis Morsa, and André Matagne
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Electrospray ,Circular dichroism ,Spectrometry, Mass, Electrospray Ionization ,Chemistry ,Myoglobin ,Protein Conformation ,Cytochromes c ,Lactoglobulins ,Molecular Dynamics Simulation ,Mass spectrometry ,Analytical Chemistry ,Molecular dynamics ,Protein structure ,Cross-Linking Reagents ,Covalent bond ,Chemical physics ,Ion Mobility Spectrometry ,Molecule ,Animals ,Gases ,Conformational isomerism - Abstract
The number of studies referring to the structural elucidation of intact biomolecular systems using mass spectrometry techniques has gradually increased in the post-2000s literature topics. As part of native mass spectrometry, this domain capitalizes on the kinetic trapping of physiological folds in view of probing solution-like conformational properties of isolated molecules or complexes after their electrospray transfer to the gas phase. Despite its efficiency for a wide array of analytes, this approach is expected to be pushed to its limits when considering highly dynamic systems or when dealing with nonideal operating conditions. To circumvent these limitations, we challenge the adequacy of an original strategy based on cross-linkers to improve the gas-phase stability of isolated proteins and ensure the preservation of folded conformations when measuring with strong transmission voltages, by spraying from denaturing solvents, or trapping for extended periods of time. Tested on cytochrome c, myoglobin, and β-lactoglobulin cross-linked using BS3, we validated the process as structurally nonintrusive in solution using far-ultraviolet circular dichroism and unraveled the preservation of folded conformations showing better resilience to denaturation on cross-linked species using ion mobility. The resulting collision cross sections were found in agreement with the native fold, and a preservation of the proteins' secondary and tertiary structures was evidenced using molecular dynamics simulations. Our results provide new insights concerning the fate of electro-sprayed cross-linked conformers in the gas phase, while constituting promising evidence for the validation of this technique as part of future structural mass spectrometry workflows.
- Published
- 2019
24. High-performance liquid chromatography/electrospray mass spectrometry for the analysis of modified bases in DNA: 7-(2-hydroxyethyl)guanine, the major ethylene oxide-DNA adduct
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Leclercq, Laurent, Laurent, Christian, and Pauw, Edwin de
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Chromatography -- Research ,Guanine -- Analysis ,Chemistry - Abstract
A method was developed for the analysis of 7-(2-hydroxyethyl)guanine (7HEG), the major DNA adduct formed after exposure to ethylene oxide (EO). The method is based on DNA neutral thermal hydrolysis, adduct microconcentration, and final characterization and quantification by HPLC coupled to single-ion monitoring electrospray mass spectrometry (HPLC/SIR-ESMS). The method was found to be selective, sensitive, and easy to handle with no need for enzymatic digestion or previous sample derivatization. Detection limit was found to be close to 1 fmol of adduct injected ([10.sup.-10] M), thus allowing the detection of approximately three modified bases on [10.sup.8] intact nucleotides in blood sample analysis. Quantification results are shown for 7HEG after calf thymus DNA and blood exposure to various doses of EO, in both cases obtaining clear dose - response relationships.
- Published
- 1997
25. Rapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect As a Filter in Mass Spectrometry Imaging
- Author
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Kune, Christopher, primary, McCann, Andréa, additional, Raphaël, La Rocca, additional, Arias, Anthony Arguelles, additional, Tiquet, Mathieu, additional, Van Kruining, Daan, additional, Martinez, Pilar Martinez, additional, Ongena, Marc, additional, Eppe, Gauthier, additional, Quinton, Loïc, additional, Far, Johann, additional, and De Pauw, Edwin, additional
- Published
- 2019
- Full Text
- View/download PDF
26. Covalent Cross-Linking as an Enabler for Structural Mass Spectrometry
- Author
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Hanozin, Emeline, primary, Grifnée, Elodie, additional, Gattuso, Hugo, additional, Matagne, André, additional, Morsa, Denis, additional, and Pauw, Edwin De, additional
- Published
- 2019
- Full Text
- View/download PDF
27. Combined Use of Ion Mobility and Collision-Induced Dissociation To Investigate the Opening of Disulfide Bridges by Electron-Transfer Dissociation in Peptides Bearing Two Disulfide Bonds
- Author
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Edwin De Pauw, Gregory Upert, Philippe Massonnet, Loïc Quinton, Nicolas Gilles, and Nicolas Smargiasso
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Collision-induced dissociation ,Stereochemistry ,Chemistry ,Molecular Sequence Data ,010401 analytical chemistry ,010402 general chemistry ,Tandem mass spectrometry ,01 natural sciences ,Electron transport chain ,Chemistry Techniques, Analytical ,Dissociation (chemistry) ,0104 chemical sciences ,Analytical Chemistry ,Electron Transport ,Electron-transfer dissociation ,Tandem Mass Spectrometry ,Drug Design ,Cleave ,Organic chemistry ,Amino Acid Sequence ,Cysteine ,Disulfides ,Peptides ,Peptide sequence - Abstract
Disulfide bonds are post-translational modifications (PTMs) often found in peptides and proteins. They increase their stability toward enzymatic degradations and provide the structure and (consequently) the activity of such folded proteins. The characterization of disulfide patterns, i.e., the cysteine connectivity, is crucial to achieve a global picture of the active conformation of the protein of interest. Electron-transfer dissociation (ETD) constitutes a valuable tool to cleave the disulfide bonds in the gas phase, avoiding chemical reduction/alkylation in solution. To characterize the cysteine pairing, the present work proposes (i) to reduce by ETD one of the two disulfide bridges of model peptides, resulting in the opening of the cyclic structures, (ii) to separate the generated species by ion mobility, and (iii) to characterize the species using collision-induced dissociation (CID). Results of this strategy applied to several peptides show different behaviors depending on the connectivity. The loss of SH· radical species, observed for all the peptides, confirms the cleavage of the disulfides during the ETD process.
- Published
- 2015
28. Multilabel Per-Pixel Quantitation in Mass Spectrometry Imaging.
- Author
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Dewez, Frédéric, De Pauw, Edwin, Heeren, Ron M. A., and Balluff, Benjamin
- Published
- 2021
- Full Text
- View/download PDF
29. MALDI-In Source Decay Applied to Mass Spectrometry Imaging: A New Tool for Protein Identification
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Marie-Claire De Pauw-Gillet, Edwin De Pauw, Loïc Quinton, Virginie Bertrand, and Delphine Debois
- Subjects
Ions ,MALDI imaging ,chemistry.chemical_classification ,Chromatography ,Databases, Factual ,Swine ,Chemistry ,Gentisates ,Biomolecule ,Molecular Sequence Data ,Proteins ,Top-down proteomics ,Mass spectrometry ,Mass Spectrometry ,Mass spectrometry imaging ,Ion source ,Analytical Chemistry ,Matrix (chemical analysis) ,Mice ,2-Naphthylamine ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Animals ,Protein identification ,Amino Acid Sequence - Abstract
Matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) imaging is a powerful technique giving access to the distribution of a large range of biomolecules directly from a tissue section, allowing, for example, the discovery of new pathological biomarkers. Nevertheless, one main difficulty lies in the identification of the detected species, especially proteins. MALDI-in source decay (ISD) is used to fragment ions directly in the mass spectrometer ion source. This technique does not require any special sample treatment but only the use of a specific MALDI matrix such as 2,5-dihydroxybenzoic acid or 1,5-diaminonaphthalene. MALDI-ISD is generally employed on classical, purified samples, but here we demonstrate that ISD can also be performed directly on mixtures and on a tissue slice leading to fragment ions, allowing the identification of major proteins without any further treatment. On a porcine eye lens slice, de novo sequencing was even performed. Crystallins not yet referenced in databases were identified by sequence homology with other mammalian species. On a mouse brain slice, we demonstrate that results obtained with ISD are comparable and even better than those obtained with a classical in situ digestion.
- Published
- 2010
30. New Approach for Pseudo-MS3 Analysis of Peptides and Proteins via MALDI In-Source Decay Using Radical Recombination with 1,5-Diaminonaphthalene
- Author
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Nicolas Smargiasso, Edwin De Pauw, and Daiki Asakawa
- Subjects
chemistry.chemical_classification ,Stereochemistry ,Chemistry ,Proteins ,Cleavage (embryo) ,Analytical Chemistry ,Ion ,Amino acid ,Adduct ,Residue (chemistry) ,2-Naphthylamine ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Organic chemistry ,Peptide bond ,Binding site ,Peptides ,Recombination - Abstract
Matrix-assisted laser desorption ionization in-source decay (MALDI-ISD) is a useful method for top-down sequencing of proteins and preferentially produces the c'/z(•) fragment pair. Subsequently, radical z(•) fragments undergo a variety of radical reactions. This work is focused on the chemical properties of the 1,5-diaminonaphthalene (1,5-DAN) adducts on z fragment ions (zn*), which are abundant in MALDI-ISD spectra. Postsource decay (PSD) of the zn* fragments resulted in specific peptide bond cleavage adjacent to the binding site of 1,5-DAN, leading to the preferential formation of y'n-1 fragments. The dominant loss of an amino acid with 1,5-DAN from zn* can be used in pseudo-MS(3) mode to identify the C-terminal side fragments from a complex MALDI-ISD spectrum or to determine missed cleavage residues using MALDI-ISD. Although the N-Cα bond at the N-terminal side of Pro is not cleaved by MALDI-ISD, pseudo-MS(3) via zn* can confirm the presence of a Pro residue.
- Published
- 2014
31. Accurate Drift Time Determination by Traveling Wave Ion Mobility Spectrometry: The Concept of the Diffusion Calibration
- Author
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Johann Far, Edwin De Pauw, and Christopher Kune
- Subjects
Resolution (mass spectrometry) ,business.industry ,Ion-mobility spectrometry ,Chemistry ,010401 analytical chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Computational physics ,Ion ,Full width at half maximum ,symbols.namesake ,Optics ,Calibration ,Gaussian function ,symbols ,Deconvolution ,Diffusion (business) ,business - Abstract
Ion mobility spectrometry (IMS) is a gas phase separation technique, which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS difference is below the instrumental resolution expressed as CCS/ΔCCS. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. This paper introduces a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly resolved or unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half-maximum (fwhm) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation, which achieves the deconvolution of ATD peaks where the fwhm is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (μ). The standard deviation parameter (correlated to fwhm) becomes a function of the drift time. This correlation function between μ and fwhm is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion under limited and controlled space charge effect using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers of crown ether complexes and peptides leading to more accurate CCS determinations in better agreement with quantum chemistry predictions.
- Published
- 2016
32. Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies
- Author
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Haler, Jean R. N., primary, Kune, Christopher, additional, Massonnet, Philippe, additional, Comby-Zerbino, Clothilde, additional, Jordens, Jan, additional, Honing, Maarten, additional, Mengerink, Ynze, additional, Far, Johann, additional, and De Pauw, Edwin, additional
- Published
- 2017
- Full Text
- View/download PDF
33. Ion Mobility Mass Spectrometry as a Potential Tool To Assign Disulfide Bonds Arrangements in Peptides with Multiple Disulfide Bridges
- Author
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Edwin De Pauw, Loïc Quinton, Nicolas Gilles, and Julien Echterbille
- Subjects
chemistry.chemical_classification ,Spectrometry, Mass, Electrospray Ionization ,Ion-mobility spectrometry ,Chemistry ,Stereochemistry ,Disulfide bond ,Analytical chemistry ,Peptide ,Tandem mass spectrometry ,Dissociation (chemistry) ,Analytical Chemistry ,Ion ,Pairing ,Cysteine ,Disulfides ,Peptides - Abstract
Disulfide bridges play a major role in defining the structural properties of peptides and proteins. However, the determination of the cysteine pairing is still challenging. Peptide sequences are usually achieved using tandem mass spectrometry (MS/MS) spectra of the totally reduced unfolded species, but the cysteine pairing information is lost. On the other hand, MS/MS experiments performed on native folded species show complex spectra composed of nonclassical ions. MS/MS alone does not allow either the cysteine pairing or the full sequence of an unknown peptide to be determined. The major goal of this work is to set up a strategy for the full structural characterization of peptides including disulfide bridges annotation in the sequence. This strategy was developed by combining ion mobility spectrometry (IMS) and collision-induced dissociation (CID). It is assumed that the opening of one S-S bridge in a peptide leads to a structural evolution which results in a modification of IMS drift time. In the presence of multiple S-S bridges, the shift in arrival time will depend on which disulfide(s) has (have) been reduced and on the shape adopted by the generated species. Due to specific fragmentations observed for each species, CID experiments performed after the mobility separation could provide not only information on peptide sequence but also on the localization of the disulfide bridges. To achieve this goal, synthetic peptides containing two disulfides were studied. The openings of the bridges were carried out following different experimental conditions such as reduction, reduction/alkylation, or oxidation. Due to disulfide scrambling highlighted with the reduction approaches, oxidation of S-S bonds into cysteic acids appeared to be the best strategy. Cysteine connectivity was then unambiguously determined for the two peptides, without any disulfide scrambling interference.
- Published
- 2013
34. Identification and Relative-Quantification of Glycans by Matrix-Assisted Laser Desorption/Ionization In-Source Decay with Hydrogen Abstraction
- Author
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Daiki Asakawa, Edwin De Pauw, and Nicolas Smargiasso
- Subjects
chemistry.chemical_classification ,Glycan ,biology ,Chemistry ,Analytical chemistry ,Glycosidic bond ,Hydrogen atom abstraction ,Mass spectrometry ,Analytical Chemistry ,carbohydrates (lipids) ,Matrix-assisted laser desorption/ionization ,Isomerism ,Fragmentation (mass spectrometry) ,Polysaccharides ,Computational chemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Ionization ,biology.protein ,Molecule ,Salicylic Acid ,Hydrogen - Abstract
The use of specific matrixes allows enhancing the scope of in-source decay (ISD) applications in matrix-assisted laser desorption/ionization (MALDI) thanks to the specificity of analyte-matrix chemistry. The use of an oxidizing matrix, 5-nitrosalicylic acid (5-NSA), for MALDI-ISD of glycans is shown to promote fragmentation pathways involving radical precursors. Both glycosidic and cross-ring cleavages are promoted by hydrogen abstraction from hydroxyl group of glycans by 5-NSA molecules. Cross-ring cleavage ions are potentially useful in linkage analysis, one of the most critical steps of glycan characterization. Moreover, we show here that isobaric glycans could be distinguished by structure specific ISD ions and that the molar ratio of glycan isomers in the mixture can be estimated from their fragment ions abundance. The use of 5-NSA also opens the possibility to perform pseudo-MS(3) analysis of glycans. Therefore, MALDI-ISD with 5-NSA is a useful method for identification of glycans and semiquantitative analysis of mixture of glycan isomers.
- Published
- 2012
35. Accurate Drift Time Determination by Traveling Wave Ion Mobility Spectrometry: The Concept of the Diffusion Calibration
- Author
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Kune, Christopher, primary, Far, Johann, additional, and De Pauw, Edwin, additional
- Published
- 2016
- Full Text
- View/download PDF
36. Selected protein monitoring in histological sections by targeted MALDI-FTICR in-source decay imaging
- Author
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Andrei Turtoi, Delphine Debois, Marie-Claire De Pauw-Gillet, David Calligaris, Edwin De Pauw, Agnès Noël, Vincenzo Castronovo, Daiki Asakawa, Virginie Bertrand, and Rémi Longuespée
- Subjects
Proteomics ,Swine ,Analytical chemistry ,Computational biology ,01 natural sciences ,Fourier transform ion cyclotron resonance ,Analytical Chemistry ,03 medical and health sciences ,Mice ,2-Naphthylamine ,Lens, Crystalline ,Animals ,Humans ,Ionization mass spectrometry ,030304 developmental biology ,0303 health sciences ,Mice, Inbred BALB C ,Enzymatic digestion ,Chemistry ,010401 analytical chemistry ,Liver Neoplasms ,Brain ,Proteins ,Middle Aged ,Maldi msi ,0104 chemical sciences ,Molecular mapping ,Rapid identification ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Female ,Ion cyclotron resonance ,Off line ,Biomarkers - Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a rapidly growing method in biomedical research allowing molecular mapping of proteins on histological sections. The images can be analyzed in terms of spectral pattern to define regions of interest. However, the identification and the differential quantitative analysis of proteins require off line or in situ proteomic methods using enzymatic digestion. The rapid identification of biomarkers holds great promise for diagnostic research, but the major obstacle is the absence of a rapid and direct method to detect and identify with a sufficient dynamic range a set of specific biomarkers. In the current work, we present a proof of concept for a method allowing one to identify simultaneously a set of selected biomarkers on histological slices with minimal sample treatment using in-source decay (ISD) MSI and MALDI-Fourier transform ion cyclotron resonance (FTICR). In the proposed method, known biomarkers are spotted next to the tissue of interest, the whole MALDI plate being coated with 1,5-diaminonaphthalene (1,5-DAN) matrix. The latter enhances MALDI radical-induced ISD, providing large tags of the amino acid sequences. Comparative analysis of ISD fragments between the reference spots and the specimen in imaging mode allows for unambiguous identification of the selected biomarker while preserving full spatial resolution. Moreover, the high resolution/high mass accuracy provided by FTICR mass spectrometry allows the identification of proteins. Well-resolved peaks and precise measurements of masses and mass differences allow the construction of reliable sequence tags for protein identification. The method will allow the use of MALDI-FTICR MSI as a method for rapid targeted biomarker detection in complement to classical histology.
- Published
- 2013
37. Combination of Capillary Zone Electrophoresis-Mass Spectrometry, Ion Mobility-Mass Spectrometry, and Theoretical Calculations for Cysteine Connectivity Identification in Peptides Bearing Two Intramolecular Disulfide Bonds
- Author
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Delvaux, Cédric, Massonnet, Philippe, Kune, Christopher, Haler, Jean R. N., Upert, Gregory, Mourier, Gilles, Gilles, Nicolas, Quinton, Loïc, De Pauw, Edwin, and Far, Johann
- Abstract
Disulfide bonds between cysteine residues are commonly involved in the stability of numerous peptides and proteins and are crucial for providing biological activities. In such peptides, the appropriate cysteine connectivity ensures the proper conformation allowing an efficient binding to their molecular targets. Disulfide bond connectivity characterization is still challenging and is a critical issue in the analysis of structured peptides/proteins targeting pharmaceutical or pharmacological utilizations. This study describes the development of new and fast gas-phase and in-solution electrophoretic methods coupled to mass spectrometry to characterize the cysteine connectivity of disulfide bonds. For this purpose, disulfide isomers of three peptides bearing two intramolecular disulfide bonds but different cysteine connectivity have been investigated. Capillary zone electrophoresis and ion mobility both coupled to mass spectrometry were used to perform the separation in both aqueous and gas phases, respectively. The separation efficiency of each technique has been critically evaluated and compared. Finally, theoretical calculations were performed to support and explain the experimental data based on the predicted physicochemical properties of the different peptides.
- Published
- 2020
- Full Text
- View/download PDF
38. Highly Sensitive Nondestructive Rare Earth Element Detection by Means of Wavelength-Dispersive X-ray Fluorescence Spectroscopy Enabled by an Energy Dispersive pn-Charge-Coupled-Device Detector
- Author
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De Pauw, Ella, Tack, Pieter, Lindner, Miles, Ashauer, Antonia, Garrevoet, Jan, Vekemans, Bart, Falkenberg, Gerald, Brenker, Frank E., and Vincze, Laszlo
- Abstract
Detection of rare earth elements (REE) is commonly performed with destructive techniques such as (LA)-ICPMS or coupled to a destructive sample preparation. When investigating unique geological samples, such as cometary, asteroidal, or interstellar material from sample return missions or inclusions in deep Earth diamonds, a nondestructive method is preferred. The presented nondestructive highly sensitive wavelength-dispersive X-ray fluorescence spectroscopy (WD-XRF) technique is designed to measure the L-lines of REE between 4.5 and 7 keV with a sensitivity down to the ppm level. REE fluorescence L-lines are often only separated by a few eV from neighboring XRF-lines and cannot be resolved by an energy dispersive approach especially in the presence of transition metal K-lines. In our spectrometer the characteristic X-rays emitted by the sample are dispersed by a fixed Ge(111) analyzer crystal over the active area of an energy dispersive pn-charge-coupled-device (pnCCD) detector, enabling high energy resolution detection of X-rays differentiated by their corresponding Bragg angles. The use of an energy-dispersive 2D detector enables the simultaneous acquiring of XRF-lines while eliminating any ambiguities due to potential contribution from higher order diffraction effects or other diffraction planes and thereby increases the sensitivity by reducing the (scatter) background. This detection method shows an energy resolution of 12 eV for the Ti–Kα fluorescence line and has a sensitivity down to 0.50 ppm for REE L-lines. The method was optimized specifically for the nondestructive analysis of inclusions in deep Earth diamonds, yielding in situquantitative information about up-to-now inaccessible elemental (REE) composition patterns together with the more abundant transition metals like Ti, Cr, Mn, and Fe. This information is of great importance to decipher the role that deep Earth plays in the global carbon and fluid cycle.
- Published
- 2020
- Full Text
- View/download PDF
39. An analytical pipeline for MALDI in-source decay mass spectrometry imaging
- Author
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Delphine Debois, Tyler A. Zimmerman, Marie-Claire De Pauw-Gillet, Gabriel Mazzucchelli, Edwin De Pauw, and Virginie Bertrand
- Subjects
MALDI imaging ,Chromatography ,Protein mass spectrometry ,Chemistry ,Swine ,Analytical chemistry ,Cytochromes c ,Mass spectrometry ,Crystallins ,Mass spectrometry imaging ,Analytical Chemistry ,Protein sequencing ,Fragmentation (mass spectrometry) ,Ionization ,2-Naphthylamine ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Mass spectrum ,Animals ,Software - Abstract
In-source decay (ISD) fragmentation as combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allows protein sequencing directly from mass spectra. Acquisition of MALDI-ISD mass spectra from tissue samples is achieved using an appropriate MALDI matrix, such as 1,5-diaminonaphthalene (DAN). Recent efforts have focused on combining MALDI-ISD with mass spectrometry imaging (MSI) to provide simultaneous sequencing and localization of proteins over a thin tissue surface. Successfully coupling these approaches requires the development of new data analysis tools, but first, investigating the properties of MALDI-ISD as applied to mixtures of protein standards reveals a high sensitivity to the relative protein ionization efficiency. This finding translates to the protein mixtures found in tissues and is used to inform the development of an analytical pipeline for data analysis in MALDI-ISD MS imaging, including software to identify the most pertinent spectra, to sequence protein mixtures, and to generate ion images for comparison with tissue morphology. The ability to simultaneously identify and localize proteins is demonstrated by using the analytical pipeline on three tissue sections from porcine eye lens, resulting in localizations for crystallins and cytochrome c. The variety of protein identifications provided by MALDI-ISD-MSI between tissue sections creates a discovery tool, and the analytical pipeline makes this process more efficient.
- Published
- 2011
40. The use of ion mobility mass spectrometry for isomer composition determination extracted from Se-rich yeast
- Author
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Edwin De Pauw, Gauthier Eppe, Johann Far, Cédric Delvaux, and Christopher Kune
- Subjects
chemistry.chemical_classification ,Chromatography ,Ion exchange ,Ion-mobility spectrometry ,Electrospray ionization ,Size-exclusion chromatography ,Analytical chemistry ,Ether ,Mass spectrometry ,Analytical Chemistry ,chemistry.chemical_compound ,chemistry ,Reagent ,Crown ether - Abstract
The isomer ratio determination of a selenium-containing metabolite produced by Se-rich yeast was performed. Electrospray ionization and ion mobility mass spectrometry (IM-MS) were unsuccessfully used in order to resolve the isomers according to their collisional cross section (CCS) difference. The isomer ratio determination of 2,3-dihydroxypropionylselenocystathionine was performed after multidimensional liquid chromatography preconcentration from a water extract of Se-rich yeast using preparative size exclusion, anion exchange, and capillary reverse phase columns coupled to IM-MS. 4'-nitrobenzo-15-crown-5 ether, a selective shift reagent (SSR), was added after the last chromatographic dimension in order to specifically increase the CCS of one of the isomers by the formation of a stable host-guest system with the crown ether. Both isomers were consequently fully resolved by IM-MS, and the relative ratio of the isomers was determined to be 11-13% and 87-89%. The present data compared favorably with the literature to support the analytical strategy despite the lack of an authentic standard for method validation. In addition, computational chemistry methods were successfully applied to design the SSR and to support the experimental data.
- Published
- 2014
41. Polymer topology revealed by ion mobility coupled with mass spectrometry
- Author
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Thomas Defize, Dominique Dehareng, Denis Morsa, Edwin De Pauw, and Christine Jérôme
- Subjects
chemistry.chemical_classification ,Ions ,Quantitative Biology::Biomolecules ,Work (thermodynamics) ,Field (physics) ,Chemistry ,Polymers ,Context (language use) ,Polymer ,Topology ,Mass spectrometry ,Mass Spectrometry ,Analytical Chemistry ,Ion ,Invariant (mathematics) ,Topology (chemistry) - Abstract
Hyperbranched and star shaped polymers have raised tremendous interest because of their unusual structural and photochemical properties, which provide them potent applications in various domains, namely in the biomedical field. In this context, the development of adequate tools aiming to probe particular three-dimensional features of such polymers is of crucial importance. In this present work, ion mobility coupled with mass spectrometry was used to experimentally derive structural information related to cationized linear and star shaped poly-ε-caprolactones as a function of their charge state and chain length. Two major conformations were observed and identified using theoretical modeling: (1) near spherical conformations whose sizes are invariant with the polymer topology for long and lightly charged chains and (2) elongated conformations whose sizes vary with the polymer topology for short and highly charged chains. These conformations were further confirmed by collisional activation experiments based on the ejection thresholds of the coordinated cations that vary according to the elongation amplitude of the polymer chains. Finally, a comparison between solution and gas-phase conformations highlights a compaction of the structure with a loss of specific chain arrangements during the ionization and desolvation steps of the electrospray process, fueling the long-time debated question related to the preservation of the analyte structure during the transfer into the mass spectrometer.
- Published
- 2014
42. Spatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging
- Author
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Marc Ongena, Edwin De Pauw, Delphine Debois, Nicolas Smargiasso, Philippe Thonart, and Emmanuel Jourdan
- Subjects
Rhizosphere ,Bacilli ,Bacillus amyloliquefaciens ,biology ,fungi ,Biofilm ,food and beverages ,Bacillus ,biology.organism_classification ,Plant Roots ,Mass spectrometry imaging ,Analytical Chemistry ,Microbiology ,Elicitor ,chemistry.chemical_compound ,chemistry ,Biofilms ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Surfactin ,Bacteria - Abstract
Some soil Bacilli living in association with plant roots can protect their host from infection by pathogenic microbes and are therefore being developed as biological agents to control plant diseases. The plant-protective activity of these bacteria has been correlated with the potential to secrete a wide array of antibiotic compounds upon growth as planktonic cells in isolated cultures under laboratory conditions. However, in situ expression of these antibiotics in the rhizosphere where bacterial cells naturally colonize root tissues is still poorly understood. In this work, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) to examine spatiotemporal changes in the secreted antibiome of Bacillus amyloliquefaciens developing as biofilms on roots. Nonribosomal lipopeptides such as the plant immunity elicitor surfactin or the highly fungitoxic iturins and fengycins were readily produced albeit in different time frames and quantities in the surrounding medium. Interestingly, tandem mass spectrometry (MS/MS) experiments performed directly from the gelified culture medium also allowed us to identify a new variant of surfactins released at later time points. However, no other bioactive compounds such as polyketides were detected at any time, strongly suggesting that the antibiome expressed in planta by B. amyloliquefaciens does not reflect the vast genetic arsenal devoted to the formation of such compounds. This first dynamic study reveals the power of MALDI MSI as tool to identify and map antibiotics synthesized by root-associated bacteria and, more generally, to investigate plant-microbe interactions at the molecular level.
- Published
- 2014
43. Supercritical Fluid Extraction and Accelerated Solvent Extraction of Dioxins from High- and Low-Carbon Fly Ash
- Author
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Steven B. Hawthorne, E. De Pauw, David J. Miller, and I. Windal
- Subjects
Matrix (chemical analysis) ,chemistry.chemical_compound ,Municipal solid waste ,Chromatography ,chemistry ,Fly ash ,Extraction (chemistry) ,Supercritical fluid extraction ,Gas chromatography ,Toluene ,Analytical Chemistry ,Incineration - Abstract
This study investigates the replacement of Soxhlet extraction by supercritical fluid extraction (SFE) or accelerated solvent extraction (ASE) for the removal of dioxins from municipal waste incinerator fly ash. SFE is very matrix dependent; higher percent recoveries versus Soxhlet extraction can be obtained for low-carbon-level fly ash, but only a few percent of dioxins can be extracted from high-carbon-level fly ash. The addition of large quantities of toluene in the extraction cell prior to extraction of high-carbon fly ash improves the recovery of the lowest chlorinated dioxins (approximately 90%), but a maximum of 20% of the octachlorodibenzo-p-dioxins can be extracted. Since large quantities of toluene are needed to improve the recoveries, ASE with toluene was tested. Recoveries similar to Soxhlet extraction can be obtained in 2 h at 80 degrees C. Increasing the temperature to 150 degrees C increases the extraction rate and yields recoveries of approximately 110-160% compared to 48-h Soxhlet extraction for all congeners for both low- and high-carbon fly ashes. These results question the choice of Soxhlet extraction as a reference method for dioxin determination.
- Published
- 2000
44. In-source decay during matrix-assisted laser desorption/ionization combined with the collisional process in an FTICR mass spectrometer
- Author
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Edwin De Pauw, Daiki Asakawa, David Calligaris, and Tyler A. Zimmerman
- Subjects
Mice, Inbred BALB C ,Fourier Analysis ,Chemistry ,Analytical chemistry ,Proteins ,Mass spectrometry ,Fourier transform ion cyclotron resonance ,Ion source ,Analytical Chemistry ,Ion ,Matrix-assisted laser desorption/ionization ,Mice ,Fragmentation (mass spectrometry) ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Mass spectrum ,Animals ,Time-of-flight mass spectrometry ,Phosphorylation ,Peptides - Abstract
The type of ions detected after in-source decay (ISD) in a MALDI source differs according to the ion source pressure and on the mass analyzer used. We present the mechanism leading to the final ISD ions for a Fourier transform-ion cyclotron resonance mass spectrometer (FTICR MS). The MALDI ion source was operated at intermediate pressure to cool the resulting ions and increase their lifetime during the long residence times in the FTICR ion optics. This condition produces not only c', z', and w fragments, but also a, y', and d fragments. In particular, d ions help to identify isobaric amino acid residues present near the N-terminal amino acid. Desorbed ions collide with background gas during desorption, leading to proton mobilization from Arg residues to a less favored protonation site. As a result, in the case of ISD with MALDI FTICR, the influence of the Arg residue in ISD fragmentation is less straightforward than for TOF MS and the sequence coverage is thus improved. MALDI-ISD combined with FTICR MS appears to be a useful method for sequencing of peptides and proteins including discrimination of isobaric amino acid residues and site determination of phosphorylation. Additionally we also used new software for in silico elimination of MALDI matrix peaks from MALDI-ISD FTICR mass spectra. The combination of high resolving power of an FTICR analyzer and matrix subtraction software helps to interpret the low m/z region of MALDI-ISD spectra. Finally, several of these developed methods are applied in unison toward a MALDI ISD FTICR imaging experiment on mouse brain to achieve better results.
- Published
- 2013
45. Optimization of matrix conditions for the control of MALDI in-source decay of permethylated glycans
- Author
-
Edwin De Pauw and Nicolas Smargiasso
- Subjects
MALDI imaging ,Analyte ,Glycan ,Chromatography ,biology ,Chemistry ,Mass spectrometry ,Methylation ,Analytical Chemistry ,Matrix (mathematics) ,Matrix-assisted laser desorption/ionization ,Mice ,Homogeneous ,Polysaccharides ,On demand ,Immunoglobulin G ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,biology.protein ,Animals ,Artifacts - Abstract
Due to its fastness and its easiness to use, MALDI-MS is currently an analytical tool widely used in glycomic applications. However, the MALDI ionization process could result in the so-called "in-source decay", or ISD, of analytes, leading to complex spectra. On the other hand, ISD opens the possibility to perform pseudo-MS(3) experiments. This phenomenon must therefore be controlled in order to be used on demand as a supplementary tool for the analysis of permethylated glycans by MALDI mass spectrometry. For this purpose, several matrices were tested and MALDI imaging was used to determine optimal conditions promoting or, inversely, avoiding ISD of permethylated glycans. 2,5-DHB was shown to be a versatile matrix allowing one to induce or prevent ISD according to the location of laser shots. Inversely, it was shown that 9-aminoacridine forms homogeneous spots and avoids completely ISD. This matrix would therefore be suitable for automatic analysis.
- Published
- 2010
46. Combined Use of Ion Mobility and Collision-Induced Dissociation To Investigate the Opening of Disulfide Bridges by Electron-Transfer Dissociation in Peptides Bearing Two Disulfide Bonds
- Author
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Massonnet, Philippe, primary, Upert, Gregory, additional, Smargiasso, Nicolas, additional, Gilles, Nicolas, additional, Quinton, Loïc, additional, and De Pauw, Edwin, additional
- Published
- 2015
- Full Text
- View/download PDF
47. Selected Protein Monitoring in Histological Sections by Targeted MALDI-FTICR In-Source Decay Imaging
- Author
-
Calligaris, David, primary, Longuespée, Rémi, additional, Debois, Delphine, additional, Asakawa, Daiki, additional, Turtoi, Andrei, additional, Castronovo, Vincent, additional, Noël, Agnès, additional, Bertrand, Virginie, additional, De Pauw-Gillet, Marie-Claire, additional, and De Pauw, Edwin, additional
- Published
- 2013
- Full Text
- View/download PDF
48. Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay
- Author
-
Valérie Gabelica, Edwin De Pauw, Kevin Demeure, and Loïc Quinton
- Subjects
Proteomics ,Chromatography ,Hydrogen radical ,Molecular Structure ,Chemistry ,Naphthalenes ,Top-down proteomics ,Mass spectrometry ,Analytical Chemistry ,Matrix (chemical analysis) ,Matrix-assisted laser desorption/ionization ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Separation method ,Insulin ,Peptides ,Picolinic Acids ,Oxidation-Reduction ,Selection (genetic algorithm) ,Hydrogen - Abstract
In-source decay (ISD) in MALDI leads to c- and z-fragment ion series enhanced by hydrogen radical donors and is a useful method for sequencing purified peptides and proteins. Until now, most efforts to improve methods using ISD concerned instrumental optimization. The most widely used ISD matrix is 2,5-dihydroxybenzoic acid (DHB). We present here a rational way to select MALDI matrixes likely to enhance ISD for top-down proteomic approaches. Starting from Takayama's model (Takayama, M. J. Am. Soc. Mass Spectrom. 2001, 12, 1044-9), according to which formation of ISD fragments (c and z) would be due to a transfer of hydrogen radical from the matrix to the analyte, we evaluated the hydrogen-donating capacities of matrixes, and thus their ISD abilities, with spirooxazines (hydrogen scavengers). The determined hydrogen-donating abilities of the matrixes are ranked as follows: picolinic acid (PA)1,5-diaminonaphtalene (1,5-DAN)DHBsinapinic acidalpha-cyano-4-hydroxycinnamic acid. The ISD enhancement obtained by using 1,5-DAN compared to DHB was confirmed with peptides and proteins. On that basis, a matrix-enhanced ISD approach was successfully applied to sequence peptides and proteins up to approximately 8 kDa. Although PA alone is not suitable for peptide and protein ionization, ISD signals could be further enhanced when PA was used as an additive to 1,5-DAN. The optimized matrix preparation was successfully applied to identify larger proteins by large ISD tag researches in protein databases (BLASTp). Coupled with an adequate separation method, ISD is a promising tool to include in a top-down proteomic strategy.
- Published
- 2007
49. An Analytical Pipeline for MALDI In-Source Decay Mass Spectrometry Imaging
- Author
-
Zimmerman, Tyler A., primary, Debois, Delphine, additional, Mazzucchelli, Gabriel, additional, Bertrand, Virginie, additional, De Pauw-Gillet, Marie-Claire, additional, and De Pauw, Edwin, additional
- Published
- 2011
- Full Text
- View/download PDF
50. Calibration of ion effective temperatures achieved by resonant activation in a quadrupole ion trap
- Author
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Edwin De Pauw, Michael Karas, Valérie Gabelica, Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Dissemin, Projet, and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)
- Subjects
Spectrometry, Mass, Electrospray Ionization ,Analytical chemistry ,010402 general chemistry ,Mass spectrometry ,01 natural sciences ,Dissociation (chemistry) ,Analytical Chemistry ,Ion ,symbols.namesake ,Reaction rate constant ,Fragmentation (mass spectrometry) ,[CHIM] Chemical Sciences ,[CHIM]Chemical Sciences ,Animals ,Quadrupole ion trap ,Amino Acids ,Arrhenius equation ,Chemistry ,010401 analytical chemistry ,Temperature ,dissemin ,0104 chemical sciences ,Calibration ,symbols ,Cattle ,Ion trap - Abstract
International audience; The present paper describes a calibration of the ion effective temperatures as a function of the resonant activation amplitude in a quadrupole ion trap mass spectrometer. MS/MS experiments are performed on leucine enkephalin (M + H)(+), bradykinin (M + H)(+), (M + 2H)(2+), and (M + 3H)(3+), and ubiquitin (M + 11H)(11+). For each amplitude, the effective temperature is calculated as the temperature that would give the same dissociation rate constant as the one observed and is calculated using published Arrhenius parameters. The effective temperature is found to be linearly dependent on the activation amplitude on the range investigated. The dependence of the slope and of the intercept of the T-eff = f (amplitude) functions on the parent ion m/z is examined and an equation is derived to calibrate the ion effective temperature between 365 and 600 K Below 365 K, a deviation from linearity is expected. Above 600 1 the validity of the equation will depend on whether the rapid energy exchange limit is still reached. Calculating backward, the Arrhenius parameters from the measured dissociation rates using this calibration show excellent agreement with the published values. The calibration can therefore be used to determine Arrhenius activation parameters from dissociation kinetics under resonant activation in quadrupole ion trap mass spectrometers.
- Published
- 2004
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