Scientific Output

Over 10.000 scientific papers have been published by members of the Materials Chain since the foundation of the University Alliance Ruhr in 2010. This tremendous output is proof of the excellent environment the Ruhr Area provides for research in the field of materials science and technology.

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  • 2021 • 185 Oxygenated PAH Formation Chemistry Investigation in Anisole Jet Stirred Reactor Oxidation by a Thermodynamic Approach
    Chen, B. and Kruse, S. and Schmid, R. and Cai, L. and Hansen, N. and Pitsch, H.
    Energy and Fuels 35 1535-1545 (2021)
    Oxygenated poly aromatic hydrocarbons (OPAH) are widely produced in biomass combustion. Recent studies suggest significantly higher toxicity for OPAH in comparison to PAH and soot. However, the present understanding of OPAH formation chemistry is rudimentary. Hence, fundamental knowledge on the formation pathways of OPAH is urgently required to develop predictive models for adequate emission control strategies on OPAH emission in biomass combustion. In this work, the OPAH formation from oxidation of anisole, a representative biomass surrogate, was studied in a jet stirred reactor (JSR). The reaction products were in-situ sampled by molecular beam (MB) and analyzed by time-of-flight mass spectrometry (TOF-MS) using synchrotron radiation as a photon ionization source. The unique experimental setup allows direct detection and identification of large OPAH molecules. Over 40 sum formula of OPAH species were detected and identified by experiments, and a computational thermodynamic approach was applied to deduce possible isomers of OPAH species. The thermodynamic modeling approach assumes that isomers with relatively lower Gibbs free energies are more likely to be present due to possible lower activation energies in the formation pathways. Furthermore, the formation pathways of elucidated OPAH structures are proposed by analogy to the literature based on the intermediate information. The joint study of OPAH by experiments and quantum chemistry advances the understanding of OPAH formation chemistry. © 2020 American Chemical Society.
    view abstractdoi: 10.1021/acs.energyfuels.0c03829
  • 2021 • 184 Plug-flow reactor and shock-tube study of the oxidation of very fuel-rich natural gas/DME/O2 mixtures
    Kaczmarek, D. and Herzler, J. and Porras, S. and Shaqiri, S. and Fikri, M. and Schulz, C. and Atakan, B. and Maas, U. and Kasper, T.
    Combustion and Flame 225 86-103 (2021)
    A polygeneration process with the ability to provide work, heat, and useful chemicals according to the specific demand is a promising alternative to traditional energy conversion systems. By implementing such a process in an internal combustion engine, products like synthesis gas or unsaturated hydrocarbons and very high exergetic efficiencies can be obtained through partial oxidation of natural gas, in addition to the already high flexibility with respect to the required type of energy. To enable compression ignition with natural gas as input, additives such as dimethyl ether are needed to increase the reactivity at low temperatures. In this study, the reaction of fuel-rich natural gas/dimethyl ether (DME) mixtures is investigated to support the further development of reaction mechanisms for these little studied reaction conditions. Temperature-resolved species concentration profiles are obtained by mass spectrometry in a plug-flow reactor at equivalence ratios ϕ = 2, 10, and 20, at temperatures between 473 and 973 K and at a pressure of 6 bar. Ignition delay times and product-gas analyses are obtained from shock-tube experiments, for ϕ = 2 and 10, at 710 – 1639 K and 30 bar. The experimental results are compared to kinetic simulations using two literature reaction mechanisms. Good agreement is found for most species. Reaction pathways are analyzed to investigate the interaction of alkanes and DME. It is found that DME forms radicals at comparatively low temperatures and initiates the conversion of the alkanes. Additionally, according to the reaction pathways, the interaction of the alkanes and DME promotes the formation of useful products such as synthesis gas, unsaturated hydrocarbons and oxygenated species. © 2020
    view abstractdoi: 10.1016/j.combustflame.2020.10.004
  • 2021 • 183 Investigation of the combustion of iron pentacarbonyl and the formation of key intermediates in iron oxide synthesis flames
    Karakaya, Y. and Kluge, S. and Wiggers, H. and Schulz, C. and Kasper, T.
    Chemical Engineering Science 230 (2021)
    The information of the gas phase kinetics are relevant for the development of detailed reaction mechanisms as well as for process design and control in flame synthesis. In this study, the decomposition of iron pentacarbonyl and the reaction pathways towards iron oxide clusters and particles in laminar H2/O2/Ar low-pressure synthesis flames are investigated. Gas-phase species are analyzed by photoionization and electron ionization mass spectrometry. The extraction of a representative sample from the particle-laden flow of a synthesis flame by an intrusive sampling technique for the analysis is challenging, because iron-intermediate species can condense easily. Cations can be extracted from the flame with a high efficient ion sampling technique that results in high sensitivity. Iron-containing cations provide evidence of the presence of key intermediates, e.g., Fe(OH)2, Fe(OH)3, Fe2O3, and larger Fe-O-clusters which are the dominant intermediates with respect to particle formation and need to be considered in future gas-phase reaction mechanisms. © 2020 Elsevier Ltd
    view abstractdoi: 10.1016/j.ces.2020.116169
  • 2021 • 182 Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins
    Pech, S. and Rehberg, M. and Janke, R. and Benndorf, D. and Genzel, Y. and Muth, T. and Sickmann, A. and Rapp, E. and Reichl, U.
    Applied Microbiology and Biotechnology (2021)
    Abstract: Adaptations of animal cells to growth in suspension culture concern in particular viral vaccine production, where very specific aspects of virus-host cell interaction need to be taken into account to achieve high cell specific yields and overall process productivity. So far, the complexity of alterations on the metabolism, enzyme, and proteome level required for adaptation is only poorly understood. In this study, for the first time, we combined several complex analytical approaches with the aim to track cellular changes on different levels and to unravel interconnections and correlations. Therefore, a Madin-Darby canine kidney (MDCK) suspension cell line, adapted earlier to growth in suspension, was cultivated in a 1-L bioreactor. Cell concentrations and cell volumes, extracellular metabolite concentrations, and intracellular enzyme activities were determined. The experimental data set was used as the input for a segregated growth model that was already applied to describe the growth dynamics of the parental adherent cell line. In addition, the cellular proteome was analyzed by liquid chromatography coupled to tandem mass spectrometry using a label-free protein quantification method to unravel altered cellular processes for the suspension and the adherent cell line. Four regulatory mechanisms were identified as a response of the adaptation of adherent MDCK cells to growth in suspension. These regulatory mechanisms were linked to the proteins caveolin, cadherin-1, and pirin. Combining cell, metabolite, enzyme, and protein measurements with mathematical modeling generated a more holistic view on cellular processes involved in the adaptation of an adherent cell line to suspension growth. Key points: • Less and more efficient glucose utilization for suspension cell growth • Concerted alteration of metabolic enzyme activity and protein expression • Protein candidates to interfere glycolytic activity in MDCK cells © 2021, The Author(s).
    view abstractdoi: 10.1007/s00253-021-11150-z
  • 2021 • 181 Insights into the mechanism of combustion synthesis of iron oxide nanoparticles gained by laser diagnostics, mass spectrometry, and numerical simulations: A mini-review
    Rahinov, I. and Sellmann, J. and Lalanne, M.R. and Nanjaiah, M. and Dreier, T. and Cheskis, S. and Wlokas, I.
    Energy and Fuels (2021)
    To fully master a scaled-up combustion synthesis of nanoparticles toward a wide library of materials with tailored functionalities, a detailed understanding of the underlying kinetic mechanism is required. In this respect, flame synthesis of iron oxide nanoparticles is a model case, being one of the better understood systems and guiding the way how other material synthesis systems could be advanced. In this mini-review, we highlight, on the example of an iron oxide system, an approach combining laser spectroscopy and mass spectrometry with detailed simulations. The experiments deliver information on time-temperature history and concentration field data for gas-phase species and condensable matter under well-defined conditions. The simulations, which can be considered as in silico experiments, combining detailed kinetic modeling with computational fluid dynamics, serve both for mechanism validation via comparison to experimental observables as well as for shedding light on quantities inaccessible by experiments. This approach shed light on precursor decomposition, initial stages of iron oxide particle formation, and precursor role in flame inhibition and provided insights into the effect of temperature-residence time history on nanoparticle formation, properties, and flame structure. © XXXX American Chemical Society.
    view abstractdoi: 10.1021/acs.energyfuels.0c03561
  • 2021 • 180 Kinetics of the Thermal Decomposition of Ethylsilane: Shock-Tube and Modeling Study
    Sela, P. and Peukert, S. and Somnitz, H. and Janbazi, H. and Wlokas, I. and Herzler, J. and Fikri, M. and Schulz, C.
    Energy and Fuels (2021)
    The thermal decomposition of ethylsilane (H3SiC2H5, EtSiH3) is investigated behind reflected shock waves and the gas composition is analyzed by gas chromatography/mass spectrometry (GC/MS) and high-repetition-rate time-of-flight mass spectrometry (HRR-TOF-MS) in a temperature range of 990-1330 K and pressure range of 1-2.5 bar. The unimolecular decomposition of EtSiH3 is considered to be initiated via a molecular elimination of H2 (H3SiC2H5 → H2 + HSiC2H5) followed by reactions of cyclic silicon-containing species. The main observed stable products were ethylene (C2H4) and silane (SiH4). Measurements are performed with a large excess of a silylene scavenger (C2H2) to suppress bimolecular reactions caused by silylene (SiH2) and to extract unimolecular rate constants. A kinetics mechanism accounting for the gas-phase chemistry of EtSiH3 is developed, which consists of 24 Si-containing species, 31 reactions of Si-containing species, and a set of new thermochemical data. The derived unimolecular rate constant is represented by the Arrhenius expression kuni(T) = 1.96 × 1012 s-1 exp(-205 kJ mol-1/RT). The experimental data is reproduced very well by simulations based on the mechanism of this work and is in very good agreement with literature values. It is shown that EtSiH3 is a promising precursor for the synthesis of SiC nanoparticles. © 2021 American Chemical Society.
    view abstractdoi: 10.1021/acs.energyfuels.0c03425
  • 2021 • 179 Time-of-flight mass spectrometry of particle emission during irradiation with slow, highly charged ions
    Skopinski, L. and Ernst, P. and Herder, M. and Kozubek, R. and Madauß, L. and Sleziona, S. and Maas, A. and Königstein, N. and Lebius, H. and Wucher, A. and Schleberger, M.
    Review of Scientific Instruments 92 (2021)
    We describe a setup for the analysis of secondary ions and neutrals emitted from solid surfaces and two-dimensional materials during irradiation with highly charged ions. The ultrahigh vacuum setup consists of an electron beam ion source to produce bunches of ions with various charge states q (e.g., Xe1+-Xe46+) and thus potential energies, a deceleration/acceleration section to tune the kinetic energy of the ions in the range of 5 keV to 20 × q keV, a sample stage for laser-cleaning and positioning of freestanding as well as supported samples, a pulsed excimer laser for post-ionization of sputtered neutrals, and a reflectron type time-of-flight mass spectrometer, enabling us to analyze mass and velocity distributions of the emitted particles. With our setup, contributions from potential and kinetic energy deposition can be studied independently of each other. Charge dependent experiments conducted at a constant kinetic energy show a clear threshold for the emission of secondary ions from SrTiO3. Data taken with the same projectile charge state, but at a different kinetic energy, reveal a difference in the ratio of emitted particles from MoS2. In addition, first results are presented, demonstrating how velocity distributions can be measured with the new setup. © 2021 Author(s).
    view abstractdoi: 10.1063/5.0025812
  • 2021 • 178 Dedicated setup to isolate plasma catalysis mechanisms
    Stewig, C. and Urbanietz, T. and Chauvet, L. and Böke, M. and Von Keudell, A.
    Journal of Physics D: Applied Physics 54 (2021)
    Plasma catalysis, the combination of plasma and catalysis, is used to achieve efficient molecule conversion, supporting the flexibility of operating parameters and feed gases. By combining plasmas with conventional thermal catalysis, the temperature windows may be changed and the process may be made insensitive to catalyst poisoning. However, understanding plasma catalysis mechanisms is extremely difficult, due to the strong coupling between plasma, gas-phase chemistry and surface. A multitude of reaction pathways may be enhanced or reduced by the presence of a plasma that provides excited species as reaction partners. We developed a robust setup to analyse those processes, based on a parallel-plate atmospheric-pressure plasma jet that allows a plug flow design. The plasma chemistry is analysed by Fourier transform infrared absorption spectroscopy and mass spectrometry. The electrodes in contact with the plasma are temperature controlled and can easily be replaced to apply a catalyst on top of them. The basic characteristics of the setup are discussed and three examples for its application are given: (a) the analysis of methane oxidation using the plug flow scheme; (b) the plasma catalytic conversion of CO2, and (c) the plasma catalytic conversion of methane in methane–oxygen mixtures. © 2021 IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6463/abd65b
  • 2021 • 177 Machine-learning-enhanced time-of-flight mass spectrometry analysis
    Wei, Y. and Varanasi, R.S. and Schwarz, T. and Gomell, L. and Zhao, H. and Larson, D.J. and Sun, B. and Liu, G. and Chen, H. and Raabe, D. and Gault, B.
    Patterns 2 (2021)
    Mass spectrometry is a widespread approach used to work out what the constituents of a material are. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based on patterns formed in their mass-to-charge ratios and relative isotopic abundances. However, this identification step still mainly relies on individual users' expertise, making its standardization challenging, and hindering efficient data processing. Here, we introduce an approach that leverages modern machine learning technique to identify peak patterns in time-of-flight mass spectra within microseconds, outperforming human users without loss of accuracy. Our approach is cross-validated on mass spectra generated from different time-of-flight mass spectrometry (ToF-MS) techniques, offering the ToF-MS community an open-source, intelligent mass spectra analysis. Time-of-flight mass spectrometry (ToF-MS) is a mainstream analytical technique widely used in biology, chemistry, and materials science. ToF-MS provides quantitative compositional analysis with high sensitivity across a wide dynamic range of mass-to-charge ratios. A critical step in ToF-MS is to infer the identity of the detected ions. Here, we introduce a machine-learning-enhanced algorithm to provide a user-independent approach to performing this identification using patterns from the natural isotopic abundances of individual atomic and molecular ions, without human labeling or prior knowledge of composition. Results from several materials and techniques are compared with those obtained by field experts. Our open-source, easy-to-implement, reliable analytic method accelerates this identification process. A wide range of ToF-MS-based applications can benefit from our approach, e.g., hunting for patterns of biomarkers or for contamination on solid surfaces in high-throughput data. A machine-learning application for the accelerated data processing and interpretation of time-of-flight mass spectrometry is presented. The machine learns patterns in a human-label-free manner, making the process easy to implement and the result highly reproducible. © 2020 The Authors
    view abstractdoi: 10.1016/j.patter.2020.100192
  • 2021 • 176 Tracer diffusion in the σ phase of the CoCrFeMnNi system
    Zhang, J. and Muralikrishna, G.M. and Asabre, A. and Kalchev, Y. and Müller, J. and Butz, B. and Hilke, S. and Rösner, H. and Laplanche, G. and Divinski, S.V. and Wilde, G.
    Acta Materialia 203 (2021)
    A single Cr-rich σ-phase alloy with a composition of Co17Cr46Fe16.3Mn15.2Ni5.5 (at.%) and a tetragonal lattice structure was produced. The tracer diffusion coefficients of Ni and Fe were measured by secondary electron mass spectroscopy using the highly enriched 64Ni and 58Fe natural isotopes. On the homologous temperature scale, Ni and Fe diffuse in the σ phase faster as compared to the corresponding diffusion rates in the equiatomic and face-centered cubic CoCrFeMnNi alloy. In contrast, on the absolute temperature scale, these elements diffuse roughly at the same rates in both materials. Factors influencing element diffusion and phase stability of the σ phase compared to the equiatomic alloy are discussed. © 2020 Acta Materialia Inc.
    view abstractdoi: 10.1016/j.actamat.2020.116498
  • 2020 • 175 Mechanochemical Grafting: A Solvent-less Highly Efficient Method for the Synthesis of Hybrid Inorganic-Organic Materials
    Amrute, A.P. and Zibrowius, B. and Schüth, F.
    Chemistry of Materials 32 4699-4706 (2020)
    Solvent-free synthetic approaches are very attractive to curtail the chemical waste generation and simplify processes. Mechanochemistry has recently shown great potential in this direction. Here, we demonstrate the mechanochemical grafting for the synthesis of hybrid inorganic-organic materials in 5 min at room temperature without the use of any solvent. The mechanochemical functionalization of different solids (SBA-15, Î-Al2O3, SiO2 gel, and TiO2) with various organosilicon compounds (alkyltrialkoxysilanes or trialkylmonohalosilane) is confirmed by characterizing the resulting composite in detail by thermogravimetric analysis coupled to mass spectrometry, 29Si magic angle spinning nuclear magnetic resonance spectroscopy, and Fourier transform infrared spectroscopy, which suggest the formation of chemical bonds between the solid surfaces and silanes. X-ray diffraction analysis shows that the original ordered mesoporous character of SBA-15 and crystalline structures of Î-Al2O3 or TiO2 are retained after grafting. N2 sorption evidences a decrease in specific surface areas, pore diameters, and pore volumes due to the silane functionalization. Our results show that the mechanochemical silylation is efficient and likely involves the direct condensation between alkoxy or halo groups of silane and surface hydroxyls of the solids. These results, providing a general, simple, highly efficient, and solvent-free alternative to solvothermal routes for the fabrication of hybrid materials, might lead to a new pathway for the preparation of different composites for various technological applications. Copyright © 2020 American Chemical Society.
    view abstractdoi: 10.1021/acs.chemmater.0c01266
  • 2020 • 174 Experimental flat flame study of monoterpenes: Insights into the combustion kinetics of α-pinene, β-pinene, and myrcene
    Bierkandt, T. and Hoener, M. and Gaiser, N. and Hansen, N. and Köhler, M. and Kasper, T.
    Proceedings of the Combustion Institute (2020)
    Pinenes and pinene dimers have similar energy densities to petroleum-based fuels and are regarded as alternative fuels. The pyrolysis of the pinenes is well studied, but information on their combustion kinetics is limited. Three stoichiometric, flat premixed flames of the C10H16 monoterpenes α-pinene, β-pinene, and myrcene were investigated by synchrotron-based photoionization molecular-beam mass spectrometry (PI-MBMS) at the Advanced Light Source (ALS). This technique allows isomer-resolved identification and quantification of the flame species formed during the combustion process. Flame-sampling molecular-beam mass spectrometry even enables the detection of very reactive radical species. Myrcene was chosen because of its known formation during β-pinene pyrolysis. The quantitative speciation data and the discussed decomposition steps of the fuels provide important information for the development of future chemical kinetic reaction mechanisms concerning pinene combustion. The main decomposition of myrcene starts with the unimolecular cleavage of the carbon-carbon single bond between the two allylic carbon atoms. Further decompositions by β-scission to stable combustion intermediates such as isoprene (C5H8), 1,2,3-butatriene (C4H4) or allene (aC3H4) are consistent with the observed species pool. Concentrations of all detected hydrocarbons in the β-pinene flame are closer to the myrcene flame than to the α-pinene flame. These similarities and the direct identification of myrcene by its photoionization efficiency spectrum during β-pinene combustion indicate that β-pinene undergoes isomerization to myrcene under the studied flame conditions. Aromatic species such as phenylacetylene (C8H6), styrene (C8H8), xylenes (C8H10), and indene (C9H8) could be clearly identified and have higher concentrations in the α-pinene flame. Consequently, a higher sooting tendency can generally be expected for this monoterpene. The presented quantitative speciation data of flat premixed flames of the three monoterpenes α-pinene, β-pinene, and myrcene give insights into their combustion kinetics. © 2020 The Combustion Institute.
    view abstractdoi: 10.1016/j.proci.2020.06.204
  • 2020 • 173 Synthesis of graphene-related carbon nanoparticles from a liquid isopropanol precursor by a one-step atmospheric plasma process
    Bodnar, W. and Schiorlin, M. and Frank, A. and Schulz, T. and Wöhrl, N. and Miron, C. and Scheu, C. and Kolb, J.F. and Kruth, A.
    Applied Surface Science 514 (2020)
    This study presents a cost-efficient single-step-method to synthesize nanographite from isopropanol by bipolar pulsed electric discharges. The influence of pulse width within the nanosecond range, repetition frequency within the kilohertz range and processing time on the product was systematically investigated by Raman spectroscopy, high-resolution transmission electron microscopy and gas chromatography - mass spectrometry. It was found that long pulses in the microsecond range promote the creation of amorphous and oxidic carbon structures. Although, hydrocarbon cracking and subsequent graphitization do occur, these process conditions are not suitable to drive intermediate reduction processes. In contrast, applying short pulses in the nanosecond regime ensures fast reduction processes and formation of graphene-related nanostructures. The number of observed nanographite layers lies in the range of 3–13 with an average interlayer spacing of 3.4(0.3) Å and an average distance between defects of 11.5(6.0) nm meaning that the produced nanographite is in the area of small defect density. Furthermore, no significant influence of process times on the product properties over a period up to 15 min was observed, indicating good process homogeneity. © 2020 Elsevier B.V.
    view abstractdoi: 10.1016/j.apsusc.2020.145926
  • 2020 • 172 Decomposition Reactions of Fe(CO)5, Fe(C5H5)2, and TTIP as Precursors for the Spray-Flame Synthesis of Nanoparticles in Partial Spray Evaporation at Low Temperatures
    Gonchikzhapov, M. and Kasper, T.
    Industrial and Engineering Chemistry Research 59 8551-8561 (2020)
    Flame spray pyrolysis is an important method of nanoparticle manufacturing. Reactions of the precursor and the solvent determine which intermediates can contribute to particle formation. To investigate the chemical interaction between the solvent and the precursor during the partial evaporation of the spray preceding ignition, precursor solutions were sprayed into an externally heated flow reactor. The thermal decomposition of the precursors Fe(CO)5, Fe(C5H5)2, and Ti(i-OC3H7)4 in solutions of xylene and ethanol was investigated. Decomposition products were analyzed by mass spectrometry. The relevance of reactions at these low temperatures for the spray-flame process is substantiated by measurements of the spatial temperature distribution of the spray flame. Depending on the relative thermal stabilities of the precursor and the solvent, the less stable component can initiate decomposition of the more stable component, resulting in different reaction patterns of the solutions. The results are discussed with regard to their potential influence on particle formation pathways. © 2020 American Chemical Society.
    view abstractdoi: 10.1021/acs.iecr.9b06667
  • 2020 • 171 Additive-free spin coating of tin oxide thin films: Synthesis, characterization and evaluation of tin β-ketoiminates as a new precursor class for solution deposition processes
    Huster, N. and Zanders, D. and Karle, S. and Rogalla, D. and Devi, A.
    Dalton Transactions 49 10755-10764 (2020)
    The fabrication of SnOx in thin film form via chemical solution deposition (CSD) processes is favored over vacuum based techniques as it is cost effective and simpler. The precursor employed plays a central role in defining the process conditions for CSD. Particularly for processing SnO2 layers that are appealing for sensor or electronic applications, there are limited precursors available for CSD. Thus the focus of this work was to develop metalorganic precursors for tin, based on the ketoiminate ligand class. By systematic molecular engineering of the ligand periphery, a series of new homoleptic Sn(ii) β-ketoiminate complexes was synthesized, namely bis[4-(2-methoxyethylimino)-3-pentanonato] tin, [Sn(MEKI)2] (1), bis[4-(2-ethoxyethylimino)-2-pentanonato] tin, [Sn(EEKI)2] (2), bis[4-(3-methoxypropylimino)-2-pentanonato] tin, [Sn(MPKI)2] (3), bis[4-(3-ethoxypropylimino)-2-pentanonato] tin, [Sn(EPKI)2] (4) and bis[4-(3-isopropoxypropylimino)-2-pentanonato] tin, [Sn(iPPKI)2] (5). All these N-side-chain ether functionalized compounds were analyzed by nuclear magnetic resonance (NMR) spectroscopy, electron impact mass spectrometry (EI-MS), elemental analysis (EA) and thermogravimetric analysis (TGA). The solid state molecular structure of [Sn(MPKI)2] (3) was eludicated by means of single crystal X-ray diffraction (SCXRD). Interestingly, this class of compounds features excellent solubility and stability in common organic solvents alongside good reactivity towards H2O and low decomposition temperatures, thus fulfilling the desired requirements for CSD of tin oxides. With compound 3 as a representative example, we have demonstrated the possibility to directly deposit SnOx layers via hydrolysis upon exposure to air followed by heat treatment under oxygen at moderate temperatures and most importantly without the need for any additive that is generally used in CSD. A range of complementary analytical methods were employed, namely X-ray diffraction (XRD), Rutherford backscattering spectrometry (RBS), nuclear reaction analysis (NRA), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) to analyse the structure, morphology and composition of the SnOx layers. This journal is © The Royal Society of Chemistry.
    view abstractdoi: 10.1039/d0dt01463j
  • 2020 • 170 Cutting the Gordian knot: early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation
    Jarmusch, S.A. and Feldmann, I. and Blank-Landeshammer, B. and Cortés-Albayay, C. and Castro, J.F. and Andrews, B. and Asenjo, J.A. and Sickmann, A. and Ebel, R. and Jaspars, M.
    Journal of Antibiotics 73 772-779 (2020)
    Lasso peptides are a diverse class of ribosomally synthesized and post-translationally modified peptides (RiPPs). Their proteolytic and thermal stability alongside their growing potential as therapeutics has increased attention to these antimicrobial peptides. With the advent of genome mining, the discovery of RiPPs allows for the accurate prediction of putatively encoded structures, however, MSn experiments only provide partial sequence confirmation, therefore 2D NMR experiments are necessary for characterisation. Multiple MS/MS techniques were applied to two structurally characterized lasso peptides, huascopeptin and leepeptin, and one uncharacterized lasso peptide, citrulassin C, which was not isolable in sufficient quantity for NMR analysis. We have shown that MS2 can be used to elucidate the full amino acid sequences previously predicted with genome mining for this compound class. HCD was able to open the macrocycles and fragment the newly opened linear peptides, confirming the complete amino acid sequences of the characterised lasso peptides. In addition, to determine if this technique could be applied at the earliest stages of the isolation process, we targeted a lasso peptide found by genome mining, citrulassin C, and were able to fully elucidate the amino acid sequence using only MS2 from a semi-crude extract of Streptomyces huasconensis HST28T. © 2020, The Author(s), under exclusive licence to the Japan Antibiotics Research Association.
    view abstractdoi: 10.1038/s41429-020-00369-z
  • 2020 • 169 Experimental and numerical study on the influence of equivalence ratio on key intermediates and silica nanoparticles in flame synthesis
    Karakaya, Y. and Janbazi, H. and Wlokas, I. and Levish, A. and Winterer, M. and Kasper, T.
    Proceedings of the Combustion Institute (2020)
    Tetramethylsilane is a precursor often used for the production of flame-synthesized silica nanoparticles or coatings. This study investigates the chemical reaction mechanism of tetramethylsilane in a series of H 2 /O 2 /Ar low-pressure (p = 30 mbar) flames from fuel-lean to slightly fuel-rich flame conditions (ϕ= 0.8, 1.0 and 1.2). Mole fraction profiles are obtained by molecular-beam mass spectrometry. The experimental data are compared to simulations using a recently published reaction mechanism. The present study reveals the influence of the flame composition on the depletion of the precursor TMS, the formation of its main carbon-containing products (e.g. CO 2 and CO) and the main silicon-containing intermediates (e.g. Si(CH 3) 3 (CH 2)OO), Si(OH) 4, SiO 2, Si 4 O 10 H 4) appearing along the routes of particle formation. TEM images of synthesized particles reveal that the nanoparticles obtained from the gas-phase synthesis are spheres with a low degree of agglomeration. The particle size distribution appears to be dependent on the equivalence ratio of the synthesis flames and the changes can tentatively be traced to different particle formation pathways. The data set provided in this work can serve a basis for improvements to the reaction mechanisms of the Si/C/H/O system that are urgently needed to improve particle synthesis processes. © 2020 The Combustion Institute. Published by Elsevier Inc.
    view abstractdoi: 10.1016/j.proci.2020.06.096
  • 2020 • 168 Isothermal pyrolysis investigation of aluminum diethylphosphinate mixed as a flame retardant additive into ultra-high molecular weight polyethylene
    Lau, S. and Atakan, B.
    Combustion and Flame 222 272-284 (2020)
    Aliphatic polymers such as polyethylene or polypropylene are widely used in spite of their high flammability and forces the introduction of flame retardants (FR), e.g. metal phosphinates, into the polymers. These flame retardants usually act in the condensed phase or may influence the gas phase mechanism of combustion. However, the modes of action are not yet understood in detail and require increasing research. In this study a contribution to the latter is made. The thermal decomposition behavior of aluminum diethylphosphinate (AlPi) as FR, mixed in ultra-high molecular weight polyethylene (UHMWPE) is investigated here by molecular beam mass spectrometry (MBMS) in an oxygen-free atmosphere. The isothermal pyrolysis experiments for this system have been systematically studied by first concentrating on each neat compound, FR and polymer, respectively, followed by the analysis of doped polyethylene blends. The aim is to detect phosphorus-containing species in the gas phase, which is the minimum requirement for a gas phase active FR. It was found that the main product of AlPi is diethylphosphinic acid, which subsequently degrades to lighter species or dimerizes. In the mixture, although the AlPi decomposition is influenced by the polymer in the condensed phase, most of the species responsible for a flame suppressant effect are still present in the gas phase. © 2020
    view abstractdoi: 10.1016/j.combustflame.2020.08.048
  • 2020 • 167 Vapor Pressure Assessment of Sulfolane-Based Eutectic Solvents: Experimental, PC-SAFT, and Molecular Dynamics
    Lima, F. and Dietz, C.H.J.T. and Silvestre, A.J.D. and Branco, L.C. and Canongia Lopes, J. and Gallucci, F. and Shimizu, K. and Held, C. and Marrucho, I.M.
    Journal of Physical Chemistry B 124 10386-10397 (2020)
    Since their discovery, deep eutectic solvents (DES) have been explored in multiple applications. However, the complete physicochemical characterization is still nonexistent for many of the proposed and used DES. In particular, vapor pressure, which is a crucial property for the application of DES as solvents, is very rarely available. In this work, the measurement of the total and partial pressures of two sulfolane-based DES, tetrabutylammonium bromide:sulfolane and tetrabutylphosphonium bromide:sulfolane, in several proportions, from 40 to 100 °C and atmospheric pressure, was performed using headspace gas chromatography mass spectrometry, HS-GC-MS. A large decrease on the total pressure was recorded which, together with the finding that total pressures showed negative deviations from Raoult's law, is indicative of the favorable, strong interactions between the two components within the DES. Additionally, the study of vapor pressure change with DES molar composition was carried out, and surprisingly, the existence of inflection points in the pressure curve was observed. Experimental results were modeled using the PC-SAFT equation of state, and in addition, MD simulations were performed to provide a molecular understanding of the pressure data. Considering the different results and insights obtained from the used strategies, it can be concluded that both DES systems have especially strong interactions between salt and sulfolane, at high sulfolane content, due to the different structural rearrangement of the liquid state. © 2020 American Chemical Society.
    view abstractdoi: 10.1021/acs.jpcb.0c04837
  • 2020 • 166 Improving identification of in-organello protein-protein interactions using an affinityenrichable, isotopically coded, and mass spectrometry-cleavable chemical crosslinker
    Makepeace, K.A.T. and Mohammed, Y. and Rudashevskaya, E.L. and Petrotchenko, E.V. and Vögtle, F.-N. and Meisinger, C. and Sickmann, A. and Borchers, C.H.
    Molecular and Cellular Proteomics 19 624-639 (2020)
    An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improvements in the application of the CLMS technique, in terms of the detection, acquisition, and identification of crosslinker-modified peptides. This approach was evaluated on intact yeast mitochondria, and the results showed that hundreds of unique protein-protein interactions could be identified on an organelle proteome-wide scale. Both known and previously unknown protein-protein interactions were identified. These interactions were assessed based on their known sub-compartmental localizations. Additionally, the identified crosslinking distance constraints are in good agreement with existing structural models of protein complexes involved in the mitochondrial electron transport chain. © 2020 Makepeace et al.
    view abstractdoi: 10.1074/mcp.RA119.001839
  • 2020 • 165 Herbivores coprolites from chehrabad salt mine of zanjan, iran (Sassanid era, 224-651 ad) reveals eggs of strongylidae and anoplocephalidae helminths
    Meigouni, M. and Makki, M. and Haniloo, A. and Askari, Z. and Mobedi, I. and Naddaf, S.R. and Boenke, N. and Stollner, T. and Aali, A. and Heidari, Z. and Mowlavi, G.
    Iranian Journal of Parasitology 15 109-114 (2020)
    Background: The ancient Chehrabad Salt mine, a well-known archaeological site in Iran, has recently received increasing interest from Iranian and international archeologists. Also, the biological remains from this site have provided valuable sources for studying the pathogenic agents of ancient times. This study aimed to identify the parasitic helminth eggs preserved in the herbivores coprolites. Methods: From 2011 to 2015, we received three coprolites belonging to herbivorous animals recovered during excavations in Chehrabad Salt mine of Zanjan, Iran. The coprolites were dated back to the Sassanid era (224-651 AD) by using radiocarbon accelerator mass spectrometry (AMS) and archeological stratigraphy methods. Following rehydration of the specimens in a 0.5% trisodium phosphate solution, the suspensions were mounted in glycerin jelly on glass slides and examined by a light microscope with 100x and 400x magnifications. Results: Two coprolites belonged to donkeys and one to an unknown herbivore species. The recovered eggs belonged to members of two helminths families, Strongylidae, and Anoplocephalidae. Also, within the two coprolites, some mites, presumably of the order Oribatida, were observed. Conclusion: The presence of two different nematodes in the equids coprolites provide clues of the burden of helminths infection on working animal at the Sassanid time and demonstrates the appropriate preservation condition of biological remains in the ancient salt mine of Chehrabad as well. © 2020, Tehran University of Medical Sciences (TUMS). All rights reserved.
    view abstractdoi: 10.18502/ijpa.v15i1.2533
  • 2020 • 164 Differentiation between Carbon Corrosion and Oxygen Evolution Catalyzed by NixB/C Hybrid Electrocatalysts in Alkaline Solution using Differential Electrochemical Mass Spectrometry
    Möller, S. and Barwe, S. and Dieckhöfer, S. and Masa, J. and Andronescu, C. and Schuhmann, W.
    ChemElectroChem 7 2680-2686 (2020)
    Carbon is a frequently used electrode material and an important additive in catalyst films. Its corrosion is often reported during electrocatalysis at high anodic potentials, especially in acidic electrolyte. Investigation of the carbon corrosion in alkaline environment is difficult due to the CO2/CO32− equilibrium. We report the on-line determination of electrolysis products generated on NixB/C hybrid electrocatalysts in alkaline electrolyte at anodic potentials using differential electrochemical mass spectrometry (DEMS). NixB/C catalyst films were obtained from mixtures containing different ratios of NiXB and benzoxazine monomers followed by polymerization and pyrolysis. The impact of the composition of the electrocatalyst on the dominant electrolysis process allows to distinguish between the oxygen evolution reaction and carbon corrosion using DEMS results as well as the catalyst surface composition evaluated from X-ray photoelectron spectra. At the imposed highly oxidative conditions, an increasing amount of NixB in the electrocatalyst leads to a suppression of carbon corrosion. © 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/celc.202000697
  • 2020 • 163 High-frequency gas effusion through nanopores in suspended graphene
    Rosłoń, I.E. and Dolleman, R.J. and Licona, H. and Lee, M. and Šiškins, M. and Lebius, H. and Madauß, L. and Schleberger, M. and Alijani, F. and van der Zant, H.S.J. and Steeneken, P.G.
    Nature Communications 11 (2020)
    Porous, atomically thin graphene membranes have interesting properties for filtration and sieving applications. Here, graphene membranes are used to pump gases through nanopores using optothermal forces, enabling the study of gas flow through nanopores at frequencies above 100 kHz. At these frequencies, the motion of graphene is closely linked to the dynamic gas flow through the nanopore and can thus be used to study gas permeation at the nanoscale. By monitoring the time delay between the actuation force and the membrane mechanical motion, the permeation time-constants of various gases through pores with diameters from 10–400 nm are shown to be significantly different. Thus, a method is presented for differentiating gases based on their molecular mass and for studying gas flow mechanisms. The presented microscopic effusion-based gas sensing methodology provides a nanomechanical alternative for large-scale mass-spectrometry and optical spectrometry based gas characterisation methods. © 2020, The Author(s).
    view abstractdoi: 10.1038/s41467-020-19893-5
  • 2020 • 162 Conversion of volatile organic compounds in a twin surface dielectric barrier discharge
    Schücke, L. and Gembus, J.-L. and Peters, N. and Kogelheide, F. and Nguyen-Smith, R.T. and Gibson, A.R. and Schulze, J. and Muhler, M. and Awakowicz, P.
    Plasma Sources Science and Technology 29 (2020)
    A voltage and power controlled surface dielectric barrier discharge for the removal of volatile organic compounds (VOCs) from gas streams is studied by means of current-voltage measurements, flame ionization detectors, and gas chromatography-mass spectrometry (GC-MS). The discharge is generated in a defined synthetic air gas stream at atmospheric pressure by application of a damped sinusoidal voltage waveform resulting from a resonant circuit. Multiple organic compounds, namely n-butane, butanol, isobutanol, ethyl acetate, diethyl ether, and butoxyethanol, are tested at concentrations of 50, 100, 200, and 400 ppm (parts per million), as well as peak-to-peak voltages of 8 to 13 kVpp and pulse repetition frequencies of 250 to 4000 Hz. The dissipated power within the system is calculated utilizing the measured voltage and current waveforms. The conversion and absolute degradation of the VOCs are determined by flame ionization detectors. An increasing concentration of VOCs is found to increase the dissipated power marginally, suggesting a higher conductivity and higher electron densities in the plasma. Of the applied VOCs, n-butane is found to be the most resistant to the plasma treatment, while higher concentrations consistently result in a lower conversion and a higher absolute degradation across all tested compounds. Corresponding amounts of converted molecules per expended joule are given as a comparable parameter by weighting the absolute degradation with the dissipated power. Finally, specific reaction products are determined by online GC-MS, further confirming carbon dioxide (CO2) as a major reaction product, alongside a variety of less prevalent side products, depending on the structure of the original compound. The findings of this study are intended to promote the development of energy efficient processes for the purification of gas streams in both, industry and consumer market. Potential applications of the presented technique could be found in car paint shops, chemical plants, hospital ventilation systems, or air purifiers for living space. © 2020 IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6595/abae0b
  • 2020 • 161 Thermal treatment of lignin, cellulose and hemicellulose in nitrogen and carbon dioxide
    Senneca, O. and Cerciello, F. and Russo, C. and Wütscher, A. and Muhler, M. and Apicella, B.
    Fuel 271 (2020)
    The paper explores the primary products from fast pyrolysis of biomass components: Lignin, Cellulose and Hemicellulose (Xylan). A heated strip reactor is employed at temperatures of 1573 K and 2073 K with N2 and CO2 atmospheres. Volatiles quench immediately after volatilization on a cold pyrex bridge, while char remains on the heated strip for 3 s. Tar, soot and char are collected and subject to chemical treatments and analyses, including gas chromatography-mass spectrometry and Size Exclusion Chromatography, Thermogravimetric analysis, Raman spectroscopy and Scanning Electron Microscopy. Fast pyrolysis of Lignin produces “Light tar” (soluble in acetone) and “Heavy tar” (soluble in NMP), char, a minor fraction of soot. The “Light tar” contains Vanillin, which can be considered the main primary depolymerization product, but also aliphatics and PAHs. Higher temperature enhances “Heavy tar” and graphitization of the char. Cellulose at 1573 K produces only “Light tar”, largely made of Levoglucosan, as the result of depolymerization. At higher temperature the tar becomes heavier. Hemicellulose has a peculiar behavior: it produces a “Light tar” which is chemically similar to that of Cellulose and, at high temperature also “Heavy tar”. Hemicellulose pyrolysis results also in the production of an atypical solid residue: swollen ad spongy at lower temperature, bright and glassy at higher temperature. CO2 affects the pyrolysis products, particularly those of Lignin, promoting tar cracking and oxygenation already at the stage of primary pyrolysis and hindering thermal annealing and structural ordering of the solid carbonaceous structure. © 2020 Elsevier Ltd
    view abstractdoi: 10.1016/j.fuel.2020.117656
  • 2020 • 160 Study of the transition from self-organised to homogeneous plasma distribution in chromium HiPIMS discharge
    Šlapanská, M. and Hecimovic, A. and Gudmundsson, J.T. and Hnilica, J. and Breilmann, W. and Vašina, P. and Von Keudell, A.
    Journal of Physics D: Applied Physics 53 (2020)
    The self-organised plasma patterns, known as spokes or ionisation zones in magnetron sputtering discharges, were observed in a wide range of power densities, from low power direct current magnetron sputtering (dcMS) discharge to high power impulse magnetron sputtering (HiPIMS) discharge. For some target materials and non-reactive gases, it was observed that at very high power densities (>3 kW cm-2) the plasma exhibits a transition from a regime where spokes are observed to a homogeneous plasma regime. In this contribution, we present a comparison of plasma properties: plasma emission (optical emission spectroscopy) and flux of argon and chromium ions (mass spectrometry), measured both in the spoke regime and in the homogeneous plasma regime, aimed to expand the understanding of the plasma transition between the two modes. A simple biased flat probe was used to distinguish between the spoke regime and the homogeneous plasma regime. It was found that the flux of multiply charged ions (Ar2+, Cr2+, Cr3+, Cr4+) increases abruptly at the transition between the spoke regime and the homogeneous plasma regime. Similarly, the emission from Cr+ ions exhibits a strong increase of about 50% when the plasma torus becomes homogeneous. These observations are interpreted as an increase in electron temperature and a change in the electron heating mode, from a combination of secondary electron heating and Ohmic heating towards pure Ohmic heating. The transition to the homogeneous plasma regime and pure Ohmic heating is only observed in non-reactive HiPIMS discharges for target atoms with the second ionisation potential higher than the first ionisation potential of Ar (15.76 eV), and a self-sputter yield larger than 1. © 2020 The Author(s). Published by IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6463/ab6a8c
  • 2020 • 159 Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies
    Xuan, Y. and Bateman, N.W. and Gallien, S. and Goetze, S. and Zhou, Y. and Navarro, P. and Hu, M. and Parikh, N. and Hood, B.L. and Conrads, K.A. and Loosse, C. and Kitata, R.B. and Piersma, S.R. and Chiasserini, D. and Zhu, H. an...
    Nature Communications 11 (2020)
    Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrate robust, sensitive, and reproducible data generation across eleven international sites on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality. © 2020, The Author(s).
    view abstractdoi: 10.1038/s41467-020-18904-9
  • 2019 • 158 High temperature pyrolysis of lignite and synthetic carbons
    Apicella, B. and Russo, C. and Ciajolo, A. and Cortese, L. and Cerciello, F. and Stanzione, F. and Wuetscher, A. and Muhler, M. and Senneca, O.
    Fuel 264-272 (2019)
    The paper explores changes in reactivity and chemico-physical characteristics of char and tar produced by severe heat treatment of lignite in both inert atmospheres and CO2 rich atmospheres. The role of mineral matter, in particular metal oxides, in catalysing chemical and physical transformations is also addressed. A Rhenish Lignite from the Garzweiler mine was studied and compared with: a) mineral-free synthetic carbon (HTC), obtained from cellulose; b) a synthetic carbon doped with iron oxide (Fe2O3). A heated strip reactor (HSR) was employed at temperatures of 1300 and 1800 °C in N2 and CO2 atmospheres. Liquid and solid products (tar and char) were analysed and compared. Tar composition was evaluated by extraction and gas chromatography-mass spectrometry, whereas the solid carbonaceous material produced by pyrolysis, mainly composed of char, was characterized regarding its thermal behaviour by thermogravimetric analysis and its structure by Raman spectroscopy and scanning electron microscopy. Results show that iron oxide exerts a catalytic influence on both pyrolysis and char oxidation. Upon severe heat treatment, it reduces char reactivity promoting graphitization and structural ordering. The overall effect on char reactivity is therefore not easy to predict. © 2018 Elsevier Ltd
    view abstractdoi: 10.1016/j.fuel.2018.12.065
  • 2019 • 157 Lead diffusion in CaTiO3: A combined study using Rutherford backscattering and TOF-SIMS for depth profiling to reveal the role of lattice strain in diffusion processes
    Beyer, C. and Dohmen, R. and Rogalla, D. and Becker, H.-W. and Marquardt, K. and Vollmer, C. and Hagemann, U. and Hartmann, N. and Chakraborty, S.
    American Mineralogist 104 557-568 (2019)
    We present experimental data on the diffusivity of Pb in CaTiO3 perovskite, which is commonly used for dating kimberlites and carbonatites. Experiments were performed on oriented synthetic and natural CaTiO3 single crystals. The Pb-source was either a laser deposited (Ca0.83Pb0.07)Ti1.05O3 thin film or a (Ca0.9Pb0.1)TiO3 powder reservoir. The crystals were annealed in a high-temperature furnace between 736 and 1135 °C and for durations from 2 to 283 h. The diffusion profiles were measured with Rutherford backscattering and time-of-flight secondary ion mass spectrometry in the depth-profiling mode. The concentration profiles measured on the same samples with the two analytical methods are in agreement. The measured concentration profiles show two regions - a steep gradient at the diffusion interface that transitions sharply (at ~50 to 150 nm from the surface) to a low concentration tail that penetrates deeper into the crystal. This diffusion behavior could be modeled best using diffusion coefficients that are a function of the Pb concentration, with a different set of diffusion coefficient for the high and the low concentration region of the profile, respectively. The diffusion coefficients extracted from the thin film and powder source experiments are similar within uncertainties. Pb diffuses slower at concentrations between 8.5 and 0.6 wt% and 1.6 to 2.6 log units faster below ~0.5 wt% Pb. Temperature dependency for each region is discussed in the text, and the Arrhenius relation for the fast diffusion regime that is most relevant for natural samples is DPbfast=2.5×10-13×exp(-158(24)kJ/mol/RT)m2/s. $$begin array D- text Pb- text fast=2.5 times 10- -13times exp Big(-158big(24big)text kJ/mol/RTBig)m-2/s. end array $$ We found a distinct change in the structure of CaTiO3 in the surface region of the single crystal that is coincidental with the change in diffusivity. This initial region is dominated by planar defects. We propose that Pb is trapped in planar defects that have formed due to the high strain introduced into the perovskite structure caused by the mismatch in the ionic radius between Ca2+ and Pb2+. The activation energies obtained here yield closure temperature for Pb in CaTiO3 between 300 and 400 °C for a range of different cooling scenarios if diffusive resetting of Pb in CaTiO3 occurs at all. At typical cooling rates of hours to days for ascending kimberlite, the age of crystal growth is preserved, with closure temperatures similar to the magma temperature. © 2019 Walter de Gruyter GmbH, Berlin/Boston 2019.
    view abstractdoi: 10.2138/am-2019-6730
  • 2019 • 156 Flame structure of laminar premixed anisole flames investigated by photoionization mass spectrometry and photoelectron spectroscopy
    Bierkandt, T. and Hemberger, P. and Oßwald, P. and Krüger, D. and Köhler, M. and Kasper, T.
    Proceedings of the Combustion Institute 37 1579-1587 (2019)
    Two laminar, premixed, fuel-rich flames fueled by anisole-oxygen-argon mixtures with the same cold gas velocity and pressure were investigated by molecular-beam mass spectrometry at two synchrotron sources where tunable vacuum-ultraviolet radiation enables isomer-resolved photoionization. Decomposition of the very weak O-CH3 bond in anisole (C6H5OCH3) by unimolecular decomposition yields the resonantly-stabilized phenoxy radical (C6H5O). This key intermediate species opens reaction routes to five-membered ring species, such as cyclopentadiene (C5H6) and cyclopentadienyl radicals (C5H5). Anisole is often discussed as model compound for lignin to study the phenolic-carbon structure in this natural polymer. Measured temperature profiles and mole fractions of many combustion intermediates give detailed information on the flame structure. A very comprehensive reaction mechanism from the literature which includes a sub-scheme for anisole combustion is used for species modeling. Species with the highest measured mole fractions (on the order of 10?3-10?2) are CH3, CH4, C2H2, C2H4, C2H6, CH2O, C5H5 (cyclopentadienyl radical), C5H6 (cyclopentadiene), C6H6 (benzene), C6H5OH (phenol), and C6H5CHO (benzaldehyde). Some are formed in the first destruction steps of anisole, e.g., phenol and benzaldehyde, and their formation will be discussed and with regard to the modeling results. There are three major routes for the fuel destruction: (1) formation of benzaldehyde (C6H5CHO), (2) formation of phenol (C6H5OH), and (3) unimolecular decomposition of anisole to phenoxy (C6H5O) and CH3 radicals. In the experiment, the phenoxy radical could be measured directly. The phenoxy radical decomposes via a bicyclic structure into the soot precursor C5H5 and CO. Formation of larger oxygenated species was observed in both flames. One of them is guaiacol (2-methoxyphenol), which decomposes into fulvenone. The presented speciation data, which contain more than 60 species mole fraction profiles of each flame, give insights into the combustion kinetics of anisole.
    view abstractdoi: 10.1016/j.proci.2018.07.037
  • 2019 • 155 Proteogenomics of colorectal cancer liver metastases: Complementing precision oncology with phenotypic data
    Blank-Landeshammer, B. and Richard, V.R. and Mitsa, G. and Marques, M. and Leblanc, A. and Kollipara, L. and Feldmann, I. and Du Tertre, M.C. and Gambaro, K. and McNamara, S. and Spatz, A. and Zahedi, R.P. and Sickmann, A. and Bat...
    Cancers 11 (2019)
    Hotspot testing for activating KRAS mutations is used in precision oncology to select colorectal cancer (CRC) patients who are eligible for anti-EGFR treatment. However, even for KRASwildtype tumors anti-EGFR response rates are <30%, while mutated-KRAS does not entirely rule out response, indicating the need for improved patient stratification. We performed proteogenomic phenotyping of KRASwildtype and KRASG12V CRC liver metastases (mCRC). Among >9000 proteins we detected considerable expression changes including numerous proteins involved in progression and resistance in CRC. We identified peptides representing a number of predicted somatic mutations, including KRASG12V. For eight of these, we developed a multiplexed parallel reaction monitoring (PRM) mass spectrometry assay to precisely quantify the mutated and canonical protein variants. This allowed phenotyping of eight mCRC tumors and six paired healthy tissues, by determining mutation rates on the protein level. Total KRAS expression varied between tumors (0.47–1.01 fmol/μg total protein) and healthy tissues (0.13–0.64 fmol/μg). In KRASG12V-mCRC, G12Vmutation levels were 42–100%, while one patient had only 10% KRASG12V but 90% KRASwildtype. This might represent a missed therapeutic opportunity: Based on hotspot sequencing, the patient was excluded from anti-EGFR treatment and instead received chemotherapy, while PRM-based tumorphenotyping indicates the patient might have benefitted from anti-EGFR therapy. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
    view abstractdoi: 10.3390/cancers11121907
  • 2019 • 154 Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials
    Chang, Y. and Lu, W. and Guénolé, J. and Stephenson, L.T. and Szczpaniak, A. and Kontis, P. and Ackerman, A.K. and Dear, F.F. and Mouton, I. and Zhong, X. and Zhang, S. and Dye, D. and Liebscher, C.H. and Ponge, D. and Korte-Ker...
    Nature Communications 10 (2019)
    Hydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale. © 2019, The Author(s).
    view abstractdoi: 10.1038/s41467-019-08752-7
  • 2019 • 153 Determination of the Total Vapor Pressure of Hydrophobic Deep Eutectic Solvents: Experiments and Perturbed-Chain Statistical Associating Fluid Theory Modeling
    Dietz, C.H.J.T. and Creemers, J.T. and Meuleman, M.A. and Held, C. and Sadowski, G. and Van Sint Annaland, M. and Gallucci, F. and Kroon, M.C.
    ACS Sustainable Chemistry and Engineering 7 4047-4057 (2019)
    Head-space gas chromatography mass spectrometry (HS-GC-MS) was used for the first time to measure the total vapor pressure of hydrophobic deep eutectic solvents (DESs). The new method was developed as a valid alternative for thermogravimetric analysis (TGA), as TGA did not allow obtaining reliable total vapor pressure data for the hydrophobic DESs studied in this work. The main advantage of HS-GC-MS is that the partial pressure of each DES constituent and the contribution of each DES constituent to the total vapor pressure of the mixture can be measured. The results give a clear indication of the interactions occurring between the DES constituents. Also, activity coefficients, enthalpies of evaporation, and activation energies for fluid displacement were obtained and correlated to the measured vapor pressure data. It was confirmed that the total vapor pressures of the hydrophobic DESs are very low in comparison to vapor pressures of commonly used volatile organic solvents like toluene. The total vapor pressures of the hydrophobic DESs were successfully predicted with perturbed-chain statistical associating fluid theory (PC-SAFT) when using PC-SAFT parameters for the individual DES constituents. © 2019 American Chemical Society.
    view abstractdoi: 10.1021/acssuschemeng.8b05449
  • 2019 • 152 Molecular cobalt corrole complex for the heterogeneous electrocatalytic reduction of carbon dioxide
    Gonglach, S. and Paul, S. and Haas, M. and Pillwein, F. and Sreejith, S.S. and Barman, S. and De, R. and Müllegger, S. and Gerschel, P. and Apfel, U.-P. and Coskun, H. and Aljabour, A. and Stadler, P. and Schöfberger, W. and Roy, S.
    Nature Communications 10 (2019)
    Electrochemical conversion of CO2 to alcohols is one of the most challenging methods of conversion and storage of electrical energy in the form of high-energy fuels. The challenge lies in the catalyst design to enable its real-life implementation. Herein, we demonstrate the synthesis and characterization of a cobalt(III) triphenylphosphine corrole complex, which contains three polyethylene glycol residues attached at the meso-phenyl groups. Electron-donation and therefore reduction of the cobalt from cobalt(III) to cobalt(I) is accompanied by removal of the axial ligand, thus resulting in a square-planar cobalt(I) complex. The cobalt(I) as an electron-rich supernucleophilic d8-configurated metal centre, where two electrons occupy and fill up the antibonding dz 2 orbital. This orbital possesses high affinity towards electrophiles, allowing for such electronically configurated metals reactions with carbon dioxide. Herein, we report the potential dependent heterogeneous electroreduction of CO2 to ethanol or methanol of an immobilized cobalt A3-corrole catalyst system. In moderately acidic aqueous medium (pH = 6.0), the cobalt corrole modified carbon paper electrode exhibits a Faradaic Efficiency (FE%) of 48 % towards ethanol production. © 2019, The Author(s).
    view abstractdoi: 10.1038/s41467-019-11868-5
  • 2019 • 151 Development and evaluation of a chemical kinetics reaction mechanism for tetramethylsilane-doped flames
    Janbazi, H. and Karakaya, Y. and Kasper, T. and Schulz, C. and Wlokas, I. and Peukert, S.
    Chemical Engineering Science 209 (2019)
    Tetramethysilane (TMS) is a precursor for flame synthesis of silica (SiO2) nanoparticles. A chemical reaction mechanism was developed for the oxidation of TMS in a lean low-pressure (p ≈ 30 mbar) H2/O2/Ar flame using species mole fractions, obtained from molecular-beam mass spectrometry (MBMS) measurements in a matrix-supported flat flame doped with 600 ppm TMS. The thermodynamic data of Si-containing species were determined from quantum-chemical calculations at the G4 level of theory. The formation and subsequent consumption of Si(OH)4, one of the main products of TMS oxidation, and the formation of Si4O10H4 clusters are hypothesized to be the primary pathway in the synthesis of silica nanoparticles. The reaction rate coefficients are either estimated via an algorithmic optimization procedure or are assumed based on analogies to similar reactions in the literature. The mechanism was further validated based on MBMS measurements with the same base flame doped with 400 and 800 ppm TMS. © 2019 Elsevier Ltd
    view abstractdoi: 10.1016/j.ces.2019.115209
  • 2019 • 150 Investigation of the partial oxidation of methane/n-heptane-mixtures and the interaction of methane and n-heptane under ultra-rich conditions
    Kaczmarek, D. and Atakan, B. and Kasper, T.
    Combustion and Flame 345-357 (2019)
    The homogeneous partial oxidation of methane is an interesting approach to obtain useful chemicals like synthesis gas, higher hydrocarbons, aldehydes or alcohols. Because of the low reactivity of methane, the homogeneous conversion needs high temperatures to proceed at reasonable reaction rates. Additives like n-heptane form reactive intermediates at comparatively low temperatures and initiate the conversion. To study the kinetics of doped conversion reactions, fuel-rich diluted methane/n-heptane/oxygen/argon-mixtures (2 ≤ Φ ≤ 20) were investigated in a plug-flow reactor at a pressure of 6 bar, at intermediate temperatures between 423 and 973 K and at relatively long residence times (7 ≤ τ ≤ 14 s). The product composition at the reactor outlet is analyzed by gas chromatography and mass spectrometry. Species profiles as a function of equivalence ratio and temperature are compared with simulations, and serve as validation data for different reaction mechanisms. Rates of production and reaction paths are analyzed to investigate the interaction of methane and n-heptane during the oxidation process. They show that the chemical interaction of the oxidation products of both fuels has a promoting effect on the formation of different useful products like carbon monoxide, methanol or ethane. To prove this observation, mole fraction profiles as a function of temperature were compared between experiments with an equivalence ratio of Φ = 8 using neat methane, neat n-heptane and methane/n-heptane mixtures as fuels. The results show that the yields of these species are much higher in case of the methane/n-heptane mixture compared to the yields obtained in the neat methane and neat n-heptane conversions or the sum of both. © 2019 The Combustion Institute
    view abstractdoi: 10.1016/j.combustflame.2019.04.005
  • 2019 • 149 Plug-Flow Reactor Study of the Partial Oxidation of Methane and Natural Gas at Ultra-Rich Conditions
    Kaczmarek, D. and Atakan, B. and Kasper, T.
    Combustion Science and Technology 191 1571-1584 (2019)
    The homogeneous partial oxidation of fuel-rich CH4/O2, CH4/C2H6/C3H8/O2 as well as CH4/C2H6/C3H8/H2/O2 mixtures is investigated in a plug-flow reactor at intermediate temperatures (473 ≤ T ≤ 973 K) and a pressure of 6 bar. Experiments are carried out at equivalence ratios (Φ) of 2, 10, and 20. Product species are analyzed using time-of-flight molecular-beam mass spectrometry. The experimental results are further compared with kinetic simulations. It was found that under the investigated conditions, the onset temperature for CH4 oxidation is above 773 K. The highest methane conversion at equivalence ratios of 10 and 20 was between 0–3% for neat methane as fuel and 10–13% for natural gas as fuel. The conversions yield useful chemicals like synthesis gas (H2/CO), C2H4, C2H6, or C3H6. Higher CH4 conversion in the natural gas mixtures results in much higher yields of all products. The natural gas components ethane and propane do not influence the reaction onset temperature. © 2019, © 2019 Taylor & Francis Group, LLC.
    view abstractdoi: 10.1080/00102202.2019.1577829
  • 2019 • 148 Investigating the Role of Mitochondria in Type 2 Diabetes – Lessons from Lipidomics and Proteomics Studies of Skeletal Muscle and Liver
    Kappler, L. and Kollipara, L. and Lehmann, R. and Sickmann, A.
    Advances in Experimental Medicine and Biology 1158 143-182 (2019)
    Mitochondrial dysfunction is discussed as a key player in the pathogenesis of type 2 diabetes mellitus (T2Dm), a highly prevalent disease rapidly developing as one of the greatest global health challenges of this century. Data however about the involvement of mitochondria, central hubs in bioenergetic processes, in the disease development are still controversial. Lipid and protein homeostasis are under intense discussion to be crucial for proper mitochondrial function. Consequently proteomics and lipidomics analyses might help to understand how molecular changes in mitochondria translate to alterations in energy transduction as observed in the healthy and metabolic diseases such as T2Dm and other related disorders. Mitochondrial lipids integrated in a tool covering proteomic and functional analyses were up to now rarely investigated, although mitochondrial lipids might provide a possible lynchpin in the understanding of type 2 diabetes development and thereby prevention. In this chapter state-of-the-art analytical strategies, pre-analytical aspects, potential pitfalls as well as current proteomics and lipidomics-based knowledge about the pathophysiological role of mitochondria in the pathogenesis of type 2 diabetes will be discussed. © 2019, Springer Nature Singapore Pte Ltd.
    view abstractdoi: 10.1007/978-981-13-8367-0_9
  • 2019 • 147 Degradation of iridium oxides via oxygen evolution from the lattice: Correlating atomic scale structure with reaction mechanisms
    Kasian, O. and Geiger, S. and Li, T. and Grote, J.-P. and Schweinar, K. and Zhang, S. and Scheu, C. and Raabe, D. and Cherevko, S. and Gault, B. and Mayrhofer, K.J.J.
    Energy and Environmental Science 12 3548-3555 (2019)
    Understanding the fundamentals of iridium degradation during the oxygen evolution reaction is of importance for the development of efficient and durable water electrolysis systems. The degradation mechanism is complex and it is under intense discussion whether the oxygen molecule can be directly released from the oxide lattice. Here, we define the extent of lattice oxygen participation in the oxygen evolution and associated degradation of rutile and hydrous iridium oxide catalysts, and correlate this mechanism with the atomic-scale structures of the catalytic surfaces. We combine isotope labelling with atom probe tomography, online electrochemical and inductively coupled plasma mass spectrometry. Our data reveal that, unlike rutile IrO2, Ir hydrous oxide contains -IrIIIOOH species which directly contribute to the oxygen evolution from the lattice. This oxygen evolution mechanism results in faster degradation and dissolution of Ir. In addition, near surface bulk regions of hydrous oxide are involved in the oxygen catalysis and dissolution, while only the topmost atomic layers of rutile IrO2 participate in both reactions. Overall our data provide a contribution to the fundamental understanding of the exceptional stability of Ir-oxides towards the oxygen evolution reaction. The proposed approach to a quantitative assessment of the degree of lattice oxygen participation in the oxygen evolution reaction can be further applied to other oxide catalyst systems. © 2019 The Royal Society of Chemistry.
    view abstractdoi: 10.1039/c9ee01872g
  • 2019 • 146 Imaging individual solute atoms at crystalline imperfections in metals
    Katnagallu, S. and Stephenson, L.T. and Mouton, I. and Freysoldt, C. and Subramanyam, A.P.A. and Jenke, J. and Ladines, A.N. and Neumeier, S. and Hammerschmidt, T. and Drautz, R. and Neugebauer, J. and Vurpillot, F. and Raabe, D. ...
    New Journal of Physics 21 (2019)
    Directly imaging all atoms constituting a material and, maybe more importantly, crystalline defects that dictate materials' properties, remains a formidable challenge. Here, we propose a new approach to chemistry-sensitive field-ion microscopy (FIM) combining FIM with time-of-flight mass-spectrometry (tof-ms). Elemental identification and correlation to FIM images enabled by data mining of combined tof-ms delivers a truly analytical-FIM (A-FIM). Contrast variations due to different chemistries is also interpreted from density-functional theory (DFT). A-FIM has true atomic resolution and we demonstrate how the technique can reveal the presence of individual solute atoms at specific positions in the microstructure. The performance of this new technique is showcased in revealing individual Re atoms at crystalline defects formed in Ni-Re binary alloy during creep deformation. The atomistic details offered by A-FIM allowed us to directly compare our results with simulations, and to tackle a long-standing question of how Re extends lifetime of Ni-based superalloys in service at high-temperature. © 2019 The Author(s). Published by IOP Publishing Ltd on behalf of the Institute of Physics and Deutsche Physikalische Gesellschaft.
    view abstractdoi: 10.1088/1367-2630/ab5cc4
  • 2019 • 145 The fate of the OH radical in molecular beam sampling experiments
    Krüger, D. and Oßwald, P. and Köhler, M. and Hemberger, P. and Bierkandt, T. and Kasper, T.
    Proceedings of the Combustion Institute 37 1563-1570 (2019)
    The collisional history of ionized molecules in a molecular beam mass spectrometric flame experiment is target of our present investigation. Measurements in a double imaging photoelectron photoion coincidence spectroscopy (i2PEPICO) were performed at the Swiss Light Source (SLS) of the Paul Scherrer Institute to use the ion imaging device for separating the molecular beam ions from rethermalized ions. This enables the precise composition study of the individual types of ions. Results show clearly for the OH radical that the complete signal is obtained from the molecular beam, while the signal from other combustion compounds features additional rethermalized molecules. As for OH radicals, the mole fraction is reduced by sampling effects and contact with the ionization vessel walls significantly. Consequently, this leads to signal loss and lower mole fractions, when using ionization cross sections for the quantification. To improve on this, a beam fraction (BF) factor is presented. The factor describes the ratio of the separated beam signal without rethermalized ions with the total ion signal, consisting of the mass to charge ratio from the molecular beam and additional rethermalized ions. Since the detected OH radicals are solely from the molecular beam, a new method of comparing two molecular beam alignments using the OH to H2O signal ratio is presented. This method has a decent potential for the optimization of the quality of molecular beams. Finally, the separated beam signal (without the rethermalized ions) was used to determine mole fraction profiles for the OH radical using ionization cross sections. These profiles are in good agreement with model predictions of the USC-II and the Aramco Mech 2.0 mechanisms, while the total signal leads to factor of 12 smaller OH mole fractions. © 2018 Elsevier Ltd.
    view abstractdoi: 10.1016/j.proci.2018.05.041
  • 2019 • 144 Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator
    Nshanian, M. and Lantz, C. and Wongkongkathep, P. and Schrader, T. and Klärner, F.-G. and Blümke, A. and Despres, C. and Ehrmann, M. and Smet-Nocca, C. and Bitan, G. and Loo, J.A.
    Journal of the American Society for Mass Spectrometry 30 16-23 (2019)
    Native top-down mass spectrometry (MS) and ion mobility spectrometry (IMS) were applied to characterize the interaction of a molecular tweezer assembly modulator, CLR01, with tau, a protein believed to be involved in a number of neurodegenerative disorders, including Alzheimer’s disease. The tweezer CLR01 has been shown to inhibit aggregation of amyloidogenic polypeptides without toxic side effects. ESI-MS spectra for different forms of tau protein (full-length, fragments, phosphorylated, etc.) in the presence of CLR01 indicate a primary binding stoichiometry of 1:1. The relatively high charging of the protein measured from non-denaturing solutions is typical of intrinsically disordered proteins, such as tau. Top-down mass spectrometry using electron capture dissociation (ECD) is a tool used to determine not only the sites of post-translational modifications but also the binding site(s) of non-covalent interacting ligands to biomolecules. The intact protein and the protein-modulator complex were subjected to ECD-MS to obtain sequence information, map phosphorylation sites, and pinpoint the sites of inhibitor binding. The ESI-MS study of intact tau proteins indicates that top-down MS is amenable to the study of various tau isoforms and their post-translational modifications (PTMs). The ECD-MS data point to a CLR01 binding site in the microtubule-binding region of tau, spanning residues K294-K331, which includes a six-residue nucleating segment PHF6 (VQIVYK) implicated in aggregation. Furthermore, ion mobility experiments on the tau fragment in the presence of CLR01 and phosphorylated tau reveal a shift towards a more compact structure. The mass spectrometry study suggests a picture for the molecular mechanism of the modulation of protein-protein interactions in tau by CLR01. [Figure not available: see fulltext.]. © 2018, American Society for Mass Spectrometry.
    view abstractdoi: 10.1007/s13361-018-2027-6
  • 2019 • 143 High-temperature gas-phase kinetics of the thermal decomposition of tetramethoxysilane
    Sela, P. and Peukert, S. and Herzler, J. and Sakai, Y. and Fikri, M. and Schulz, C.
    Proceedings of the Combustion Institute 37 1133-1141 (2019)
    The decomposition of tetramethoxysilane (Si(OCH3)4, TMOS) was studied in shock-tube experiments in the 1131-1610 K temperature range at pressures ranging from 1.9 to 2.3 bar behind reflected shock waves combining gas chromatography/mass spectrometry (GC/MS) and high-repetition-rate time-of-flight mass spectrometry (HRR-TOF-MS). The initial reaction is a four-center elimination to form methanol. At elevated temperatures, TMOS also decomposes via a O-C bond scission forming a methyl (CH3) and the corresponding OSi(OCH3)3 radical. The main observed products were methane (CH4), methanol (CH3OH), ethylene (C2H4), and ethane (C2H6). The yields of these products increase with temperature. A kinetics mechanism from literature (Chu et al. 1995), which quantitatively accounts for the observed products in the decomposition of TMOS, was adopted and updated. The mechanism contains 13 silicon species and 24 reactions with silicon-containing species. It was combined with the methanol mechanism of Burke et al. (2006). The measured global rate constant for TMOS decomposition was found to be koverall[TMOS→products] = 2.9 × 1011exp(- 225 kJ mol-1/RT)s-1. © 2018 The Combustion Institute.
    view abstractdoi: 10.1016/j.proci.2018.05.084
  • 2019 • 142 High-Temperature Unimolecular Decomposition of Diethyl Ether: Shock-Tube and Theory Studies
    Sela, P. and Sakai, Y. and Choi, H.S. and Herzler, J. and Fikri, M. and Schulz, C. and Peukert, S.
    Journal of Physical Chemistry A 123 6813-6827 (2019)
    The unimolecular decomposition of diethyl ether (DEE; C2H5OC2H5) is considered to be initiated via a molecular elimination and a C-O and a C-C bond fission step: C2H5OC2H5 → C2H4 + C2H5OH (1), C2H5OC2H5 → C2H5 + C2H5O (2), and C2H5OC2H5 → CH3 + C2H5OCH2 (3). In this work, two shock-tube facilities were used to investigate these reactions via (a) time-resolved H-atom concentration measurements by H-ARAS (atomic resonance absorption spectrometry), (b) time-resolved DEE-concentration measurements by high repetition-rate time-of-flight mass spectrometry (HRR-TOF-MS), and (c) product-composition measurements via gas chromatography/MS (GC/MS) after quenching the test gas. The experiments were conducted at temperatures ranging from 1054 to 1505 K and at pressures between 1.2 and 2.5 bar. Initial DEE mole fractions between 0.4 and 9300 ppm were used to perform the kinetics experiments by H-ARAS (0.4 ppm), GC/MS (200-500 ppm), and HRR-TOF-MS (7850-9300 ppm). The rate constants, ktotal (ktotal = k1 + k2 + k3) derived from the GC/MS and HRR-TOF-MS experiments agree well with each other and can be described by the Arrhenius expression, ktotal(1054-1467 K; 1.3-2.5 bar) = 1012.81±0.22 exp(-240.27 ± 5.11 kJ mol-1/RT) s-1. From the H-ARAS experiments, overall rate constants for the bond fission channels, k2+3 = k2 + k3 have been extracted. The k2+3 data can be well described by the Arrhenius equation, k2+3(1299-1505 K; 1.3-2.5 bar) = 1014.43±0.33 exp(-283.27 ± 8.78 kJ mol-1/RT) s-1. A master-equation analysis was performed using CCSD(T)/aug-cc-pvtz//B3LYP/aug-cc-pvtz and CASPT2/aug-cc-pvtz//B3LYP/aug-cc-pvtz molecular properties and energies for the three primary thermal decomposition processes in DEE. The derived experimental data is very well reproduced by the simulations with the mechanism of this work. With regard to the branching ratios between bond fissions and elimination channels, uncertainties remain. Copyright © 2019 American Chemical Society.
    view abstractdoi: 10.1021/acs.jpca.9b04186
  • 2019 • 141 Enhancing the Selectivity between Oxygen and Chlorine towards Chlorine during the Anodic Chlorine Evolution Reaction on a Dimensionally Stable Anode
    Wintrich, D. and Öhl, D. and Barwe, S. and Ganassin, A. and Möller, S. and Tarnev, T. and Botz, A. and Ruff, A. and Clausmeyer, J. and Masa, J. and Schuhmann, W.
    ChemElectroChem 6 3108-3112 (2019)
    The selectivity of the chlorine evolution reaction over the oxygen evolution reaction during the electrolysis of aqueous NaCl is, despite being very high, still insufficient to prevent expensive separation of the formed Cl2 and O2 by means of liquefaction. We hypothesize that, by decreasing the local activity of H2O near the anode surface by substantially increasing the ionic strength of the electrolyte, the oxygen evolution reaction would be suppressed, leading concomitantly to a higher selectivity of Cl2 over O2 formation. Hence, the influence of the ionic strength on the competition between electrochemical evolution of O2 and Cl2 at dimensionally stable anodes (DSAs) was investigated. Addition of a high concentration of NaNO3, an inert electrolyte additive, increases the selectivity for chlorine at high current density, as determined by means of online electrochemical mass spectrometry and UV-vis spectroscopy. We propose conditions in which free water is suppressed, owing to under-coordination of the solvation shells of ions, as a general concept to modulate the selectivity of competing electrochemical reactions. © 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
    view abstractdoi: 10.1002/celc.201900784
  • 2019 • 140 Targeting the MKK7-JNK (Mitogen-Activated Protein Kinase Kinase 7-c-Jun N-Terminal Kinase) Pathway with Covalent Inhibitors
    Wolle, P. and Hardick, J. and Cronin, S.J.F. and Engel, J. and Baumann, M. and Lategahn, J. and Penninger, J.M. and Rauh, D.
    Journal of Medicinal Chemistry 62 2843-2848 (2019)
    The protein kinase MKK7 is linked to neuronal development and the onset of cancer. The field, however, lacks high-quality functional probes that would allow for the dissection of its detailed functions. Against this background, we describe an effective covalent inhibitor of MKK7 based on the pyrazolopyrimidine scaffold. © 2019 American Chemical Society.
    view abstractdoi: 10.1021/acs.jmedchem.9b00102
  • 2018 • 139 Fasciola hepatica eggs in paleofaeces of the Persian onager Equus hemionus onager, a donkey from Chehrabad archaeological site, dating back to the Sassanid Empire (224–651 AD), in ancient Iran
    Askari, Z. and Mas-Coma, S. and Bouwman, A.S. and Boenke, N. and Stöllner, T. and Aali, A. and Rezaiian, M. and Mowlavi, G.
    Infection, Genetics and Evolution 62 233-243 (2018)
    Fascioliasis is a highly pathogenic zoonotic disease caused by the liver trematodes Fasciola hepatica and F. gigantica. Within the multidisciplinary initiative against this disease, there is the aim of understanding how this disease reached a worldwide distribution, with important veterinary and medical repercussions, by elucidating the spreading steps followed by the two fasciolids from their paleobiogeograhical origins. Fasciola eggs were detected in paleofaeces of a donkey, probably the present-day endangered Persian onager Equus hemionus onager, found in the Chehrabad salt mine archaeological site, Zanjan province, northwestern Iran. The biological remains dated back to the Sassanid period, 224–651 AD. Egg characteristics allowed for their specific ascription to F. hepatica. The interest of this finding relies on the fact of being the first archaeological finding of Fasciola in Asia and the Near East. Moreover, it allows to reach many conclusions about historical, epidemiological and spreading aspects of the disease. The finding in Chehrabad indicates that, at that time, this fasciolid had already spread through the Zagros mountains eastward from the Fertile Crescent. In that region and in ancient Egypt, livestock domestication played a crucial role in facilitating the disease spread during the postdomestication period. Donkeys appear at present to be usually infected by fasciolids in countries of the Fertile Crescent - Ancient Egypt region or neighbouring that region, with prevalences from low to very high. The high pathogenicity and mortality induced by Fasciola in these equines should be considered as an additional potential factor among the causes of the extinctions of E. h. hemippus in Syria, E. h. hydruntinus in the Anatolia-Balkans area, E. h. onager in the Caucasus and maybe also its decline in Iran. Indeed, Eurasiatic wild asses were present in the region and neighbourhood of the Fertile Crescent when the domestication of the livestock reservoirs of Fasciola began. © 2018 Elsevier B.V.
    view abstractdoi: 10.1016/j.meegid.2018.04.028
  • 2018 • 138 An N-Heterocyclic Carbene Based Silver Precursor for Plasma-Enhanced Spatial Atomic Layer Deposition of Silver Thin Films at Atmospheric Pressure
    Boysen, N. and Hasselmann, T. and Karle, S. and Rogalla, D. and Theirich, D. and Winter, M. and Riedl, T. and Devi, A.
    Angewandte Chemie - International Edition 57 16224-16227 (2018)
    A new N-heterocyclic carbene (NHC)-based silver amide compound, 1,3-di-tert-butyl-imidazolin-2-ylidene silver(I) 1,1,1-trimethyl-N-(trimethylsilyl)silanaminide [(NHC)Ag(hmds)] was synthesized and analyzed by single-crystal X-ray diffraction, 1H and 13C NMR spectroscopy, as well as EI mass spectrometry, and subsequently evaluated for its thermal characteristics. This new halogen- and phosphine-free Ag atomic layer deposition (ALD) precursor was tested successfully for silver thin film growth in atmospheric pressure plasma enhanced spatial (APP-ALD). High-purity conductive Ag thin films with a low sheet resistance of 0.9 Ω/sq (resistivity: 10−5 Ωcm) were deposited at 100 °C and characterized by X-ray photoelectron spectroscopy, scanning electron microscopy, optical transmittance, and Rutherford back-scattering techniques. The carbene-based Ag precursor and the new APP-ALD process are significant developments in the field of precursor chemistry as well as metal ALD processing. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
    view abstractdoi: 10.1002/anie.201808586
  • 2018 • 137 Enhanced selective cellular proliferation by multi-biofunctionalization of medical implant surfaces with heterodimeric BMP-2/6, fibronectin, and FGF-2
    Ettelt, V. and Belitsky, A. and Lehnert, M. and Loidl-Stahlhofen, A. and Epple, M. and Veith, M.
    Journal of Biomedical Materials Research - Part A 106 2910-2922 (2018)
    Increasing cell adhesion on implant surfaces is an issue of high biomedical importance. Early colonization with endogenous cells reduces the risk of bacterial contamination and enhances the integration of an implant into the diverse cellular tissues surrounding it. In vivo integration of implants is controlled by a complex spatial and temporal interplay of cytokines and adhesive molecules. The concept of a multi-biofunctionalized TiO2 surface for stimulating bone and soft tissue growth is presented here. All supramolecular architectures were built with a biotin–streptavidin coupling system. Biofunctionalization of TiO2 with immobilized FGF-2 and heparin could be shown to selectively increase the proliferation of fibroblasts while immobilized BMP-2 only stimulated the growth of osteoblasts. Furthermore, TiO2 surfaces biofunctionalized with either the BMP-2 or BMP-2/6 growth factor and the cell adhesion-enhancing protein fibronectin showed higher osteoblast adhesion than a TiO2 surface functionalized with only one of these proteins. In conclusion, the presented immobilization strategy is applicable in vivo for a selective surface coating of implants in both hard and connective tissue. The combined immobilization of different extracellular proteins on implants has the potential to further influence cell-specific reactions. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2910–2922, 2018. © 2018 Wiley Periodicals, Inc.
    view abstractdoi: 10.1002/jbm.a.36480
  • 2018 • 136 Hydrogen abstraction ratios: A systematic iPEPICO spectroscopic investigation in laminar flames
    Krüger, D. and Oßwald, P. and Köhler, M. and Hemberger, P. and Bierkandt, T. and Karakaya, Y. and Kasper, T.
    Combustion and Flame 191 343-352 (2018)
    The radicals produced by hydrogen abstraction in the initial fuel decomposition step are essential in combustion kinetics, but their experimental detection is very challenging. Imaging photoelectron photoion coincidence spectroscopy enables the detection and identification of even these isomeric radicals. Laminar low-pressure (40 mbar) hydrogen flames doped with different alkanes and alkenes are investigated systematically with the goal to identify the formation pathways and the fate of fuel radicals formed in hydrogen abstraction reactions. The abstraction reactions of primary, secondary, tertiary, and vinylic H atoms were never target of a systematic, direct semiquantitative investigation in a flame environment and this paper describes such a study for the first time. Performing the measurements at the vacuum ultraviolet beamline located at the Swiss Light Source enables isomer-selective detection of reactive radical species by imaging photoelectron photoion coincidence spectroscopy. For unambiguous identification of several isomeric radicals, threshold photoelectron spectra were compared with reference photoelectron spectra. H-abstraction ratios of isomeric radicals were determined and compared to literature reaction barriers and rate coefficients. In addition to the quantitative information, the peak positions of the profiles of radicals formed by hydrogen abstraction or addition to the fuel molecules as function of distance from the burner show faster H-abstraction for unbranched alkanes and alkenes than for branched fuels and faster H-addition than H-abstraction, respectively. © 2018 The Combustion Institute
    view abstractdoi: 10.1016/j.combustflame.2017.12.025
  • 2018 • 135 Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry
    Mnatsakanyan, R. and Shema, G. and Basik, M. and Batist, G. and Borchers, C.H. and Sickmann, A. and Zahedi, R.P.
    Expert Review of Proteomics 15 515-535 (2018)
    Introduction: Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information—for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)—holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays—particularly targeted MS, MALDI imaging, and immuno-MALDI—may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies. © 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
    view abstractdoi: 10.1080/14789450.2018.1483340
  • 2018 • 134 Comparative study on the deposition of silicon oxide permeation barrier coatings for polymers using hexamethyldisilazane (HMDSN) and hexamethyldisiloxane (HMDSO)
    Mitschker, F. and Schücke, L. and Hoppe, C. and Jaritz, M. and Dahlmann, R. and De Los Arcos, T. and Hopmann, C. and Grundmeier, G. and Awakowicz, P.
    Journal of Physics D: Applied Physics 51 (2018)
    The effect of the selection of hexamethyldisiloxane (HMDSO) and hexamethyldisilazane (HMDSN) as a precursor in a microwave driven low pressure plasma on the deposition of silicon oxide barrier coatings and silicon based organic interlayers on polyethylene terephthalate (PET) and polypropylene (PP) substrates is investigated. Mass spectrometry is used to quantify the absolute gas density and the degree of depletion of neutral precursor molecules under variation of oxygen admixture. On average, HMDSN shows a smaller density, a higher depletion and the production of smaller fragments. Subsequently, this is correlated with barrier performance and chemical structure as a function of barrier layer thickness and oxygen admixture on PET. For this purpose, the oxygen transmission rate (OTR) is measured and Fourier transformed infrared (FTIR) spectroscopy as well as x-ray photoelectron spectroscopy (XPS) is performed. HMDSN based coatings exhibit significantly higher barrier performances for high admixtures of oxygen (200 sccm). In comparison to HMDSO based processes, however, a higher supply of oxygen is necessary to achieve a sufficient degree of oxidation, cross-linking and, therefore, barrier performance. FTIR and XPS reveal a distinct carbon content for low oxygen admixtures (10 and 20 sccm) in case of HMDSN based coatings. The variation of interlayer thickness also reveals significantly higher OTR for HMDSO based coatings on PET and PP. Barrier performance of HMDSO based coatings improves with increasing interlayer thickness up to 10 nm for PET and PP. HMDSN based coatings exhibit a minimum of OTR without interlayer on PP and for 2 nm interlayer thickness on PET. Furthermore, HMDSN based coatings show distinctly higher bond strengths to the PP substrate. © 2018 IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6463/aac0ab
  • 2018 • 133 Direct Measurement of High-Temperature Rate Constants of the Thermal Decomposition of Dimethoxymethane, a Shock Tube and Modeling Study
    Peukert, S. and Sela, P. and Nativel, D. and Herzler, J. and Fikri, M. and Schulz, C.
    Journal of Physical Chemistry A 122 7559-7571 (2018)
    Shock-tube experiments have been performed to investigate the thermal decomposition of the oxygenated hydrocarbon dimethoxymethane (DMM; CH 3 OCH 2 OCH 3 ). The primary initial reaction channels of DMM decomposition are considered to be the two bond fissions: CH 3 OCH 2 OCH 3 → CH 3 O + CH 2 OCH 3 (1) and CH 3 OCH 2 OCH 3 → CH 3 + OCH 2 OCH 3 (2). In the present work, two shock-tube facilities and three different detection techniques have been combined: Behind reflected shock waves, we have carried out time-resolved measurements of (i) the formation of H atoms using the highly sensitive H-ARAS (Atomic Resonance Absorption Spectrometry) technique and (ii) the depletion of the DMM reactant by high-repetition-rate time-of-flight mass spectrometry (HRR-TOF-MS). In addition, (iii) the temperature-dependent composition of stable reaction products was measured in single-pulse shock-tube experiments via gas chromatography (GC/MS). The experiments span a temperature range of 1100-1430 K, a pressure range of 1.2-2.5 bar, and initial reactant mole fractions from 0.5 ppm (for H-ARAS experiments) up to 10 000 ppm (for HRR-TOF-MS experiments). Experimental rate constants k total , k total = k 1 + k 2 , obtained from these three completely different methods were in excellent agreement among each other, i.e., deviations are within ±30-40%, and they can be well represented by the Arrhenius expression k total (T) = 10 13.28±0.27 exp(-247.90 ± 6.36 kJ mol -1 /RT) s -1 (valid over the 1100-1400 K temperature and the 1.2-2.5 bar pressure range). By replacing the respective k total values used in a recently published DMM chemical kinetics combustion mechanism (Vermeire et al. Combust. Flame 2018, 190, 270-283), it was also possible to successfully reproduce measured product distributions. © 2018 American Chemical Society.
    view abstractdoi: 10.1021/acs.jpca.8b06558
  • 2018 • 132 Omics-based responses induced by bosentan in human hepatoma HepaRG cell cultures
    Rodrigues, R.M. and Kollipara, L. and Chaudhari, U. and Sachinidis, A. and Zahedi, R.P. and Sickmann, A. and Kopp-Schneider, A. and Jiang, X. and Keun, H. and Hengstler, J. and Oorts, M. and Annaert, P. and Hoeben, E. and Gijbels,...
    Archives of Toxicology 92 1939-1952 (2018)
    Bosentan is well known to induce cholestatic liver toxicity in humans. The present study was set up to characterize the hepatotoxic effects of this drug at the transcriptomic, proteomic, and metabolomic levels. For this purpose, human hepatoma-derived HepaRG cells were exposed to a number of concentrations of bosentan during different periods of time. Bosentan was found to functionally and transcriptionally suppress the bile salt export pump as well as to alter bile acid levels. Pathway analysis of both transcriptomics and proteomics data identified cholestasis as a major toxicological event. Transcriptomics results further showed several gene changes related to the activation of the nuclear farnesoid X receptor. Induction of oxidative stress and inflammation were also observed. Metabolomics analysis indicated changes in the abundance of specific endogenous metabolites related to mitochondrial impairment. The outcome of this study may assist in the further optimization of adverse outcome pathway constructs that mechanistically describe the processes involved in cholestatic liver injury. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
    view abstractdoi: 10.1007/s00204-018-2214-z
  • 2018 • 131 On the Ni-Ion release rate from surfaces of binary NiTi shape memory alloys
    Ševčíková, J. and Bártková, D. and Goldbergová, M. and Kuběnová, M. and Čermák, J. and Frenzel, J. and Weiser, A. and Dlouhý, A.
    Applied Surface Science 427 434-443 (2018)
    The study is focused on Ni-ion release rates from NiTi surfaces exposed in the cell culture media and human vascular endothelial cell (HUVEC) culture environments. The NiTi surface layers situated in the depth of 70 μm below a NiTi oxide scale are affected by interactions between the NiTi alloys and the bio-environments. The finding was proved with use of inductively coupled plasma mass spectrometry and electron microscopy experiments. As the exclusive factor controlling the Ni-ion release rates was not only thicknesses of the oxide scale, but also the passivation depth, which was two-fold larger. Our experimental data strongly suggested that some other factors, in addition to the Ni concentration in the oxide scale, admittedly hydrogen soaking deep below the oxide scale, must be taken into account in order to rationalize the concentrations of Ni-ions released into the bio-environments. The suggested role of hydrogen as the surface passivation agent is also in line with the fact that the Ni-ion release rates considerably decrease in NiTi samples that were annealed in controlled hydrogen atmospheres prior to bio-environmental exposures. © 2017 Elsevier B.V.
    view abstractdoi: 10.1016/j.apsusc.2017.08.235
  • 2018 • 130 Co2+-Doping of Magic-Sized CdSe Clusters: Structural Insights via Ligand Field Transitions
    Yang, J. and Muckel, F. and Choi, B.K. and Lorenz, S. and Kim, I.Y. and Ackermann, J. and Chang, H. and Czerney, T. and Kale, V.S. and Hwang, S.-J. and Bacher, G. and Hyeon, T.
    Nano Letters 18 7350-7357 (2018)
    Magic-sized clusters represent materials with unique properties at the border between molecules and solids and provide important insights into the nanocrystal formation process. However, synthesis, doping, and especially structural characterization become more and more challenging with decreasing cluster size. Herein, we report the successful introduction of Co2+ ions into extremely small-sized CdSe clusters with the intention of using internal ligand field transitions to obtain structural insights. Despite the huge mismatch between the radii of Cd2+ and Co2+ ions (>21%), CdSe clusters can be effectively synthesized with a high Co2+ doping concentration of ∼10%. Optical spectroscopy and mass spectrometry suggest that one or two Co2+ ions are substitutionally embedded into (CdSe)13 clusters, which is known as one of the smallest CdSe clusters. Using magnetic circular dichroism spectroscopy on the intrinsic ligand field transitions between the different 3d orbitals of the transition metal dopants, we demonstrate that the Co2+ dopants are embedded on pseudotetrahedral selenium coordinated sites despite the limited number of atoms in the clusters. A significant shortening of Co-Se bond lengths compared to bulk or nanocrystals is observed, which results in the metastability of Co2+ doping. Our results not only extend the doping chemistry of magic-sized semiconductor nanoclusters, but also suggest an effective method to characterize the local structure of these extremely small-sized clusters. © 2018 American Chemical Society.
    view abstractdoi: 10.1021/acs.nanolett.8b03627
  • 2017 • 129 Insights in m-xylene decomposition under fuel-rich conditions by imaging photoelectron photoion coincidence spectroscopy
    Bierkandt, T. and Hemberger, P. and Oßwald, P. and Köhler, M. and Kasper, T.
    Proceedings of the Combustion Institute 36 1223-1232 (2017)
    A fuel-rich (Φ=1.79) m-xylene flame (7.3% m-C8H10, 42.7% O2, 50.0% Ar) at low-pressure (40mbar) was investigated with focus on the reactive fuel radicals (C8H9) and the first decomposition steps leading to C8H8 isomers. The results show that an isomerization of the m-xylyl radical to o- and p-xylyl must take place to explain the observed intermediates in agreement with pyrolysis experiments. Important higher polycyclic aromatic hydrocarbons (PAHs) relevant to soot formation were also identified. All Measurements were performed with a molecular-beam mass spectrometry (MBMS) setup at the Swiss Light Source (SLS), where single-photon ionization with VUV radiation offers soft ionization of the sampled species. Isomer-selective detection with unprecedented resolution is achieved by a combination of time-of-flight mass spectrometry and imaging photoelectron photoion coincidence (iPEPICO) spectroscopy. In principle, species can be identified by comparison of measured ionization efficiency (PIE) curves with known or calculated ionization energies of expected species. For convoluted signals of several species, this procedure works well for the isomer with the lowest ionization energy. Changes in the slopes of the ionization efficiency curve do not necessarily correlate with ionization thresholds of other isomers and the assignment of higher thresholds can become difficult. PEPICO spectrometry, which detects the electrons that are produced in the ionization process in coincidence with the ions, enables the measurement of mass-selected threshold photoelectron spectra (ms-TPES). These spectra improve the detection capability of isomers because vibrational transitions from the neutral into ionic states can be observed and used as a fingerprint of a specific molecule. The obtained ms-TPES are compared with reference spectra from the literature or Franck-Condon simulations. Quantification of the major species as well as several intermediate species for this fuel-rich m-xylene flame yields a data set for model validation and experimental results are compared with five kinetic reaction models from the literature. © 2016.
    view abstractdoi: 10.1016/j.proci.2016.06.143
  • 2017 • 128 Influence of nitrogen admixture to argon on the ion energy distribution in reactive high power pulsed magnetron sputtering of chromium
    Breilmann, W. and Maszl, C. and Hecimovic, A. and Von Keudell, A.
    Journal of Physics D: Applied Physics 50 (2017)
    Reactive high power impulse magnetron sputtering (HiPIMS) of metals is of paramount importance for the deposition of various oxides, nitrides and carbides. The addition of a reactive gas such as nitrogen to an argon HiPIMS plasma with a metal target allows the formation of the corresponding metal nitride on the substrate. The addition of a reactive gas introduces new dynamics into the plasma process, such as hysteresis, target poisoning and the rarefaction of two different plasma gases. We investigate the dynamics for the deposition of chromium nitride by a reactive HiPIMS plasma using energy- and time-resolved ion mass spectrometry, fast camera measurements and temporal and spatially resolved optical emission spectroscopy. It is shown that the addition of nitrogen to the argon plasma gas significantly changes the appearance of the localized ionization zones, the so-called spokes, in HiPIMS plasmas. In addition, a very strong modulation of the metal ion flux within each HiPIMS pulse is observed, with the metal ion flux being strongly suppressed and the nitrogen molecular ion flux being strongly enhanced in the high current phase of the pulse. This behavior is explained by a stronger return effect of the sputtered metal ions in the dense plasma above the racetrack. This is best observed in a pure nitrogen plasma, because the ionization zones are mostly confined, implying a very high local plasma density and consequently also an efficient scattering process. © 2017 IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6463/aa5bfc
  • 2017 • 127 Experimental and numerical study of a HMDSO-seeded premixed laminar low-pressure flame for SiO2 nanoparticle synthesis
    Feroughi, O.M. and Deng, L. and Kluge, S. and Dreier, T. and Wiggers, H. and Wlokas, I. and Schulz, C.
    Proceedings of the Combustion Institute 36 1045-1053 (2017)
    Silicon dioxide nanoparticles are generated in a lean hydrogen/oxygen flat flame doped with small amounts of hexamethyldisiloxane (HMDSO) stabilized by a water-cooled sintered bronze matrix. The burner is housed in an optically-accessible low-pressure (3kPa) chamber. Temperature fields were determined via multi-line laser-induced fluorescence (LIF) using added NO as target species. Gas-phase silicon oxide (SiO) was detected via laser-induced fluorescence (LIF) by exciting the weakly temperature-dependent rovibrational Q11(32) transition in the A-X (0,0) vibronic band system at 235.087nm. Semi-quantitative concentration profiles as a function of height-above-burner (HAB) were obtained after exploiting the measured temperature fields and correcting measured LIF intensities for the temperature-dependence of the ground-state population and collisional quenching using measured effective fluorescence lifetimes. Particle sizes were determined as a function of HAB via molecular-beam sampling with subsequent particle mass spectrometry (PMS). The experimental data were used to develop a simple kinetics model of HMDSO combustion and SiO2 particle precursor formation with subsequent nucleation and particle growth in the H2/O2 flame. The model was incorporated in a CFD simulation to account for facility effects that arise from modified flow fields and heat transfer between the flame and the reactor chamber. © 2016 Elsevier Ltd.
    view abstractdoi: 10.1016/j.proci.2016.07.131
  • 2017 • 126 The proteome of baker's yeast mitochondria
    Gonczarowska-Jorge, H. and Zahedi, R.P. and Sickmann, A.
    Mitochondrion 33 15-21 (2017)
    In the past decade mass spectrometry-based proteomics has greatly contributed to shaping our knowledge about . Saccharomyces cerevisiae mitochondria, from the initial identification of novel essential components in purified protein complexes, to the actual characterization of the mitochondrial proteome, the specific analysis of mitochondrial subcompartment proteomes, and the study of regulatory mechanisms that govern mitochondrial homeostasis. Here, we provide an overview of relevant mitochondrial proteome studies and furthermore discuss future possibilities how proteomics will further improve our existing understanding of mitochondria. Although mitochondria were the first organelles that have been intensively studied using proteomics, indeed the recent progress and development of more powerful and sensitive methods, instrumentation and data analysis strategies indicate that we are only beginning to exploit the full potential of mitochondrial proteomics and its possibilities to decipher cell biology. Beside mere (quantitative) inventory under different conditions, this will for instance include studying the role of multiple post-translational modifications in mitochondrial homeostasis as well as the system-wide mapping of protein-protein complexes and protein-lipid interactions. © 2016.
    view abstractdoi: 10.1016/j.mito.2016.08.007
  • 2017 • 125 Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin
    Gonczarowska-Jorge, H. and Loroch, S. and Dell'Aica, M. and Sickmann, A. and Roos, A. and Zahedi, R.P.
    Analytical Chemistry 89 13137-13145 (2017)
    Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, nonunique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as Glu-C, Asp-N, Lys-N, Arg-C, LysargiNase has been reported. Here, we present how the broad-specificity protease subtilisin enables mapping of previously hidden areas of the proteome. We systematically evaluated its digestion efficiency and reproducibility and compared it to the gold standard in the field, trypsin. Notably, subtilisin allows reproducible near-complete digestion of cells lysates in 1-5 min. As expected from its broad specificity the generation of overlapping peptide sequences reduces the number of identified proteins compared to trypsin (8363 vs 6807; 1% protein FDR). However, subtilisin considerably improved the coverage of missing and particularly proline-rich areas of the proteome. Along 14:628 high confidence phosphorylation sites identified in total, only 33% were shared between both enzymes, while 37% were exclusive to subtilisin. Notably, 926 of these were not even accessible by additional in silico digestion with either Asp-N, Arg-C, Glu-C, Lys-C, or Lys-N. Thus, subtilisin might be particularly beneficial for system-wide profiling of post-translational modification sites. Finally, we demonstrate that subtilisin can be used for reporter-ion based in-depth quantification, providing a precision comparable to trypsin - despite broad specificity and fast digestion that may increase technical variance. © 2017 American Chemical Society.
    view abstractdoi: 10.1021/acs.analchem.7b02395
  • 2017 • 124 Synthesis and evaluation of new copper ketoiminate precursors for a facile and additive-free solution-based approach to nanoscale copper oxide thin films
    Karle, Sarah and Rogalla, Detlef and Ludwig, Arne and Becker, Hans-Werner and Wieck, Andreas Dirk and Grafen, Markus and Ostendorf, Andreas and Devi, Anjana
    Dalton Transactions 46 2670--2679 (2017)
    Novel copper ketoiminate compounds were synthesized and for the first time applied for additive-free solution-based deposition of nanoscale copper oxide thin films. The two closely related compounds, namely the bis[4-(2-ethoxyethyl-imino)-3-pentanonato] copper, [Cu(EEKI)(2)], and bis[4-(3-methoxypropylimino)- 3-pentanonato] copper, [Cu(MPKI)(2)], were characterized by means of elemental and thermogravimetric analysis (TGA), as well as electron impact mass spectrometry (EI-MS). The advantages of these compounds are that they are liquid and possess excellent solubility in common organic solvents in addition to an optimum reactivity towards ambient moisture that enables a facile solution-based approach to nanoscale copper oxide thin films. Moreover, no additives or aging is needed to stabilize the solution processing of the copper oxide layers. [Cu(MPKI)(2)] was tested in detail for the deposition of copper oxide thin films by spin coating. Upon one-step annealing, high-quality, uniform, crystalline copper oxide thin films were deposited on Si, SiO2, as well as on quartz substrates. Structural, morphological and compositional characteristics of the copper oxide nanostructures were investigated in detail by means of X-ray diffraction (XRD), scanning electron microscopy (SEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and a combined analysis using Rutherford backscattering spectroscopy (RBS) and nuclear reaction analysis (NRA). It was possible to control the copper oxide phases (CuO and Cu2O) by systematic tuning of the post-deposition annealing conditions. The functional properties in terms of optical band gap were investigated using UV/Vis spectroscopy, while the transport properties, such as resistivity, mobility and carrier concentration were analyzed employing Hall measurements, which confirmed the p-type conductivity of the copper oxide layers.
    view abstractdoi: 10.1039/c6dt04399b
  • 2017 • 123 Mass spectrometric analysis of clusters and nanoparticles during the gas-phase synthesis of tungsten oxide
    Kluge, S. and Wiggers, H. and Schulz, C.
    Proceedings of the Combustion Institute 36 1037-1044 (2017)
    The combustion synthesis of nanoscale tungsten-oxide particles from tungsten hexafluoride is investigated in a low-pressure hydrogen/oxygen flat flame. The reactor is equipped with molecular-beam sampling of post-flame gases at variable height above burner (HAB). Main species of the flame, intermediate tungsten species, and tungsten-oxide clusters are studied with time-of-flight mass spectrometry (TOF-MS) as a function of HAB. Various WO x (OH) y are identified within the flame front. With increasing HAB, (WO3) n clusters with increasing cluster size appear in the burnt gases at the expense of the concentration of W1 species. Clusters with n =3-7 arise at 70mm HAB, followed by larger clusters at even larger heights. Clusters up to (WO3)38 were identified. The subsequent formation of nanoparticles is detected with particle mass spectrometry (PMS) and a quartz crystal microbalance (QCM) from 120mm HAB and the increasing particle size and mass flux have been determined. © 2016.
    view abstractdoi: 10.1016/j.proci.2016.06.165
  • 2017 • 122 Recent progress in microstructural hydrogen mapping in steels: quantification, kinetic analysis, and multi-scale characterisation
    Koyama, M. and Rohwerder, M. and Tasan, C.C. and Bashir, A. and Akiyama, E. and Takai, K. and Raabe, D. and Tsuzaki, K.
    Materials Science and Technology (United Kingdom) 1-16 (2017)
    This paper gives an overview of recent progress in microstructure-specific hydrogen mapping techniques. The challenging nature of mapping hydrogen with high spatial resolution, i.e. at the scale of finest microstructural features, led to the development of various methodologies: thermal desorption spectrometry, silver decoration, the hydrogen microprint technique, secondary ion mass spectroscopy, atom probe tomography, neutron radiography, and the scanning Kelvin probe. These techniques have different characteristics regarding spatial and temporal resolution associated with microstructure-sensitive hydrogen detection. Employing these techniques in a site-specific manner together with other microstructure probing methods enables multi-scale, quantitative, three-dimensional, high spatial, and kinetic resolution hydrogen mapping, depending on the specific multi-probe approaches used. Here, we present a brief overview of the specific characteristics of each method and the progress resulting from their combined application to the field of hydrogen embrittlement. © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
    view abstractdoi: 10.1080/02670836.2017.1299276
  • 2017 • 121 Deciphering lymphoma pathogenesis via state-of-the-art mass spectrometry-based quantitative proteomics
    Psatha, K. and Kollipara, L. and Voutyraki, C. and Divanach, P. and Sickmann, A. and Rassidakis, G.Z. and Drakos, E. and Aivaliotis, M.
    Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences 1047 2-14 (2017)
    Mass spectrometry-based quantitative proteomics specifically applied to comprehend the pathogenesis of lymphoma has incremental value in deciphering the heterogeneity in complex deregulated molecular mechanisms/pathways of the lymphoma entities, implementing the current diagnostic and therapeutic strategies. Essential global, targeted and functional differential proteomics analyses although still evolving, have been successfully implemented to shed light on lymphoma pathogenesis to discover and explore the role of potential lymphoma biomarkers and drug targets. This review aims to outline and appraise the present status of MS-based quantitative proteomic approaches in lymphoma research, introducing the current state-of-the-art MS-based proteomic technologies, the opportunities they offer in biological discovery in human lymphomas and the related limitation issues arising from sample preparation to data evaluation. It is a synopsis containing information obtained from recent research articles, reviews and public proteomics repositories (PRIDE). We hope that this review article will aid, assimilate and assess all the information aiming to accelerate the development and validation of diagnostic, prognostic or therapeutic targets for an improved and empowered clinical proteomics application in lymphomas in the nearby future. © 2016 Elsevier B.V.
    view abstractdoi: 10.1016/j.jchromb.2016.11.005
  • 2017 • 120 DISMS2: A flexible algorithm for direct proteome- Wide distance calculation of LC-MS/MS runs
    Rieder, V. and Blank-Landeshammer, B. and Stuhr, M. and Schell, T. and Biß, K. and Kollipara, L. and Meyer, A. and Pfenninger, M. and Westphal, H. and Sickmann, A. and Rahnenführer, J.
    BMC Bioinformatics 18 (2017)
    Background: The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra. Methods: We present DISMS2, a new algorithm to calculate proteome-wide distances directly from MS/MS data, extending the algorithm compareMS2, an approach that also uses a spectral comparison pipeline. Results: Our new more flexible algorithm, DISMS2, allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be tailored to specific situations by parameter optimization. Conclusions: DISMS2 performs well for samples from species with and without database annotation and thus has clear advantages over methods that are purely based on database search. © 2017 The Author(s).
    view abstractdoi: 10.1186/s12859-017-1514-2
  • 2017 • 119 Comparison of the quantitative analysis performance between pulsed voltage atom probe and pulsed laser atom probe
    Takahashi, J. and Kawakami, K. and Raabe, D.
    Ultramicroscopy 175 105-110 (2017)
    The difference in quantitative analysis performance between the voltage-mode and laser-mode of a local electrode atom probe (LEAP3000X HR) was investigated using a Fe-Cu binary model alloy. Solute copper atoms in ferritic iron preferentially field evaporate because of their significantly lower evaporation field than the matrix iron, and thus, the apparent concentration of solute copper tends to be lower than the actual concentration. However, in voltage-mode, the apparent concentration was higher than the actual concentration at 40 K or less due to a detection loss of matrix iron, and the concentration decreased with increasing specimen temperature due to the preferential evaporation of solute copper. On the other hand, in laser-mode, the apparent concentration never exceeded the actual concentration, even at lower temperatures (20 K), and this mode showed better quantitative performance over a wide range of specimen temperatures. These results indicate that the pulsed laser atom probe prevents both detection loss and preferential evaporation under a wide range of measurement conditions. © 2017 Elsevier B.V.
    view abstractdoi: 10.1016/j.ultramic.2017.01.015
  • 2017 • 118 Enrichment of Cross-Linked Peptides Using Charge-Based Fractional Diagonal Chromatography (ChaFRADIC)
    Tinnefeld, V. and Venne, A.S. and Sickmann, A. and Zahedi, R.P.
    Journal of Proteome Research 16 459-469 (2017)
    Chemical cross-linking of proteins is an emerging field with huge potential for the structural investigation of proteins and protein complexes. Owing to the often relatively low yield of cross-linking products, their identification in complex samples benefits from enrichment procedures prior to mass spectrometry analysis. So far, this is mainly accomplished by using biotin moieties in specific cross-linkers or by applying strong cation exchange chromatography (SCX) for a relatively crude enrichment. We present a novel workflow to enrich cross-linked peptides by utilizing charge-based fractional diagonal chromatography (ChaFRADIC). On the basis of two-dimensional diagonal SCX separation, we could increase the number of identified cross-linked peptides for samples of different complexity: pure cross-linked BSA, cross-linked BSA spiked into a simple protein mixture, and cross-linked BSA spiked into a HeLa lysate. We also compared XL-ChaFRADIC with size exclusion chromatography-based enrichment of cross-linked peptides. The XL-ChaFRADIC approach is straightforward, reproducible, and independent of the cross-linking chemistry and cross-linker properties. © 2016 American Chemical Society.
    view abstractdoi: 10.1021/acs.jproteome.6b00587
  • 2017 • 117 Absolutely calibrated mass spectrometry measurement of reactive and stable plasma chemistry products in the effluent of a He/H2O atmospheric plasma
    Willems, G. and Benedikt, J. and Von Keudell, A.
    Journal of Physics D: Applied Physics 50 (2017)
    Mass spectrometry has been used to analyse the effluent of a micro-scaled atmospheric plasma jet operated in helium with a controlled concentration of water vapour. Absolute densities of H2O2 and OH have been measured as function of water vapour concentration and distance from the jet nozzle. The trend for both species densities are correlated and after an initial increase, the densities of H2O2 and OH saturate around 5000 ppm to 6000 ppm of water admixture. The largest densities for H2O2 (2.37 × 1014 cm-3) and OH (1.96 × 1014 cm-3) were measured at 7980 ppm water admixture and 2 mm distance from the jet. Densities of HO2 (1 × 1014 cm-3) and O2 (4 × 1014 cm-3) have been measured as well, although no trend could be observed. The direct electron impact ionisation cross-section of H2O2 at 70 eV electron energy was experimentally determined to be 1.02 × 1016 cm2. The measured densities and profiles have been compared to a 2D axially symmetric fluid model of species transport and recombination reactions. The effluent reaction chemistry is dominated by the hydroxyl radical, where the hydrogen atoms seem to play an important role as well. The analysis of neutral plasma chemistry products have been complemented by measurements of qualitative ion signals. © 2017 IOP Publishing Ltd.
    view abstractdoi: 10.1088/1361-6463/aa77ca
  • 2017 • 116 Chemical Synthesis, Doping, and Transformation of Magic-Sized Semiconductor Alloy Nanoclusters
    Yang, J. and Muckel, F. and Baek, W. and Fainblat, R. and Chang, H. and Bacher, G. and Hyeon, T.
    Journal of the American Chemical Society 139 6761-6770 (2017)
    doi: 10.1021/jacs.7b02953
  • 2016 • 115 Zeolite Beta Formation from Clear Sols: Silicate Speciation, Particle Formation and Crystallization Monitored by Complementary Analysis Methods
    Castro, M. and Haouas, M. and Lim, I. and Bongard, H.J. and Schüth, F. and Taulelle, F. and Karlsson, G. and Alfredsson, V. and Breyneart, E. and Kirschhock, C.E.A. and Schmidt, W.
    Chemistry - A European Journal 22 15307-15319 (2016)
    The formation of silicate nanoaggregates (NAs) at the very early stages of precursor sols and zeolite beta crystallization from silicate nanoparticles (NPs) are investigated in detail using a combination of different analysis methods, including liquid-state29Si,27Al,14N, and1H NMR spectroscopy, mass spectrometry (MS), small-angle X-ray scattering (SAXS), X-ray diffraction (XRD), and transmission electron microscopy at cryogenic temperatures (cryo-TEM). Prior to hydrothermal treatment, silicate NAs are observed if the Si/OH ratio in the reaction mixture is greater than 1. Condensation of oligomers within the NAs then generates NPs. Aluminum doped into the synthesis mixtures is located exclusively in the NPs, and is found exclusively in a state that is fourfold connected to silicate, favoring their condensation and aggregation. These results are in agreement with general trends observed for other systems. Silicate NAs are essential intermediates for zeolite formation and are generated by the aggregation of hydrated oligomers, aluminate, and templating cations. Subsequent further intra-nanoaggregate silicate condensation results in the formation of NPs.1H and14N liquid NMR as well as diffusion ordered spectroscopy (DOSY) experiments provide evidence for weakly restricted rotational and translational mobility of the organic template within NAs as a consequence of specific silicate–template interactions. NAs thus appear as key species in clear sols, and their presence in the precursor sol favors silicate condensation and further crystallization, promoted either by increasing the Si/OH ratio or by heating. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
    view abstractdoi: 10.1002/chem.201600511
  • 2016 • 114 Degradation of Polymeric Brominated Flame Retardants: Development of an Analytical Approach Using PolyFR and UV Irradiation
    Koch, C. and Dundua, A. and Aragon-Gomez, J. and Nachev, M. and Stephan, S. and Willach, S. and Ulbricht, M. and Schmitz, O. J. and Schmidt, T. C. and Sures, B.
    Environmental Science & Technology 50 12912--12920 (2016)
    Many well-established methods for studying the degradation of brominated flame retardants are not useful when working with polymeric and water insoluble species. An example for this specific class of flame retardants is PoIyFR (polymeric flame retardant; CAS No 1195978-93-8), which is used as a substituent for hexabromocyclododecane. Although it has been on the market for two years now, almost no information is available about its long time behavior in the environment. Within this study, we focus on how to determine a possible degradation of both pure PolyFR as well as PolyFR in the final insulation product, expanded polystyrene foam. Therefore, we chose UV radiation followed by analyses of the total bromine content at different time points via ICP-MS and identified possible degradation products such as 2,4,6-tribromophenol through LC-MS. These results were then linked with measurements of the adsorbable organically bound bromine and total organic carbon in order to estimate their concentrations. With respect to the obtained H-1 NMR, GPC, and contact angle results, the possibility for further degradation was discussed, as UV irradiation can influence the decomposition of molecules in combination with other environmental factors like biodegradation.
    view abstractdoi: 10.1021/acs.est.6b04083
  • 2016 • 113 FTIR spectroscopy of cysteine as a ready-to-use method for the investigation of plasma-induced chemical modifications of macromolecules
    Kogelheide, F. and Kartaschew, K. and Strack, M. and Baldus, S. and Metzler-Nolte, N. and Havenith, M. and Awakowicz, P. and Stapelmann, K. and Lackmann, J.-W.
    Journal of Physics D: Applied Physics 49 (2016)
    A rapid screening method for the investigation of plasma-induced chemical modifications was developed by analyzing cysteine using Fourier Transform Infrared (FTIR) spectroscopy. Cysteine is a key amino acid in proteins due to the presence of a thiol group which provides unique structural features by offering the possibility to form disulfide bonds. Its chemical composition makes cysteine a well-suited model for the investigation of plasma-induced modifications at three functional groups - the amino, the carboxyl and the thiol group - all highly abundant in proteins. FTIR spectroscopy is present in most physical laboratories and offers a fast way to assess changes in the chemical composition of cysteine substrates due to plasma treatment and to compare different treatment conditions or plasma sources with each other. Significant changes in the fingerprint spectra of cysteine samples treated with a dielectric barrier discharge (DBD) compared to untreated controls were observed using a FTIR spectrometer. The loss of the thiol signal and the simultaneous increase of bands originating from oxidized sulfur and nitrogen species indicate that the thiol group of cysteine is modified by reactive oxygen and nitrogen species during DBD treatment. Furthermore, other plasma-induced modifications, such as changes of the amino and carbonyl groups, could be observed. Complementary mass spectrometry measurements confirmed these results. © 2016 IOP Publishing Ltd.
    view abstractdoi: 10.1088/0022-3727/49/8/084004
  • 2016 • 112 Preparation of pulsed DC magnetron deposited Fe-doped SnO2 coatings
    Kormunda, M. and Fischer, D. and Hertwig, A. and Beck, U. and Sebik, M. and Esser, N.
    Physica Status Solidi (A) Applications and Materials Science 213 2303-2309 (2016)
    Iron-doped SnO2 coatings were deposited in a 50 kHz DC-pulsed magnetron sputtering discharge. The pulses had a duration of 4 μs in selected gas mixtures from pure argon up to 60% of oxygen at a constant total pressure of 0.2 Pa. A single target of SnO2 with Fe inset was used. The mass spectrometry study detected the gas-related ions Ar+, O2 + and O+, where the last one becomes the dominant positive ion at higher oxygen contents. Atomic oxygen ions had a higher energy as it resulted from the collision-caused dissociation on the target surface. The tin-related species were detected as Sn+ and SnO+. SnO2 + species were not detected. The deposition rate decreased by using gas mixtures with oxygen as well as the corresponding amount of Sn-related species in the plasma. The increase of oxygen also increased significantly the sheet resistance of the films. The XPS study showed that the iron concentration decreased by using additional oxygen. But the O/Sn ratio in the coatings was constant, contrary to the increased FeO/Fe ratio in the films. An additional analysis of the coatings by spectroscopic ellipsometry has shown a dependence of the polarizability and the permittivity on the amount of oxygen used during the deposition. In contrast, the study has found no such dependence for the absorption of the layers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
    view abstractdoi: 10.1002/pssa.201532882
  • 2016 • 111 A pioneer protein is part of a large complex involved in trans-splicing of a group II intron in the chloroplast of Chlamydomonas reinhardtii
    Lefebvre-Legendre, L. and Reifschneider, O. and Kollipara, L. and Sickmann, A. and Wolters, D. and Kück, U. and Goldschmidt-Clermont, M.
    Plant Journal 85 57-69 (2016)
    Splicing of organellar introns requires the activity of numerous nucleus-encoded factors. In the chloroplast of Chlamydomonas reinhardtii, maturation of psaA mRNA encoding photosystem I subunit A involves two steps of trans-splicing. The exons, located on three separate transcripts, are flanked by sequences that fold to form the conserved structures of two group II introns. A fourth transcript contributes to assembly of the first intron, which is thus tripartite. The raa7 mutant (RNA maturation of psaA 7) is deficient in trans-splicing of the second intron of psaA, and may be rescued by transforming the chloroplast genome with an intron-less version of psaA. Using mapped-based cloning, we identify the RAA7 locus, which encodes a pioneer protein with no previously known protein domain or motif. The Raa7 protein, which is not associated with membranes, localizes to the chloroplast. Raa7 is a component of a large complex and co-sediments in sucrose gradients with the previously described splicing factors Raa1 and Raa2. Based on tandem affinity purification of Raa7 and mass spectrometry, Raa1 and Raa2 were identified as interacting partners of Raa7. Yeast two-hybrid experiments indicate that the interaction of Raa7 with Raa1 and Raa2 may be direct. We conclude that Raa7 is a component of a multimeric complex that is required for trans-splicing of the second intron of psaA. The characterization of this psaA trans-splicing complex is also of interest from an evolutionary perspective because the nuclear spliceosomal introns are thought to derive from group II introns, with which they show mechanistic and structural similarity. © 2015 The Authors The Plant Journal.
    view abstractdoi: 10.1111/tpj.13089
  • 2016 • 110 Copper(II), zinc(II) and copper(II)/zinc(II)-containing carbonate-substituted hydroxyapatite: Synthesis, characterization and thermal behaviour
    Livitska, O. and Strutynska, N. and Zatovsky, I. and Nikolenko, I. and Slobodyanik, N. and Prylutskyy, Y. and Epple, M. and Prymak, O. and Byeda, A.
    Materialwissenschaft und Werkstofftechnik 47 85-91 (2016)
    A new approach for the preparation of nanoscale copper- and zinc-containing sodium- and carbonate-substituted apatites is presented. The thermal transformations of the samples in the temperature range 80-1000 °C were determined by temperature-programmed desorption mass spectroscopy and thermogravimetry. The chemical and phase compositions of the copper- and zinc-containing sodium- and carbonate-substituted apatites were studied by atomic absorption spectroscopy and X-ray diffraction, respectively. The degree and nature of the carbonate substitution were determined by elemental analysis (C, H, N) and infrared spectroscopy, respectively. In addition, scanning electron microscopy (SEM) showed nanoparticles (about 10-20 nm in diameter) with a stability to aggregation under processes by microwave radiation. Samples annealed at 700 °C were crystalline and had an apatite structure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/mawe.201600460
  • 2016 • 109 A new setup for the investigation of swift heavy ion induced particle emission and surface modifications
    Meinerzhagen, F. and Breuer, L. and Bukowska, H. and Bender, M. and Severin, D. and Herder, M. and Lebius, H. and Schleberger, M. and Wucher, A.
    Review of Scientific Instruments 87 (2016)
    The irradiation with fast ions with kinetic energies of >10 MeV leads to the deposition of a high amount of energy along their trajectory (up to several ten keV/nm). The energy is mainly transferred to the electronic subsystem and induces different secondary processes of excitations, which result in significant material modifications. A new setup to study these ion induced effects on surfaces will be described in this paper. The setup combines a variable irradiation chamber with different techniques of surface characterizations like scanning probe microscopy, time-of-flight secondary ion, and neutral mass spectrometry, as well as low energy electron diffraction under ultra high vacuum conditions, and is mounted at a beamline of the universal linear accelerator (UNILAC) of the GSI facility in Darmstadt, Germany. Here, samples can be irradiated with high-energy ions with a total kinetic energy up to several GeVs under different angles of incidence. Our setup enables the preparation and in situ analysis of different types of sample systems ranging from metals to insulators. Time-of-flight secondary ion mass spectrometry enables us to study the chemical composition of the surface, while scanning probe microscopy allows a detailed view into the local electrical and morphological conditions of the sample surface down to atomic scales. With the new setup, particle emission during irradiation as well as persistent modifications of the surface after irradiation can thus be studied. We present first data obtained with the new setup, including a novel measuring protocol for time-of-flight mass spectrometry with the GSI UNILAC accelerator. © 2016 AIP Publishing LLC.
    view abstractdoi: 10.1063/1.4939899
  • 2016 • 108 Digital Doping in Magic-Sized CdSe Clusters
    Muckel, F. and Yang, J. and Lorenz, S. and Baek, W. and Chang, H. and Hyeon, T. and Bacher, G. and Fainblat, R.
    ACS Nano 10 7135-7141 (2016)
    Magic-sized semiconductor clusters represent an exciting class of materials located at the boundary between quantum dots and molecules. It is expected that replacing single atoms of the host crystal with individual dopants in a one-by-one fashion can lead to unique modifications of the material properties. Here, we demonstrate the dependence of the magneto-optical response of (CdSe)13 clusters on the discrete number of Mn2+ ion dopants. Using time-of-flight mass spectrometry, we are able to distinguish undoped, monodoped, and bidoped cluster species, allowing for an extraction of the relative amount of each species for a specific average doping concentration. A giant magneto-optical response is observed up to room temperature with clear evidence that exclusively monodoped clusters are magneto-optically active, whereas the Mn2+ ions in bidoped clusters couple antiferromagnetically and are magneto-optically passive. Mn2+-doped clusters therefore represent a system where magneto-optical functionality is caused by solitary dopants, which might be beneficial for future solotronic applications. © 2016 American Chemical Society.
    view abstractdoi: 10.1021/acsnano.6b03348
  • 2016 • 107 A single-pulse shock tube coupled with high-repetition-rate time-of-flight mass spectrometry and gas chromatography for high-temperature gas-phase kinetics studies
    Sela, P. and Shu, B. and Aghsaee, M. and Herzler, J. and Welz, O. and Fikri, M. and Schulz, C.
    Review of Scientific Instruments 87 (2016)
    Shock tubes are frequently used to investigate the kinetics of chemical reactions in the gas phase at high temperatures. Conventionally, two complementary arrangements are used where either time-resolved intermediate species measurements are conducted after the initiation of the reaction or where the product composition is determined after rapid initiation and quenching of the reaction through gas-dynamic processes. This paper presents a facility that combines both approaches to determine comprehensive information. A single-pulse shock tube is combined with high-sensitivity gas chromatography/mass spectrometry for product composition and concentration measurement as well as high-repetition-rate time-of-flight mass spectrometry for time-dependent intermediate concentration determination with 10 μs time resolution. Both methods can be applied simultaneously. The arrangement is validated with investigations of the well-documented thermal unimolecular decomposition of cyclohexene towards ethylene and 1,3-butadiene at temperatures between 1000 and 1500 K and pressures ranging from 0.8 to 2.4 bars. The comparison shows that the experimental results for both detections are in very good agreement with each other and with literature data. © 2016 Author(s).
    view abstractdoi: 10.1063/1.4963844
  • 2016 • 106 Shock-tube and plug-flow reactor study of the oxidation of fuel-rich CH4/O2 mixtures enhanced with additives
    Sen, F. and Shu, B. and Kasper, T. and Herzler, J. and Welz, O. and Fikri, M. and Atakan, B. and Schulz, C.
    Combustion and Flame 169 307-320 (2016)
    Partial oxidation of hydrocarbons under well-controlled conditions opens a path to higher-value chemicals from natural gas with small exergy losses if the chemical conversion proceeds in an internal combustion engine as a polygeneration process (Gossler et al., 2015). For the relevant reaction conditions, kinetics models are not sufficiently validated due to the atypical reaction conditions, e.g., high equivalence ratios and pressures. The purpose of this study is to obtain experimental validation data for chemical reaction mechanisms that can be used to predict polygeneration processes in practical applications. In case of methane these processes proceed under fuel-rich conditions and yield primarily syngas (CO/H2). In this study, the partial oxidation of methane was investigated for an equivalence ratio of φ=2 in a shock-tube and a plug-flow reactor (PFR) in order to cover a wide temperature range. Time-resolved CO mole fractions were measured in shock-heated mixtures between 1600 and 2100K at ~1bar. Good agreement was found between the experiment and the models (Yasunaga et al., 2010; Burke et al., 2015; Zhao et al., 2008). Stable reaction products were monitored by time-of-flight mass spectrometry between 532 and 992K at 6bar in a tubular flow reactor at reaction times >4s. The influence of dimethyl ether (DME) and n-heptane addition on methane reactivity and conversion was investigated. The additives significantly lower the initial reaction temperature by producing significant amounts of OH. The results were compared to simulations and serve as validation data for the development of reaction mechanisms for these atypical reaction conditions. Good agreement was found between the experiment and the models for most of species. © 2016 The Combustion Institute.
    view abstractdoi: 10.1016/j.combustflame.2016.03.030
  • 2016 • 105 Multi-scale and spatially resolved hydrogen mapping in a Ni-Nb model alloy reveals the role of the δ phase in hydrogen embrittlement of alloy 718
    Tarzimoghadam, Z. and Rohwerder, M. and Merzlikin, S.V. and Bashir, A. and Yedra, L. and Eswara, S. and Ponge, D. and Raabe, D.
    Acta Materialia 109 69-81 (2016)
    We investigated the hydrogen distribution and desorption behavior in an electrochemically hydrogen-charged binary Ni-Nb model alloy to study the role of δ phase in hydrogen embrittlement of alloy 718. We focus on two aspects, namely, (1) mapping the hydrogen distribution with spatial resolution enabling the observation of the relations between desorption profiles and desorption sites; and (2) correlating these observations with mechanical testing results to reveal the degradation mechanisms. The trapping states of hydrogen in the alloy were globally analyzed by Thermal Desorption Spectroscopy (TDS). Additionally, spatially resolved hydrogen mapping was conducted using silver decoration, Scanning Kelvin Probe Force Microscopy (SKPFM) and Secondary Ion Mass Spectrometry (SIMS): The Ag decoration method revealed rapid effusion of hydrogen at room temperature from the γ-matrix. The corresponding kinetics was resolved in both, space and time by the SKPFM measurements. At room temperature the hydrogen release from the γ-matrix steadily decreased until about 100 h and then was taken over by the δ phase from which the hydrogen was released much slower. For avoiding misinterpretation of hydrogen signals stemming from environmental effects we also charged specimens with deuterium. The deuterium distribution in the microstructure was studied by SIMS. The combined results reveal that hydrogen dissolves more preferably inside the γ-matrix and is diffusible at room temperature while the δ phase acts as a deeper trapping site for hydrogen. With this joint and spatially resolving approach we observed the microstructure- and time-dependent distribution and release rate of hydrogen with high spatial and temporal resolution. Correlating the obtained results with mechanical testing of the hydrogen-charged samples shows that hydrogen enhanced decohesion (HEDE) occurring at the δ/matrix interfaces promotes the embrittlement. © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
    view abstractdoi: 10.1016/j.actamat.2016.02.053
  • 2016 • 104 In Situ EPR Study of the Redox Properties of CuO-CeO2 Catalysts for Preferential CO Oxidation (PROX)
    Wang, F. and Büchel, R. and Savitsky, A. and Zalibera, M. and Widmann, D. and Pratsinis, S.E. and Lubitz, W. and Schüth, F.
    ACS Catalysis 6 3520-3530 (2016)
    Understanding the redox properties of metal oxide based catalysts is a major task in catalysis research. In situ electron paramagnetic resonance (EPR) spectroscopy is capable of monitoring the change of metal ion valences and formation of active sites during redox reactions, allowing for the identification of ongoing redox pathways. Here in situ EPR spectroscopy combined with online gas analysis, supported by ex situ X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), temporal analysis of product (TAP), and mass spectrometry (MS) studies, was utilized to study the redox behavior of CuO-CeO2 catalysts under PROX conditions (preferential oxidation of carbon monoxide in hydrogen). Two redox mechanisms are revealed: (i) a synergetic mechanism that involves the redox pair Ce4+/Ce3+ during oxidation of Cu0/Cu+ species to Cu2+ and (ii) a direct mechanism that bypasses the redox pair Ce4+/Ce3+. In addition, EPR experiments with isotopically enriched 17O2 established the synergetic mechanism as the major redox reaction pathway. The results emphasize the importance of the interactions between Cu and Ce atoms for catalyst performance. With the guidance of these results, an optimized CuO-CeO2 catalyst could be designed. A rather wide temperature operation window of 11 K (from 377 to 388 K), with 99% conversion efficiency and 99% selectivity, was achieved for the preferential oxidation of CO in a H2 feed. © 2016 American Chemical Society.
    view abstractdoi: 10.1021/acscatal.6b00589
  • 2016 • 103 Influence of agglomeration and specific lung lining lipid/protein interaction on short-term inhalation toxicity
    Wohlleben, W. and Driessen, M.D. and Raesch, S. and Schaefer, U.F. and Schulze, C. and Vacano, B.V. and Vennemann, A. and Wiemann, M. and Ruge, C.A. and Platsch, H. and Mues, S. and Ossig, R. and Tomm, J.M. and Schnekenburger, J. ...
    Nanotoxicology 10 970-980 (2016)
    Abstract: Lung lining fluid is the first biological barrier nanoparticles (NPs) encounter during inhalation. As previous inhalation studies revealed considerable differences between surface functionalized NPs with respect to deposition and toxicity, our aim was to investigate the influence of lipid and/or protein binding on these processes. Thus, we analyzed a set of surface functionalized NPs including different SiO2 and ZrO2 in pure phospholipids, CuroSurfTM and purified native porcine pulmonary surfactant (nS). Lipid binding was surprisingly low for pure phospholipids and only few NPs attracted a minimal lipid corona. Additional presence of hydrophobic surfactant protein (SP) B in CuroSurfTM promoted lipid binding to NPs functionalized with Amino or PEG residues. The presence of the hydrophilic SP A in nS facilitated lipid binding to all NPs. In line with this the degree of lipid and protein affinities for different surface functionalized SiO2 NPs in nS followed the same order (SiO2 Phosphate ∼ unmodified SiO2 < SiO2 PEG < SiO2 Amino NPs). Agglomeration and biomolecule interaction of NPs in nS was mainly influenced by surface charge and hydrophobicity. Toxicological differences as observed in short-term inhalation studies (STIS) were mainly influenced by the core composition and/or surface reactivity of NPs. However, agglomeration in lipid media and lipid/protein affinity appeared to play a modulatory role on short-term inhalation toxicity. For instance, lipophilic NPs like ZrO2, which are interacting with nS to a higher extent, exhibited a far higher lung burden than their hydrophilic counterparts, which deserves further attention to predict or model effects of respirable NPs. © 2016 Informa UK Limited, trading as Taylor & Francis Group.
    view abstractdoi: 10.3109/17435390.2016.1155671
  • 2015 • 102 Stability of Dealloyed Porous Pt/Ni Nanoparticles
    Baldizzone, C. and Gan, L. and Hodnik, N. and Keeley, G.P. and Kostka, A. and Heggen, M. and Strasser, P. and Mayrhofer, K.J.J.
    ACS Catalysis 5 5000-5007 (2015)
    We provide a comprehensive durability assessment dedicated to a promising class of electrocatalysts for the oxygen reduction reaction (i.e., porous platinum nanoparticles). The stability of these nanoengineered open structures is tested under two accelerated degradation test conditions (ADT), particularly selected to mimic the potential regimes experienced by the catalyst during the operative life of a fuel cell (i.e., load cycles (up to 1.0 V<inf>RHE</inf>) and start-up cycles (up to 1.4 V<inf>RHE</inf>)). To understand the evolution of the electrochemical performance, the catalyst properties are investigated by means of fundamental rotating disc electrode studies, identical location-transmission electron microscopy (IL-TEM) coupled with electron energy loss spectroscopy chemical mapping (IL-EELS), and post-use chemical analysis and online highly sensitive potential resolved dissolution concentration monitoring by scanning flow cell inductively coupled plasma-mass spectrometry (SFC-ICP-MS). The experimental results on the nanoporous Pt revealed distinctive degradation mechanisms that could potentially affect a wide range of other nanoengineered open structures. The study concludes that, although providing promising activity performance, under the relevant operational conditions of fuel cells, the nanoporosity is only metastable and subjected to a progressive reorganization toward the minimization of the nanoscale curvature. The rate and pathways of this specific degradation mechanism together with other well-known degradation mechanisms like carbon corrosion and platinum dissolution are strongly dependent on the selected upper limit potential, leading to distinctly different durability performance. © 2015 American Chemical Society.
    view abstractdoi: 10.1021/acscatal.5b01151
  • 2015 • 101 Structure-based design and synthesis of covalent-reversible inhibitors to overcome drug resistance in EGFR
    Basu, D. and Richters, A. and Rauh, D.
    Bioorganic and Medicinal Chemistry 23 2767-2780 (2015)
    The clinical success of covalent kinase inhibitors in the treatment of EGFR-dependent non-small cell lung cancer (NSCLC) has rejuvenated the appreciation of reactive small molecules. Acquired drug resistance against first-line EGFR inhibitors remains the major bottleneck in NSCLC and is currently addressed by the application of fine-tuned covalent drugs. Here we report the design, synthesis and biochemical evaluation of a novel class of EGFR inhibitors with a covalent yet reversible warhead. A series of WZ4002 analogs, derived from anilinopyrimidine and 3-substituted-2-cyanoacrylamide scaffolds, exhibit strong and selective inhibitory activity against clinically relevant EGFRL858R and EGFRL858R/T790M. © 2015 Elsevier Ltd. All rights reserved.
    view abstractdoi: 10.1016/j.bmc.2015.04.038
  • 2015 • 100 Investigation of the sampling nozzle effect on laminar flat flames
    Deng, L. and Kempf, A. and Hasemann, O. and Korobeinichev, O.P. and Wlokas, I.
    Combustion and Flame 162 1737-1747 (2015)
    Sampling probes used for the mass spectrometric sampling of a flame can affect the flame's flow field. Although this effect is already compensated for by heuristic correction functions, state of the art 3-D simulations may permit an even better consideration of this effect. This work has investigated the perturbations induced by sampling probes in burner-stabilized, laminar, flat flames using numerical simulations. Any deviations in the flow and temperature fields from the ideal, one-dimensional flat flame were generated here by a perforated burner plate; they are also examined. Corresponding mass spectrometric measurements were performed in flames of CH4/O2/Ar and H2/O2/N2, burning under atmospheric conditions. In the present study, heat transfer from the flame to the sampling nozzle was studied with a conjugate heat transfer model. Combustion was described using a finite rate chemistry model, employing a detailed reaction mechanism for a H2/O2/N2 flame and a reduced mechanism for a CH4/O2/Ar flame. Compared to the ideal, one-dimensional, and unperturbed flame, the probe was found to affect the measurements of the concentrations of some species by up to 50%. The results highlight the value of supporting numerical simulations of both the flow and combustion for such measurements with invasive probing. © 2014 The Combustion Institute.
    view abstractdoi: 10.1016/j.combustflame.2014.11.035
  • 2015 • 99 Mass spectrometry-based proteomics for relative protein quantification and biomarker identification in primary human hepatocytes
    Dietz, L. and Sickmann, A.
    Methods in Molecular Biology 1250 251-265 (2015)
    Liquid chromatography-tandem mass spectrometry-based proteomics is a highly sensitive and effective tool to identify and quantify potential biomarkers in repeated dose toxicity studies using primary cell culture systems. In this respect, 8-plex isobaric tag for relative and absolute quantification labeling is the method of choice for relative quantification. After cell lysis and tryptic protein digestion, an individual isobaric tag is added to the amine groups of arginine and lysine. Then, up to eight differentially labeled samples are mixed and analyzed together in a mass spectrometry experiment. During peptide fragmentation in the mass spectrometer, the individual tag intensity of each identified peptide could be detected, reflecting the peptide intensities in the eight samples. The identified peptides are matched to their specific protein using specific search engines and finally to eight individual relative protein quantities. The twodimensional fractionation of complex peptide mixtures minimizes the possibility of co-fragmentation of peptides from different origin in the mass spectrometer, which leads to a higher number of peptide search matches and therefore to better identification and quantification results. © Springer Science+Business Media New York 2015.
    view abstractdoi: 10.1007/978-1-4939-2074-7_18
  • 2015 • 98 Mass spectrometry of atmospheric pressure plasmas
    Grosse-Kreul, S. and Hubner, S. and Schneider, S. and Ellerweg, D. and von Keudell, A. and Matejcik, S. and Benedikt, J.
    Plasma Sources Science & Technology 24 044008 (2015)
    Atmospheric pressure non-equilibrium plasmas (APPs) are effective source of radicals, metastables and a variety of ions and photons, ranging into the vacuum UV spectral region. A detailed study of these species is important to understand and tune desired effects during the interaction of APPs with solid or liquid materials in industrial or medical applications. In this contribution, the opportunities and challenges of mass spectrometry for detection of neutrals and ions from APPs, fundamental physical phenomena related to the sampling process and their impact on the measured densities of neutrals and fluxes of ions, will be discussed. It is shown that the measurement of stable neutrals and radicals requires a proper experimental design to reduce the beam-to-background ratio, to have little beam distortion during expansion into vacuum and to carefully set the electron energy in the ionizer to avoid radical formation through dissociative ionization. The measured ion composition depends sensitively on the degree of impurities present in the feed gas as well as on the setting of the ion optics used for extraction of ions from the expanding neutral-ion mixture. The determination of the ion energy is presented as a method to show that the analyzed ions are originating from the atmospheric pressure plasma.
    view abstractdoi: 10.1088/0963-0252/24/4/044008
  • 2015 • 97 Guided mass spectrum labelling in atom probe tomography
    Haley, D. and Choi, P. and Raabe, D.
    Ultramicroscopy 159 338-345 (2015)
    Atom probe tomography (APT) is a valuable near-atomic scale imaging technique, which yields mass spectrographic data. Experimental correctness can often pivot on the identification of peaks within a dataset, this is a manual process where subjectivity and errors can arise. The limitations of manual procedures complicate APT experiments for the operator and furthermore are a barrier to technique standardisation. In this work we explore the capabilities of computer-guided ranging to aid identification and analysis of mass spectra. We propose a fully robust algorithm for enumeration of the possible identities of detected peak positions, which assists labelling. Furthermore, a simple ranking scheme is developed to allow for evaluation of the likelihood of each possible identity being the likely assignment from the enumerated set. We demonstrate a simple, yet complete work-chain that allows for the conversion of mass-spectra to fully identified APT spectra, with the goal of minimising identification errors, and the inter-operator variance within APT experiments. This work chain is compared to current procedures via experimental trials with different APT operators, to determine the relative effectiveness and precision of the two approaches. It is found that there is little loss of precision (and occasionally gain) when participants are given computer assistance. We find that in either case, inter-operator precision for ranging varies between 0 and 2 "significant figures" (2 σ confidence in the first n digits of the reported value) when reporting compositions. Intra-operator precision is weakly tested and found to vary between 1 and 3 significant figures, depending upon species composition levels. Finally it is suggested that inconsistencies in inter-operator peak labelling may be the largest source of scatter when reporting composition data in APT. © 2015 Elsevier B.V.
    view abstractdoi: 10.1016/j.ultramic.2015.03.005
  • 2015 • 96 MOCVD of TiO2 thin films from a modified titanium alkoxide precursor
    Kim, S.J. and Dang, V.-S. and Xu, K. and Barreca, D. and Maccato, C. and Carraro, G. and Bhakta, R.K. and Winter, M. and Becker, H.-W. and Rogalla, D. and Sada, C. and Fischer, R.A. and Devi, A.
    Physica Status Solidi (A) Applications and Materials Science 212 1563-1570 (2015)
    A new titanium precursor, [Ti(OPri)<inf>2</inf>(deacam)<inf>2</inf>] (deacam = N,N-diethylacetoacetamide), was developed by the reaction of the parent Ti alkoxide with the β-ketoamide. The compound, obtained as a monomeric six-coordinated complex, was used in metal organic chemical vapor deposition (MOCVD) of TiO<inf>2</inf> both as a single source precursor (SSP) and in the presence of oxygen. The high thermal stability of [Ti(OPri)<inf>2</inf>(deacam)<inf>2</inf>] enabled the fabrication of TiO<inf>2</inf> films over a wide temperature range, with steady growth rates between 500 and 800 °C. The microstructure of the obtained systems was analyzed by X-ray diffraction (XRD) and Raman spectroscopy, whereas atomic force microscopy (AFM) and field emission-scanning electron microscopy (FE-SEM) measurements were performed to investigate the surface morphology and nanoorganization. Film composition was investigated by complementary techniques like Rutherford backscattering spectrometry (RBS), nuclear reaction analysis (NRA), X-ray photoelectron spectroscopy (XPS), and secondary ion mass spectrometry (SIMS). The electrical properties of the layers were investigated by performing capacitance voltage (C-V) and leakage current measurements. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/pssa.201532271
  • 2015 • 95 A dielectric barrier discharge terminally inactivates RNase A by oxidizing sulfur-containing amino acids and breaking structural disulfide bonds
    Lackmann, J.-W. and Baldus, S. and Steinborn, E. and Edengeiser, E. and Kogelheide, F. and Langklotz, S. and Schneider, S. and Leichert, L.I.O. and Benedikt, J. and Awakowicz, P. and Bandow, J.E.
    Journal of Physics D: Applied Physics 48 (2015)
    RNases are among the most stable proteins in nature. They even refold spontaneously after heat inactivation, regaining full activity. Due to their stability and universal presence, they often pose a problem when experimenting with RNA. We investigated the capabilities of nonthermal atmospheric-pressure plasmas to inactivate RNase A and studied the inactivation mechanism on a molecular level. While prolonged heating above 90°C is required for heat inactivating RNase A, direct plasma treatment with a dielectric barrier discharge (DBD) source caused permanent inactivation within minutes. Circular dichroism spectroscopy showed that DBD-treated RNase A unfolds rapidly. Raman spectroscopy indicated methionine modifications and formation of sulfonic acid. A mass spectrometry-based analysis of the protein modifications that occur during plasma treatment over time revealed that methionine sulfoxide formation coincides with protein inactivation. Chemical reduction of methionine sulfoxides partially restored RNase A activity confirming that sulfoxidation is causal and sufficient for RNase A inactivation. Continued plasma exposure led to over-oxidation of structural disulfide bonds. Using antibodies, disulfide bond over-oxidation was shown to be a general protein inactivation mechanism of the DBD. The antibody's heavy and light chains linked by disulfide bonds dissociated after plasma exposure. Based on their ability to inactivate proteins by oxidation of sulfur-containing amino acids and over-oxidation of disulfide bonds, DBD devices present a viable option for inactivating undesired or hazardous proteins on heat or solvent-sensitive surfaces. © 2015 IOP Publishing Ltd.
    view abstractdoi: 10.1088/0022-3727/48/49/494003
  • 2015 • 94 Atomic scale investigation of non-equilibrium segregation of boron in a quenched Mo-free martensitic steel
    Li, Y.J. and Ponge, D. and Choi, P. and Raabe, D.
    Ultramicroscopy 159 240-247 (2015)
    B-added low carbon steels exhibit excellent hardenability. The reason has been frequently attributed to B segregation at prior austenite grain boundaries, which prevents the austenite to ferrite transformation and favors the formation of martensite. The segregation behavior of B at prior austenite grain boundaries is strongly influenced by processing conditions such as austenitization temperatures and cooling rates and by alloying elements such as Mo, Cr, and Nb. Here an local electrode atom probe was employed to investigate the segregation behavior of B and other alloying elements (C, Mn, Si, and Cr) in a Cr-added Mo-free martensitic steel. Similar to our previous results on a Mo-added steel, we found that in both steels B is segregated at prior austenite grain boundaries with similar excess values, whereas B is neither detected in the martensitic matrix nor at martensite-martensite boundaries at the given cooling rate of 30 K/s. These results are in agreement with the literature reporting that Cr has the same effect on hardenability of steels as Mo in the case of high cooling rates. The absence of B at martensite-martensite boundaries suggests that B segregates to prior austenite grain boundaries via a non-equilibrium mechanism. Segregation of C at all boundaries such as prior austenite grain boundaries and martensite-martensite boundaries may occur by an equilibrium mechanism. © 2015 Elsevier B.V.
    view abstractdoi: 10.1016/j.ultramic.2015.03.009
  • 2015 • 93 Phase transitions during formation of Ag nanoparticles on In2S3 precursor layers
    Liu, Y. and Fu, Y. and Dittrich, T. and Sáez-Araoz, R. and Schmid, M. and Hinrichs, V. and Lux-Steiner, M.C. and Fischer, C.-H.
    Thin Solid Films 590 54-59 (2015)
    Phase transitions have been investigated for silver deposition onto In<inf>2</inf>S<inf>3</inf> precursor layers by spray chemical vapor deposition from a trimethylphosphine (hexafluoroacetylacetonato) silver (Ag(hfacac)(PMe<inf>3</inf>)) solution. The formation of Ag nanoparticles (Ag NPs) on top of the semiconductor layer set on concomitant with the formation of AgIn<inf>5</inf>S<inf>8</inf>. The increase of the diameter of Ag NPs was accompanied by the evolution of orthorhombic AgInS<inf>2</inf>. The formation of Ag<inf>2</inf>S at the interface between Ag NPs and the semiconductor layer was observed. Surface photovoltage spectroscopy indicated charge separation and electronic transitions in the ranges of corresponding band gaps. The phase transition approach is aimed to be applied for the formation of plasmonic nanostructures on top of extremely thin semiconducting layers. © 2015 Elsevier B.V.
    view abstractdoi: 10.1016/j.tsf.2015.07.021
  • 2015 • 92 Multidimensional electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research
    Loroch, S. and Schommartz, T. and Brune, W. and Zahedi, R.P. and Sickmann, A.
    Biochimica et Biophysica Acta - Proteins and Proteomics 1854 460-468 (2015)
    Quantitative proteomics and phosphoproteomics have become key disciplines in understanding cellular processes. Fundamental research can be done using cell culture providing researchers with virtually infinite sample amounts. In contrast, clinical, pre-clinical and biomedical research is often restricted to minute sample amounts and requires an efficient analysis with only micrograms of protein. To address this issue, we generated a highly sensitive workflow for combined LC-MS-based quantitative proteomics and phosphoproteomics by refining an ERLIC-based 2D phosphoproteomics workflow into an ERLIC-based 3D workflow covering the global proteome as well. The resulting 3D strategy was successfully used for an in-depth quantitative analysis of both, the proteome and the phosphoproteome of murine cytomegalovirus-infected mouse fibroblasts, a model system for host cell manipulation by a virus. In a 2-plex SILAC experiment with 150 μg of a tryptic digest per condition, the 3D strategy enabled the quantification of ∼ 75% more proteins and even ∼ 134% more peptides compared to the 2D strategy. Additionally, we could quantify ∼ 50% more phosphoproteins by non-phosphorylated peptides, concurrently yielding insights into changes on the levels of protein expression and phosphorylation. Beside its sensitivity, our novel three-dimensional ERLIC-strategy has the potential for semi-automated sample processing rendering it a suitable future perspective for clinical, pre-clinical and biomedical research. © 2015 Published by Elsevier B.V.
    view abstractdoi: 10.1016/j.bbapap.2015.01.006
  • 2015 • 91 Assembling Paramagnetic Ceruloplasmin at Electrode Surfaces Covered with Ferromagnetic Nanoparticles. Scanning Electrochemical Microscopy in the Presence of a Magnetic Field
    Matysiak, E. and Botz, A.J.R. and Clausmeyer, J. and Wagner, B. and Schuhmann, W. and Stojek, Z. and Nowicka, A.M.
    Langmuir 31 8176-8183 (2015)
    Adsorption of ceruloplasmin (Cp) at a gold electrode modified with ferromagnetic iron nanoparticles encapsulated in carbon (Fe@C Nps) leads to a successful immobilization of the enzyme in its electroactive form. The proper placement of Cp at the electrode surface on top of the nanocapsules containing an iron core allowed a preorientation of the enzyme, hence allowing direct electron transfer between the electrode and the enzyme. Laser ablation coupled with inductively coupled plasma mass spectrometry indicated that Cp was predominantly located at the paramagnetic nanoparticles. Scanning electrochemical microscopy measurements in the sample-generation/tip-collection mode proved that Cp was ferrooxidative inactive if it was immobilized on the bare gold surface and reached the highest activity if it was adsorbed on Fe@C Nps in the presence of a magnetic field. © 2015 American Chemical Society.
    view abstractdoi: 10.1021/acs.langmuir.5b01155
  • 2015 • 90 On the mechanism of Zn4O-acetate precursors ripening to ZnO: How dimerization is promoted by hydroxide incorporation
    Milek, T. and Kirschbaum, R.W. and Gernler, M.S.V. and Lübbert, C. and Segets, D. and Drewello, T. and Peukert, W. and Zahn, D.
    Journal of Chemical Physics 143 (2015)
    We report on a combined experimental and molecular modelling study on Zn<inf>4</inf>O ion clusters stabilized by acetate molecules (OAc). In particular, ab initio calculations of acetate substitution by hydroxide ions are compared with mass spectrometry data. Though quantum calculations in the gas phase indicate strong energetic preference, no experimental evidence of stable Zn<inf>4</inf>O(OAc)<inf>6-x</inf>(OH)<inf>x</inf> clusters in ethanolic solutions could be observed. This apparent contradiction is rationalized by identifying the supportive role of hydroxide ions for the association of (OAc- → OH- substituted) Zn<inf>4</inf>O(OAc)<inf>6</inf> and Zn<inf>4</inf>O(OAc)<inf>5</inf>+ clusters. Mass spectrometry and quantum calculations hint at the stability of (Zn<inf>4</inf>O)<inf>2</inf>(OAc)<inf>12-x</inf>(OH)<inf>x</inf> dimers with x = 1, 2. Therein, the hydroxide ions establish salt-bridges that allow for the formation of additional Zn<inf>3</inf> motifs with the OH above the triangle center - a structural motif close to that of the ZnO-crystal. The association of Zn<inf>4</inf>O(OAc)<inf>6</inf> clusters is thus suggested to involve OAc- → OH- substitution as an activation step, quickly followed by dimerization and the subsequent agglomeration of oligomers. © 2015 AIP Publishing LLC.
    view abstractdoi: 10.1063/1.4928190
  • 2015 • 89 Current strategies and findings in clinically relevant post-translational modification-specific proteomics
    Pagel, O. and Loroch, S. and Sickmann, A. and Zahedi, R.P.
    Expert Review of Proteomics 12 235-253 (2015)
    Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research. © Informa Uk, Ltd.
    view abstractdoi: 10.1586/14789450.2015.1042867
  • 2015 • 88 Identification of proteins involved in inhibition of spheroid formation under microgravity
    Riwaldt, S. and Pietsch, J. and Sickmann, A. and Bauer, J. and Braun, M. and Segerer, J. and Schwarzwälder, A. and Aleshcheva, G. and Corydon, T.J. and Infanger, M. and Grimm, D.
    Proteomics 15 2945-2952 (2015)
    Many types of cells transit in vitro from a two- to a three-dimensional growth, when they are exposed to microgravity. The underlying mechanisms are not yet understood. Hence, we investigated the impact of microgravity on protein content and growth behavior. For this purpose, the human thyroid cancer cells FTC-133 were seeded either in recently developed cell containers that can endure enhanced physical forces and perform media changes and cell harvesting automatically or in T-25 culture flasks. All cells were cultured for five days at 1g. Afterwards, a part of the cell containers were flown to the International Space Station, while another part was kept on the ground. T-25 flasks were mounted on and next to a Random Positioning Machine. The cells were cultured for 12 days under the various conditions, before they were fixed with RNAlater. All fixed cultures showed monolayers, but three-dimensional aggregates were not detected. In a subsequent protein analysis, 180 proteins were identified by mass spectrometry. These proteins did not indicate significant differences between cells exposed to microgravity and their 1g controls. However, they suggest that an enhanced production of proteins related to the extracellular matrix could detain the cells from spheroid formation, while profilin-1 is phosphorylated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201500067
  • 2015 • 87 PeptideShaker enables reanalysis of MS-derived proteomics data sets: To the editor
    Vaudel, M. and Burkhart, J.M. and Zahedi, R.P. and Oveland, E. and Berven, F.S. and Sickmann, A. and Martens, L. and Barsnes, H.
    Nature Biotechnology 33 22-24 (2015)
    doi: 10.1038/nbt.3109
  • 2015 • 86 Chemical vapor deposition of Si/SiC nano-multilayer thin films
    Weber, A. and Remfort, R. and Wöhrl, N. and Assenmacher, W. and Schulz, S.
    Thin Solid Films 593 44-52 (2015)
    Stoichiometric SiC films were deposited with the commercially available single source precursor Et3SiH by classical thermal chemical vapor deposition (CVD) as well as plasma-enhanced CVD at low temperatures in the absence of any other reactive gases. Temperature-variable deposition studies revealed that polycrystalline films containing different SiC polytypes with a Si to carbon ratio of close to 1:1 are formed at 1000°C in thermal CVD process and below 100°C in the plasma-enhanced CVD process. The plasma enhanced CVD process enables the reduction of residual stress in the deposited films and offers the deposition on temperature sensitive substrates in the future. In both deposition processes the film thickness can be controlled by variation of the process parameters such as the substrate temperature and the deposition time. The resulting material films were characterized with respect to their chemical composition and their crystallinity using scanning electron microscope, energy dispersive X-ray spectroscopy (XRD), atomic force microscopy, X-ray diffraction, grazing incidence X-ray diffraction, secondary ion mass spectrometry and Raman spectroscopy. Finally, Si/SiC multilayers of up to 10 individual layers of equal thickness (about 450 nm) were deposited at 1000°C using Et3SiH and SiH4. The resulting multilayers features amorphous SiC films alternating with Si films, which feature larger crystals up to 300 nm size as measured by transmission electron microscopy as well as by XRD. XRD features three distinct peaks for Si(111), Si(220) and Si(311). © 2015 Published by Elsevier B.V.
    view abstractdoi: 10.1016/j.tsf.2015.08.042
  • 2015 • 85 Amyloid β-Protein Assembly: The Effect of Molecular Tweezers CLR01 and CLR03
    Zheng, X. and Liu, D. and Klärner, F.-G. and Schrader, T. and Bitan, G. and Bowers, M.T.
    Journal of Physical Chemistry B 119 4831-4841 (2015)
    The early oligomerization of amyloid β-protein (Aβ) has been shown to be an important event in the pathology of Alzheimer's disease (AD). Designing small molecule inhibitors targeting Aβ oligomerization is one attractive and promising strategy for AD treatment. Here we used ion mobility spectrometry coupled to mass spectrometry (IMS-MS) to study the different effects of the molecular tweezers CLR01 and CLR03 on Aβ self-assembly. CLR01 was found to bind to Aβ directly and disrupt its early oligomerization. Moreover, CLR01 remodeled the early oligomerization of Aβ42 by compacting the structures of dimers and tetramers and as a consequence eliminated higher-order oligomers. Unexpectedly, the negative-control derivative, CLR03, which lacks the hydrophobic arms of the tweezer structure, was found to facilitate early Aβ oligomerization. Our study provides an example of IMS as a powerful tool to study and better understand the interaction between small molecule modulators and Aβ oligomerization, which is not attainable by other methods, and provides important insights into therapeutic development of molecular tweezers for AD treatment. (Graph Presented). © 2015 American Chemical Society.
    view abstractdoi: 10.1021/acs.jpcb.5b00692
  • 2014 • 84 Molecular basis for preventing α-synuclein aggregation by a molecular tweezer
    Acharya, S. and Safaie, B.M. and Wongkongkathep, P. and Ivanova, M.I. and Attar, A. and Klärner, F.-G. and Schrader, T. and Loo, J.A. and Bitan, G. and Lapidus, L.J.
    Journal of Biological Chemistry 289 10727-10737 (2014)
    Recent work on α-synuclein has shown that aggregation is controlled kinetically by the rate of reconfiguration of the unstructured chain, such that the faster the reconfiguration, the slower the aggregation. In this work we investigate this relationship by examining α-synuclein in the presence of a small molecular tweezer, CLR01, which binds selectively to Lys side chains. We find strong binding to multiple Lys within the chain as measured by fluorescence and mass-spectrometry and a linear increase in the reconfiguration rate with concentration of the inhibitor. Top-down mass-spectrometric analysis shows that the main binding of CLR01 to α-synuclein occurs at the N-terminal Lys-10/Lys- 12. Photo-induced cross-linking of unmodified proteins (PICUP) analysis shows that under the conditions used for the fluorescence analysis, α-synuclein ispredominantlymonomeric.Theresultscan be successfully modeled using a kineticschemein which two aggregation- pronemonomerscanformanencountercomplexthat leads to further oligomerization but can also dissociate back to monomers if the reconfiguration rate is sufficiently high.Takentogether, the data provide important insights into the preferred binding site of CLR01 on α-synuclein and the mechanism by which the molecular tweezer prevents self-assembly into neurotoxic aggregates by α-synuclein and presumably other amyloidogenic proteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
    view abstractdoi: 10.1074/jbc.M113.524520
  • 2014 • 83 Influence of molecular hydrogen on acetylene pyrolysis: Experiment and modeling
    Aghsaee, M. and Dürrstein, S.H. and Herzler, J. and Böhm, H. and Fikri, M. and Schulz, C.
    Combustion and Flame 161 2263-2269 (2014)
    The effect of molecular hydrogen on the formation of molecular carbonaceous species important for soot formation is studied through a combination of shock-tube experiments with high-repetition-rate time-of-flight mass spectrometry and detailed chemistry modeling. The experiment allows to simultaneously measure the concentration-time profiles for various species with a time resolution of 10μs. Concentration histories of reactants and polyacetylene intermediates (C2xH2, x=1-4) are measured during the pyrolysis of acetylene with and without H2 added to the gas mixture for a wide range of conditions. In the 1760-2565K temperature range, reasonable agreement between the experiment and the model predictions for C2H2, C4H2, C6H2, and C8H2 is achieved. H2 addition leads to the depletion of important building blocks for particle formation, namely of polyacetylenes due to an enhanced consumption of important radicals by H2, which are required for the fast build-up of carbonaceous material. © 2014 The Combustion Institute.
    view abstractdoi: 10.1016/j.combustflame.2014.03.012
  • 2014 • 82 Novel β-ketoiminato complexes of zirconium: Synthesis, characterization and evaluation for solution based processing of ZrO2 thin films
    Banerjee, M. and Seidel, R.W. and Winter, M. and Becker, H.-W. and Rogalla, D. and Devi, A.
    Dalton Transactions 43 2384-2396 (2014)
    Treatment of tetrakis(diethylamido)zirconium(iv); [Zr(NEt2) 4] with a series of β-ketoimines ({[RHN]C(CH3)C(H) C(CH3)O} where R is a functionalized side-chain; 4-(2- methoxyethylamino)pent-3-en-2-one, Hmeap; 4-(3-methoxypropylamino)pent-3-en-2- one, Hmpap; 4-(2-(dimethylamino)ethylamino)pent-3-en-2-one, Hdeap; 4-(3-(dimethylamino)propylamino)pent-3-en-2-one, Hdpap) leads to an amine substitution reaction that yielded novel monomeric heteroleptic mixed amido-ketoiminato complexes of the type bis(4-(2-methoxyethylamino)pent-3-en-2- onato)bis(diethylamido)zirconium(iv) (1), bis(4-(3-methoxypropylamino)pent-3-en- 2-onato)bis(diethylamido)zirconium(iv) (2), and bis(4-(3-(dimethylamino) propylamino)pent-3-en-2-onato)bis(diethylamido)zirconium(iv) (3), and eight-coordinated homoleptic complexes tetrakis(4-(2-methoxyethylamino)pent-3- en-2-onato)zirconium(iv) (4) and tetrakis(4-(2-(dimethylamino)ethylamino)pent-3- en-2-onato)zirconium(iv) (5), depending on the ratio of the ligand to zirconium. Adopting a similar strategy with zirconium alkoxide, namely [Zr(O iPr)4·iPrOH], with β-ketoimine Hmeap, leads to the formation of a dimer, bis(μ2-isopropoxo)bis(4- (2-methoxyethylamino)pent-3-en-2-onato)tetrakis(isopropoxo)dizirconium(iv) (6). The newly synthesised complexes were characterized by NMR spectroscopy, mass spectrometry, single crystal X-ray diffraction, elemental analysis and thermal analysis. The low decomposition temperature facilitated by the stepwise elimination of the ketominate ligand from the complex and the stability of the complexes obtained in air as well as in solution makes them highly suitable for solution based processing of ZrO2 thin films, which is demonstrated using compound 5 on Si(100) substrates. High quality ZrO2 films were obtained and were investigated for their structure, morphology, composition and optical properties. Low temperature crystallisation of ZrO2 is achieved by a simple chemical deposition process using the new class of Zr precursors and the films exhibit an optical transmittance above 90%. © 2014 The Royal Society of Chemistry.
    view abstractdoi: 10.1039/c3dt52335g
  • 2014 • 81 Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways
    Beck, F. and Geiger, J. and Gambaryan, S. and Veit, J. and Vaudel, M. and Nollau, P. and Kohlbacher, O. and Martens, L. and Walter, U. and Sickmann, A. and Zahedi, R.P.
    Blood 123 e1-e10 (2014)
    One of the most important physiological platelet inhibitors is endothelium-derived prostacyclin which stimulates the platelet cyclic adenosine monophosphate/protein kinase A (cAMP/PKA)-signaling cascade and inhibits virtually all platelet-activating key mechanisms. Using quantitative mass spectrometry, we analyzed time-resolved phosphorylation patterns in human platelets after treatment with iloprost, a stable prostacyclin analog, for 0, 10, 30, and 60 seconds to characterize key mediators of platelet inhibition and activation in 3 independent biological replicates. We quantified over 2700 different phosphorylated peptides of which 360 were significantly regulated upon stimulation. This comprehensive and time-resolved analysis indicates that platelet inhibition is a multipronged process involving different kinases and phosphatases aswell asmany previously unanticipated proteins and pathways. © 2014 by The American Society of Hematology.
    view abstractdoi: 10.1182/blood-2013-07-512384
  • 2014 • 80 Tribenzotriquinacene receptors for C60 fullerene rotors: Towards C3 symmetrical chiral stators for unidirectionally operating nanoratchets
    Bredenkötter, B. and Grzywa, M. and Alaghemandi, M. and Schmid, R. and Herrebout, W. and Bultinck, P. and Volkmer, D.
    Chemistry - A European Journal 20 9100-9110 (2014)
    The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (7) for C60 fullerene, possessing C3 point group symmetry, by threefold condensation of C2-symmetric 1,2-diketone synthons (5) and a hexaaminotribenzotriquinacene core (6) is described. The chiral diketone was synthesized in a five-step reaction sequence starting from C2h-symmetric 2,6-di-tert-butylanthracene. The highly diastereo-discriminating Diels-Alder reaction of 2,6-di-tert-butylanthracene with fumaric acid di(-)menthyl ester, catalyzed by aluminium chloride, is the relevant stereochemistry introducing step. The structure of the fullerene receptor was verified by 1H and 13C NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. VCD and ECD spectra were recorded, which were corroborated by ab initio DFT calculations, establishing the chiral nature of 7 with about 99.7 % ee, based on the ee (99.9 %) of the chiral synthon (1). The absolute configuration of 7 could thus be established as all-S [(2S,7S,16S,21S,30S,35S)-(7)]. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with either pure fullerene (C60) or fullerene derivatives, such as rotor 1'-(4-nitrophenyl)-3'-(4-N,N- dimethylaminophenyl)-pyrazolino[4',5':1,2][60]fullerene (R). The complex stability constants of the complexes dissolved in CHCl3/CS 2 (1:1 vol. %) are K([C60-7])=319(±156) M -1 and K([R-7])=110(±50) M-1. With molecular dynamics simulations using a first-principles parameterized force field the asymmetry of the rotational potential for [R-7] was shown, demonstrating the potential suitability of receptor 7 to act as a stator in a unidirectionally operating nanoratchet. Going through the motions: The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (1) for C 60 fullerenes is described. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with fullerenes. Molecular dynamics simulations show the asymmetry of the rotational potential for [R-1], demonstrating the potential suitability of receptor 1 to act as a stator in a unidirectionally operating nanoratchet (see figure). © 2014 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/chem.201304980
  • 2014 • 79 What can proteomics tell us about platelets?
    Burkhart, J.M. and Gambaryan, S. and Watson, S.P. and Jurk, K. and Walter, U. and Sickmann, A. and Heemskerk, J.W.M. and Zahedi, R.P.
    Circulation Research 114 1204-1219 (2014)
    More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein-protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.
    view abstractdoi: 10.1161/CIRCRESAHA.114.301598
  • 2014 • 78 Multidiagnostic analysis of silicate speciation in clear solutions/sols for zeolite synthesis
    Castro, M. and Haouas, M. and Taulelle, F. and Lim, I. and Breynaert, E. and Brabants, G. and Kirschhock, C.E.A. and Schmidt, W.
    Microporous and Mesoporous Materials 189 158-162 (2014)
    The formation of zeolites in presence of tetraalkylammonium cations from so-called clear solutions using silicon alkoxides is a highly complex process which challenges experimental chemistry. Most clear solutions are better described as clear sols as they contain nanosized silicate particles, which are formed during hydrolysis of the Si source before self-assembly into the zeolite framework. This process spans multiple time- and length-scales and only a combination of different analysis methods allows revelation of molecular level zeolite formation mechanisms. On the example of the early stages of the formation of zeolite beta from clear solutions/sols the different windows of observation of liquid-state 29Si and 27Al nuclear magnetic resonance (NMR) spectroscopy, small angle X-ray scattering (SAXS), dynamic light scattering (DLS) and mass spectrometry (MS) are demonstrated. Each diagnostic means by itself needs to be carefully assessed for its window of temporal and spatial resolution which can be achieved by exploiting the overlapping information available from their combination. © 2013 Elsevier Ltd. All rights reserved.
    view abstractdoi: 10.1016/j.micromeso.2013.08.027
  • 2014 • 77 Using the first steps of hydration for the determination of molecular conformation of a single molecule
    Henzl, J. and Boom, K. and Morgenstern, K.
    Journal of the American Chemical Society 136 13341-13347 (2014)
    Determination of the exact structure of individual molecules is the ultimate goal of high-resolution microscopy. However, the resolution of scanning tunneling microscopy (STM) is intrinsically limited to the extent of molecular orbitals, which frequently do not differ for small changes in the molecular conformation. Here we use the position of water molecules during the first hydration steps of an azobenzene derivative on Au(111) to determine not only the orientation of the end groups with respect to the phenyl rings but also the orientation of the two phenyl rings with respect to the azo group. We investigate the co-adsorption of 4,4'-hydroxy-azobenzene and water molecules on Au(111) by low-temperature STM. The water molecules are attached exclusively to the hydroxyl end groups of the azobenzene derivatives. Predominantly the trans-azobenzene molecule with the two hydroxyl groups pointing into opposite directions is adsorbed. As corroborated by the attachment of a single water molecule to 4-anilino-4?-nitro azobenzene on the same inert surface, the method is generally applicable for structure determination of molecules with appropriate end groups. Our study thus gives unprecedented information about the intramolecular orientation based on the first real space observation of the hydration of a functional molecule. © 2014 American Chemical Society.
    view abstractdoi: 10.1021/ja506762t
  • 2014 • 76 Role and evolution of nanoparticle structure and chemical state during the oxidation of NO over size- and shape-controlled Pt/γ-Al2O 3 catalysts under operando conditions
    Lira, E. and Merte, L.R. and Behafarid, F. and Ono, L.K. and Zhang, L. and Roldan Cuenya, B.
    ACS Catalysis 4 1875-1884 (2014)
    The structure and chemical state of size-selected Pt nanoparticles (NPs) supported on γ-Al2O3 were studied during the oxidation of NO using X-ray absorption near-edge spectroscopy and extended X-ray absorption fine-structure spectroscopy measurements under operando conditions. The data revealed the formation of PtOx species in the course of the reaction that remained present at the maximum temperature studied, 350 °C. The PtOx species were found in all samples, but those with the smallest NPs showed the highest degree of oxidation. Moreover, NO-induced nanoparticle redispersion was observed at temperatures below 150 °C for all catalysts studied. Catalytic tests showed activity toward the oxidation of NO for all samples. Nevertheless, the catalyst with the smallest NPs was found to be the least active, which is explained by a more extensive formation of PtOx species in this catalyst and their detrimental contribution to the oxidation of NO. © 2014 American Chemical Society.
    view abstractdoi: 10.1021/cs500137r
  • 2014 • 75 Origin of the energetic ions at the substrate generated during high power pulsed magnetron sputtering of titanium
    Maszl, C. and Breilmann, W. and Benedikt, J. and von Keudell, A.
    Journal of Physics D-applied Physics 47 224002 (2014)
    High power impulse magnetron sputtering (HiPIMS) plasmas generate energetic metal ions at the substrate as a major difference to conventional direct current magnetron sputtering (dcMS). The origin of these very energetic ions in HiPIMS is still an open issue, which is unravelled using two fast diagnostics: time-resolved mass spectrometry with a temporal resolution of 2 mu s and phase resolved optical emission spectroscopy with a temporal resolution of 1 mu s. A power scan from dcMS-like to HiPIMS plasmas was performed, with a 2 inch magnetron and a titanium target as sputter source and argon as working gas. Clear differences in the transport as well as the energetic properties of Ar+, Ar2+, Ti+ and Ti2+ were observed. For discharges with highest peak power densities a high energetic group of Ti+ and Ti2+ could be identified with energies of approximately 25 eV and of 50 eV, respectively. A cold group of ions was always present. It is found that hot ions are observed only when the plasma enters the spokes regime, which can be monitored by oscillations in the IV characteristics in the MHz range that are picked up by the used VI probes. These oscillations are correlated with the spokes phenomenon and are explained as an amplification of the Hall current inside the spokes as hot ionization zones. To explain the presence of energetic ions, we propose a double layer (DL) confining the hot plasma inside a spoke: if an atom becomes ionized inside the spokes region it is accelerated because of the DL to higher energies whereas its energy remains unchanged if it is ionized outside. In applying this DL model to our measurements the observed phenomena as well as several measurements from other groups can be explained. Only if spokes and a DL are present can the confined particles gain enough energy to leave the magnetic trap. We conclude from our findings that the spoke phenomenon represents the essence of HiPIMS plasmas, explaining their good performance for material synthesis applications.
    view abstractdoi: 10.1088/0022-3727/47/22/224002
  • 2014 • 74 Composition-Dependent Oxygen Reduction Activity and Stability of Pt-Cu Thin Films
    Schuppert, A.K. and Topalov, A.A. and Savan, A. and Ludwig, Al. and Mayrhofer, K.J.J.
    ChemElectroChem 1 358-361 (2014)
    Catalyst considerations: Pt-Cu alloys are prepared as a thin-film material library with a composition gradient. By using a scanning flow cell coupled to on-line mass spectrometry, this library can be screened over to measure the activity towards the oxygen reduction reaction as well as the time-resolved dissolution of both alloy components in parallel. This results in comprehensive insights into the composition-dependent performance of the Pt-Cu system. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/celc.201300078
  • 2014 • 73 A H2 very high frequency capacitively coupled plasma inactivates glyceraldehyde 3-phosphate dehydrogenase(GapDH) more efficiently than UV photons and heat combined
    Stapelmann, K. and Lackmann, J.-W. and Buerger, I. and Bandow, J.E. and Awakowicz, P.
    Journal of Physics D: Applied Physics 47 (2014)
    Plasma sterilization is a promising alternative to commonly used sterilization techniques, because the conventional methods suffer from certain limitations, e.g. incompatibility with heat-sensitive materials, or use of toxic agents. However, plasma-based sterilization mechanisms are not fully understood yet. A low-pressure very high frequency capacitively coupled plasma is used to investigate the impact of a hydrogen discharge on the protein glyceraldehyde 3-phosphate dehydrogenase (GapDH). GapDH is an enzyme of glycolysis. As a part of the central metabolism, it occurs in nearly all organisms from bacteria to humans. The plasma is investigated with absolutely calibrated optical emission spectroscopy in order to identify and to quantify plasma components that can contribute to enzyme inactivation. The contribution of UV photons and heat to GapDH inactivation is investigated separately, and neither seems to be a major factor. In order to investigate the mechanisms of GapDH inactivation by the hydrogen discharge, samples are investigated for etching, induction of amino acid backbone breaks, and chemical modifications. While neither etching nor strand breaks are observed, chemical modifications occur at different amino acid residues of GapDH. Deamidations of asparagines as well as methionine and cysteine oxidations are detected after VHF-CCP treatment. In particular, oxidation of the cysteine in the active centre is known to lead to GapDH inactivation. © 2014 IOP Publishing Ltd.
    view abstractdoi: 10.1088/0022-3727/47/8/085402
  • 2014 • 72 Thermokinetic investigation of binary Cu/Zn hydroxycarbonates as precursors for Cu/ZnO catalysts
    Tarasov, A. and Schumann, J. and Girgsdies, F. and Thomas, N. and Behrens, M.
    Thermochimica Acta 591 1-9 (2014)
    A combination of thermogravimetric analysis (TG) and differential scanning calorimetry (DSC) coupled to mass spectrometry has been applied to study the thermal decomposition of Cu/Zn hydroxycarbonates, which are used as a precursor for the active methanol synthesis catalyst. Original TG and DSC profiles and results of a formal kinetic analysis of the calcination process are compared with transformations occurring in the solid phase, which has been studied by means of in situ XRD. A series of hydroxycarbonate precursors with different Cu/Zn molar ratios (40/60, 70/30, 80/20) were synthesized under conditions reported as optimum for catalytic performance. The samples contain primarily two crystalline phases, aurichalcite (Cu,Zn)5(CO3) 2(OH)6 and zincian malachite (Cu,Zn)2CO 3(OH)2. At least four formal decomposition stages of CO2 and H2O evolution cause the major mass loss in the TG experiments. The best-fit quality for all the studied samples was obtained for a four-step competitive reaction model. The experimental TG dependences are adequately described by the n-th order equation and 3D Jander diffusion equation. The effects of the gas flow, sample mass, and water transfer conditions on the reaction pathway were studied. The presence of H2O vapor in the reaction feed accelerates the decomposition and dramatically changes the reaction TG profile. The decomposition enthalpy of mixed Cu/Zn (80/20) hydroxycarbonate was determined, and the formation enthalpy of the decomposition intermediate, a carbonate-modified oxide, was calculated to be ΔHf° = -633.7 ± 5.6 kJ/mol. © 2014 Elsevier B.V. All rights reserved.
    view abstractdoi: 10.1016/j.tca.2014.04.025
  • 2014 • 71 Catch me if you can: Challenges and applications of cross-linking approaches
    Tinnefeld, V. and Sickmann, A. and Ahrends, R.
    European Journal of Mass Spectrometry 20 99-116 (2014)
    Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications. © 2014 IM Publications LLP.
    view abstractdoi: 10.1255/ejms.1259
  • 2014 • 70 Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
    Vaudel, M. and Sickmann, A. and Martens, L.
    Biochimica et Biophysica Acta - Proteins and Proteomics 1844 12-20 (2014)
    With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways. In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the post-processing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. © 2013 Elsevier B.V. All rights reserved.
    view abstractdoi: 10.1016/j.bbapap.2013.06.019
  • 2014 • 69 Proteomics - moving from inventory to personalized medicine?
    Zahedi, R.P. and Ueffing, M. and Sickmann, A.
    Proteomics 14 1953 (2014)
    doi: 10.1002/pmic.201470133
  • 2013 • 68 Dynamic of the growth flux at the substrate during high-power pulsed magnetron sputtering (HiPIMS) of titanium
    Breilmann, W. and Maszl, C. and Benedikt, J. and von Keudell, A.
    Journal of Physics D-applied Physics 46 485204 (2013)
    The temporal distribution of the incident fluxes of argon and titanium ions on the substrate during an argon HiPIMS pulse to sputter titanium with pulse lengths between 50 to 400 mu s and peak powers up to 6 kW are measured by energy-resolved ion mass spectrometry with a temporal resolution of 2 mu s. The data are correlated with time-resolved growth rates and with phase-resolved optical emission spectra. Four ion contributions impinging on the substrate at different times and energies are identified: (i) an initial argon ion burst after ignition, (ii) a titanium and argon ion flux in phase with the plasma current due to ionized neutrals in front of the target, (iii) a small energetic burst of ions after plasma shut off, and (iv) cold ions impinging on the substrate in the late afterglow showing a pronounced maximum in current. The last contribution originates from ions generated during the plasma current maximum at 50 mu s after ignition in the magnetic trap in front of the target. They require long transport times of a few 100 mu s to reach the substrate. All energy distributions can be very well fitted with a shifted Maxwellian indicating an efficient thermalization of the energetic species on their travel from target to substrate. The energy of titanium is higher than that of argon, because they originate from energetic neutrals of the sputter process. The determination of the temporal sequence of species, energies and fluxes in HiPIMS may lead to design rules for the targeted generation of these discharges and for synchronized biasing concepts to further improve the capabilities of high-power impulse magnetron sputtering (HiPIMS) processes.
    view abstractdoi: 10.1088/0022-3727/46/48/485204
  • 2013 • 67 Adenylylation, MS, and proteomics-Introducing a "new" modification to bottom-up proteomics
    Hansen, T. and Albers, M. and Hedberg, C. and Sickmann, A.
    Proteomics 13 955-963 (2013)
    Although the addition of a 5′-adenosine phosphodiester group to proteins, called adenylylation, has been known for decades, the possibility that adenylylation could be a molecular switch in cellular signaling pathways has emerged recently. The distinct mass shift upon adenylation of threonine or tyrosine residues renders it a good target for MS detection and identification; however, the fragmentation of adenylylated peptides derived from proteolytic digestion of adenylylated proteins has not yet been systematically investigated. Here, we demonstrate that adenylylated peptides show loss of parts of the adenosine monophosphate (AMP) upon different fragmentation techniques. As expected, causing the least fragmentation of the AMP group, electron transfer dissociation yields less complicated spectra. In contrast, CID and higher energy collision (HCD) fragmentation caused AMP to fragment, generating characteristic ions that could be utilized in the specific identification of adenylylated peptides. The characteristic ions and losses upon CID and higher energy collision fragmentation from the AMP group turned out to be highly dependent on which amino acid was adenylylated, with different reporter ions for adenylylated threonine and tyrosine. We also investigated how adenylylation is best incorporated into search engines, exemplified by Mascot and showed that it is possible to identify adenylylation by search engines. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201200344
  • 2013 • 66 Measurement of the silver ion concentration in wound fluids after implantation of silver-coated megaprostheses: Correlation with the clinical outcome
    Hussmann, B. and Johann, I. and Kauther, M.D. and Landgraeber, S. and Jäger, M. and Lendemans, S.
    BioMed Research International 2013 (2013)
    Background. Tumor patients and patients after traumas are endangered by a reduced immune defense, and a silver coating on their megaprostheses may reduce their risks of infection. The aim of this study was to determine the silver ion concentration directly measured from the periprosthetic tissue and the influence on the clinical outcome. Material and Methods. Silver ions were evaluated in 5 mL wound fluids two days postoperatively and in blood patients 7 and 14 days after surgery using inductively coupled plasma emission spectrometry in 18 patients who underwent total joint replacement with a silver-coated megaendoprosthesis. Results. The concentration of silver ions averaged 0.08 parts per million. Patients who showed an increased silver concentration in the blood postoperatively presented a lower silver concentration in the wound fluids and a delayed decrease in C-reactive protein levels. There were significantly fewer reinfections and shorter hospitalization in comparison with a group that did not receive a silver-coated megaprosthesis. Conclusion. An increased concentration of silver in the immediate surroundings of silver-coated prostheses was demonstrated for the first time in cohorts of patients with trauma or tumors. An elevated concentration of silver ions in the direct periprosthetic tissue may have reduced the infection rate. © 2013 B. Hussmann et al.
    view abstractdoi: 10.1155/2013/763096
  • 2013 • 65 Developmental changes of the protein repertoire in the rat auditory brainstem: A comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ
    Kaltwaßer, B. and Schulenborg, T. and Beck, F. and Klotz, M. and Schäfer, K.-H. and Schmitt, M. and Sickmann, A. and Friauf, E.
    Journal of Proteomics 79 43-59 (2013)
    Protein profiles of developing neural circuits undergo manifold changes. The aim of this proteomic analysis was to quantify postnatal changes in two auditory brainstem areas in a comparative approach. Protein samples from the inferior colliculus (IC) and the superior olivary complex (SOC) were obtained from neonatal (P4) and young adult (P60) rats. The cytosolic fractions of both areas were examined by 2-D DIGE, and the plasma membrane-enriched fraction of the IC was analyzed via iTRAQ. iTRAQ showed a regulation in 34% of the quantified proteins. DIGE revealed 12% regulated spots in both the SOC and IC and, thus, numeric congruency. Although regulation in KEGG pathways displayed a similar pattern in both areas, only 13 of 71 regulated DIGE proteins were regulated in common, implying major area-specific differences. 89% of regulated glycolysis/gluconeogenesis and citrate cycle proteins were up-regulated in the SOC or IC, suggesting a higher energy demand in adulthood. Seventeen cytoskeleton proteins were regulated, consistent with complex morphological reorganization between P4 and P60. Fourteen were uniquely regulated in the SOC, providing further evidence for area-specific differences. Altogether, we provide the first elaborate catalog of proteins involved in auditory brainstem development, several of them possibly of particular developmental relevance. © 2012 Elsevier B.V.
    view abstractdoi: 10.1016/j.jprot.2012.11.018
  • 2013 • 64 Flame chemistry of tetrahydropyran as a model heteroatomic biofuel
    Labbe, N.J. and Seshadri, V. and Kasper, T. and Hansen, N. and Oßwald, P. and Westmoreland, P.R.
    Proceedings of the Combustion Institute 34 259-267 (2013)
    The flame chemistry of tetrahydropyran (THP), a cyclic ether, has been examined using vacuum-ultraviolet (VUV)-photoionization molecular-beam mass spectrometry (PI-MBMS) and flame modeling, motivated by the need to understand and predict the combustion of oxygen-containing, biomass-derived fuels. Species identifications and mole-fraction profiles are presented for a fuel-rich (U = 1.75), laminar premixed THP-oxygen-argon flame at 2.66 kPa (20.0 Torr). Flame species with up to six heavy atoms have been detected. A detailed reaction set was developed for THP combustion that captures relevant features of the THP flame quite well, allowing analysis of the dominant kinetic pathways for THP combustion. Necessary rate coefficients and transport parameters were calculated or were estimated by analogies with a recent reaction set [Li et al., Combust. Flame 158 (2011) 2077-2089], and necessary thermochemical properties were computed using the CBS-QB3 method. Our results show that under the low-pressure conditions, THP destruction is dominated by H-abstraction, and the three resulting THP-yl radicals decompose primarily by b-scissions to two- and four-heavy-atom species that are generally destroyed by b-scission, abstraction, or oxidation. © 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
    view abstractdoi: 10.1016/j.proci.2012.07.027
  • 2013 • 63 The formation of zeolites from solution - Analysis by mass spectrometry
    Lim, I.H. and Schrader, W. and Schüth, F.
    Microporous and Mesoporous Materials 166 20-36 (2013)
    Speciation of silicate in solution has been studied for a long time, but due to the complexity of such solutions, many questions are still open. A correlated problem, the mechanism of zeolite nucleation, remains one of the most challenging problems in zeolitic science. This is partly attributed to analytical limitations, which prevents the analysis of the crucial species involved in the process. Electrospray ionisation mass spectrometry (ESI-MS) has been successfully employed to monitor silicate speciation in prenucleating and nucleation zeolitic solutions. In this review, we present the application of mass spectrometry in studying zeolite formation. Discussion will include instrumentation, structural analysis by tandem mass spectrometry (MS/MS), dynamics of silicate species, heteroelement incorporation, and the study of nucleating solutions. © 2012 Elsevier Inc. All rights reserved.
    view abstractdoi: 10.1016/j.micromeso.2012.04.059
  • 2013 • 62 Phosphoproteomics-More than meets the eye
    Loroch, S. and Dickhut, C. and Zahedi, R.P. and Sickmann, A.
    Electrophoresis 34 1483-1492 (2013)
    PTMs enable cells to adapt to internal and external stimuli in the milliseconds to seconds time regime. Protein phosphorylation is probably the most important of these modifications as it affects protein structure and interactions, critically influencing the life cycle of a cell. In the last 15 years, new insights into phosphorylation have been provided by highly sensitive MS-based approaches combined with specific phosphopeptide enrichment strategies. Although so far research has mainly focused on the discovery and characterization of O-phosphorylation, this review also briefly outlines the current knowledge about N-phosphorylation depicting its ubiquitous relevance. Further, common pitfalls in sample preparation, LC-MS analysis, and subsequent data analysis are discussed as well as issues regarding quality and comparability of studies on protein phosphorylation. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/elps.201200710
  • 2013 • 61 Method and platform standardization in MRM-based quantitative plasma proteomics
    Percy, A.J. and Chambers, A.G. and Yang, J. and Jackson, A.M. and Domanski, D. and Burkhart, J. and Sickmann, A. and Borchers, C.H.
    Journal of Proteomics 95 66-76 (2013)
    There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. Biological significance: The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. © 2013 Elsevier B.V.
    view abstractdoi: 10.1016/j.jprot.2013.07.026
  • 2013 • 60 Interaction of proteins identified in human thyroid cells
    Pietsch, J. and Riwaldt, S. and Bauer, J. and Sickmann, A. and Weber, G. and Grosse, J. and Infanger, M. and Eilles, C. and Grimm, D.
    International Journal of Molecular Sciences 14 1164-1178 (2013)
    Influence of gravity forces on the regulation of protein expression by healthy and malignant thyroid cells was studied with the aim to identify protein interactions. Western blot analyses of a limited number of proteins suggested a time-dependent regulation of protein expression by simulated microgravity. After applying free flow isoelectric focusing and mass spectrometry to search for differently expressed proteins by thyroid cells exposed to simulated microgravity for three days, a considerable number of candidates for gravi-sensitive proteins were detected. In order to show how proteins sensitive to microgravity could directly influence other proteins, we investigated all polypeptide chains identified with Mascot scores above 100, looking for groups of interacting proteins. Hence, UniProtKB entry numbers of all detected proteins were entered into the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and processed. The program indicated that we had detected various groups of interacting proteins in each of the three cell lines studied. The major groups of interacting proteins play a role in pathways of carbohydrate and protein metabolism, regulation of cell growth and cell membrane structuring. Analyzing these groups, networks of interaction could be established which show how a punctual influence of simulated microgravity may propagate via various members of interaction chains. © 2013 by the authors; licensee MDPI, Basel, Switzerland.
    view abstractdoi: 10.3390/ijms14011164
  • 2013 • 59 Cytomegalovirus Downregulates IRE1 to Repress the Unfolded Protein Response
    Stahl, S. and Burkhart, J.M. and Hinte, F. and Tirosh, B. and Mohr, H. and Zahedi, R.P. and Sickmann, A. and Ruzsics, Z. and Budt, M. and Brune, W.
    PLoS Pathogens 9 (2013)
    During viral infection, a massive demand for viral glycoproteins can overwhelm the capacity of the protein folding and quality control machinery, leading to an accumulation of unfolded proteins in the endoplasmic reticulum (ER). To restore ER homeostasis, cells initiate the unfolded protein response (UPR) by activating three ER-to-nucleus signaling pathways, of which the inositol-requiring enzyme 1 (IRE1)-dependent pathway is the most conserved. To reduce ER stress, the UPR decreases protein synthesis, increases degradation of unfolded proteins, and upregulates chaperone expression to enhance protein folding. Cytomegaloviruses, as other viral pathogens, modulate the UPR to their own advantage. However, the molecular mechanisms and the viral proteins responsible for UPR modulation remained to be identified. In this study, we investigated the modulation of IRE1 signaling by murine cytomegalovirus (MCMV) and found that IRE1-mediated mRNA splicing and expression of the X-box binding protein 1 (XBP1) is repressed in infected cells. By affinity purification, we identified the viral M50 protein as an IRE1-interacting protein. M50 expression in transfected or MCMV-infected cells induced a substantial downregulation of IRE1 protein levels. The N-terminal conserved region of M50 was found to be required for interaction with and downregulation of IRE1. Moreover, UL50, the human cytomegalovirus (HCMV) homolog of M50, affected IRE1 in the same way. Thus we concluded that IRE1 downregulation represents a previously undescribed viral strategy to curb the UPR. © 2013 Stahl et al.
    view abstractdoi: 10.1371/journal.ppat.1003544
  • 2013 • 58 Phosphorylation of CalDAG-GEFI by protein kinase A prevents Rap1b activation
    Subramanian, H. and Zahedi, R.P. and Sickmann, A. and Walter, U. and Gambaryan, S.
    Journal of Thrombosis and Haemostasis 11 1574-1582 (2013)
    Background: Signaling via protein kinase A (PKA) and protein kinase G (PKG) is critical for maintaining platelets in the resting state. Both kinases down-regulate the activity of the small GTPase Rap1b, a critical signaling switch for integrin activation and platelet aggregation. However, the mechanism of Rap1b regulation by PKA and PKG is largely unknown. Objective: To identify the PKA phosphorylation sites in calcium and diacylglycerol-regulated guanine nucleotide exchange factor I (CalDAG-GEFI), the main GEF for Rap1b in platelets, and the effect of CalDAG-GEFI phosphorylation in Rap1b activation. Methods: The phosphorylation sites in CalDAG-GEFI were identified by radio-active phosphate incorporation assay and mass spectrometry. Phospho-antibody was developed to detect CalDAG-GEFI phosphorylation in Western blots. Rap1b activation was detected by Rap1-GTP pull-down assay. Results: S587 was identified as the major PKA phosphorylation site in CalDAG-GEFI, while S116/117 was weakly phosphorylated. Phosphorylation of S587 correlated with the inhibitory effect of PKA on Rap1b activation in platelets. In HEK293 cells, expression of a phospho-mimetic mutant of CalDAG-GEFI (S587D) abolished agonist-induced Rap1b activation. Mutation of S587 to alanine partially reversed the inhibitory effect of PKA signaling on Rap1b activation, while mutation of S116, S117 and S587 to alanine completely abolished the inhibitory effect of PKA on Rap1b activation. Conclusion: Our study strongly suggests that phosphorylation of CalDAG-GEFI is a critical mechanism by which PKA controls Rap1b-dependent platelet aggregation. © 2013 International Society on Thrombosis and Haemostasis.
    view abstractdoi: 10.1111/jth.12271
  • 2013 • 57 Buoyancy induced limits for nanoparticle synthesis experiments in horizontal premixed low-pressure flat-flame reactors
    Weise, C. and Faccinetto, A. and Kluge, S. and Kasper, T. and Wiggers, H. and Schulz, C. and Wlokas, I. and Kempf, A.
    Combustion Theory and Modelling 17 504-521 (2013)
    Premixed low-pressure flat-flame reactors can be used to investigate the synthesis of nanoparticles. The present work examines the flow field inside such a reactor during the formation of carbon (soot) and iron oxide (from Fe(CO)5) nanoparticles, and how it affects the measurements of nanoparticle size distribution. The symmetry of the flow and the impact of buoyancy were analysed by three-dimensional simulations and the nanoparticle size distribution was obtained by particle mass spectrometry (PMS) via molecular beam sampling at different distances from the burner. The PMS measurements showed a striking, sudden increase in particle size at a critical distance from the burner, which could be explained by the flow field predicted in the simulations. The simulation results illustrate different fluid mechanical phenomena which have caused this sudden rise in the measured particle growth. Up to the critical distance, buoyancy does not affect the flow, and an (almost) linear growth is observed in the PMS experiments. Downstream of this critical distance, buoyancy deflects the hot gas stream and leads to an asymmetric flow field with strong recirculation. These recirculation zones increase the particle residence time, inducing very large particle sizes as measured by PMS. This deviation from the assumed symmetric, one-dimensional flow field prevents the correct interpretation of the PMS results. To overcome this problem, modifications to the reactor were investigated; their suitability to reduce the flow asymmetry was analysed. Furthermore, 'safe' operating conditions were identified for which accurate measurements are feasible in premixed low-pressure flat-flame reactors that are transferrable to other experiments in this type of reactor. The present work supports experimentalists to find the best setup and operating conditions for their purpose. © 2013 Copyright Taylor and Francis Group, LLC.
    view abstractdoi: 10.1080/13647830.2013.781224
  • 2013 • 56 Mechanism of iron oxide formation from iron pentacarbonyl-doped low-pressure hydrogen/oxygen flames
    Wlokas, I. and Faccinetto, A. and Tribalet, B. and Schulz, C. and Kempf, A.
    International Journal of Chemical Kinetics 45 487-498 (2013)
    A chemical reaction mechanism was developed for the formation of iron oxide (Fe2O3) from iron pentacarbonyl (Fe(CO)5) in a low-pressure hydrogen-oxygen flame reactor. In this paper, we describe an extensive approach for the flame-precursor chemistry and the development of a novel model for the formation of Fe2O3 from the gas phase. The detailed reaction mechanism is reduced for the implementation in two-dimensional, reacting flow simulations. The comprehensive simulation approach is completed by a model for the formation and growth of the iron oxide nanoparticles. The exhaustive and compact reaction mechanism is validated using experimental data from iron-atom laser-induced fluorescence imaging. The particle formation and growth model are verified with new measurements from particle mass spectrometry. © 2013 Wiley Periodicals, Inc.
    view abstractdoi: 10.1002/kin.20786
  • 2013 • 55 Analysis of Post-translational Modifications
    Zahedi, R. and Sickmann, A.
    Proteomics 13 901-903 (2013)
    doi: 10.1002/pmic.201370054
  • 2012 • 54 Chemical vapor functionalization: A continuous production process for functionalized ZnO nanoparticles
    Ali, M. and Donakowski, M.D. and Mayer, C. and Winterer, M.
    Journal of Nanoparticle Research 14 (2012)
    The continuous functionalization of nanoparticles in the gas-phase directly after their generation, chemical vapor functionalization, is studied with ZnO and 1-hexanol as a model system using two reactors in series. In the first reactor ZnO nanoparticles are synthesized in the gas-phase from diethylzinc and oxygen at 1,073 K with grain sizes of 13 nm as determined by Rietveld refinement of X-ray diffractograms. The second reactor, connected at the exit of the first reactor and kept at lower temperatures (573, 673, and 773 K), is used as a functionalization chamber. At the connection point of the two reactors, the vapor of 1-hexanol is injected to react with the surface of ZnO nanoparticles in the gas phase. The process has been analyzed by quadrupole mass spectrometry to obtain information about optimal conditions for functionalization. Dynamic light scattering data show that the functionalized particles have substantially improved colloidal dispersibility with hydrodynamic diameters of 60 nm. Diffuse reflectance fourier transform infrared spectra and 1H nuclear magnetic resonance spectra are consistent with 1-hexanol adsorbed at the particle surface acting as a functionalizing agent. The agglomerate size is substantially reduced owing to chemical vapor functionalization. © Springer Science+Business Media B.V. 2012.
    view abstractdoi: 10.1007/s11051-011-0689-0
  • 2012 • 53 Intestinal aspartate proteases TiCatD and TiCatD2 of the haematophagous bug Triatoma infestans (Reduviidae): Sequence characterisation, expression pattern and characterisation of proteolytic activity
    Balczun, C. and Siemanowski, J. and Pausch, J.K. and Helling, S. and Marcus, K. and Stephan, C. and Meyer, H.E. and Schneider, T. and Cizmowski, C. and Oldenburg, M. and Höhn, S. and Meiser, C.K. and Schuhmann, W. and Schaub, G.A.
    Insect Biochemistry and Molecular Biology 42 240-250 (2012)
    Two aspartate protease encoding complementary deoxyribonucleic acids (cDNA) were characterised from the small intestine (posterior midgut) of Triatoma infestans and the corresponding genes were named TiCatD and TiCatD2. The deduced 390 and 393 amino acid sequences of both enzymes contain two regions characteristic for cathepsin D proteases and the conserved catalytic aspartate residues forming the catalytic dyad, but only TiCatD2 possesses an entire C-terminal proline loop. The amino acid sequences of TiCatD and TiCatD2 show 51-58% similarity to other insect cathepsin D-like proteases and, respectively, 88 and 58% similarity to the aspartate protease ASP25 from T. infestans available in the GenBank database. In phylogenetic analysis, TiCatD and ASP25 clearly separate from cathepsin D-like sequences of other insects, TiCatD2 groups with cathepsin D-like proteases with proline loop. The activity of purified TiCatD and TiCatD2 was highest between pH 2 and 4, respectively, and hence, deviate from the pH values of the lumen of the small intestine, which varied in correlation with the time after feeding between pH 5.2 and 6.7 as determined by means of micro pH electrodes. Both cathepsins, TiCatD and TiCatD2, were purified from the lumen of the small intestine using pepstatin affinity chromatography and identified by nanoLC-ESI-MS/MS analysis as those encoded by the cDNAs. The proteolytic activity of the purified enzymes is highest at pH 3 and the respective genes are expressed in the both regions of the midgut, stomach (anterior midgut) and small intestine, not in the rectum, salivary glands, Malpighian tubules or haemocytes. The temporal expression pattern of both genes in the small intestine after feeding revealed a feeding dependent regulation for TiCatD but not for TiCatD2. © 2011 Elsevier Ltd.
    view abstractdoi: 10.1016/j.ibmb.2011.12.006
  • 2012 • 52 Quadrupole mass spectrometry of reactive plasmas
    Benedikt, J. and Hecimovic, A. and Ellerweg, D. and von Keudell, A.
    Journal of Physics D-applied Physics 45 403001 (2012)
    Reactive plasmas are highly valued for their ability to produce large amounts of reactive radicals and of energetic ions bombarding surrounding surfaces. The non-equilibrium electron driven plasma chemistry is utilized in many applications such as anisotropic etching or deposition of thin films of high-quality materials with unique properties. However, the non-equilibrium character and the high power densities make plasmas very complex and hard to understand. Mass spectrometry (MS) is a very versatile diagnostic method, which has, therefore, a prominent role in the characterization of reactive plasmas. It can access almost all plasma generated species: stable gas-phase products, reactive radicals, positive and negative ions or even internally excited species such as metastables. It can provide absolute densities of neutral particles or energy distribution functions of energetic ions. In particular, plasmas with a rich chemistry, such as hydrocarbon plasmas, could not be understood without MS. This review focuses on quadrupole MS with an electron impact ionization ion source as the most common MS technique applied in plasma analysis. Necessary information for the understanding of this diagnostic and its application and for the proper design and calibration procedure of an MS diagnostic system for quantitative plasma analysis is provided. Important differences between measurements of neutral particles and energetic ions and between the analysis of low pressure and atmospheric pressure plasmas are described and discussed in detail. Moreover, MS-measured ion energy distribution functions in different discharges are discussed and the ability of MS to analyse these distribution functions with time resolution of several microseconds is presented.
    view abstractdoi: 10.1088/0022-3727/45/40/403001
  • 2012 • 51 Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics
    Burkhart, J.M. and Schumbrutzki, C. and Wortelkamp, S. and Sickmann, A. and Zahedi, R.P.
    Journal of Proteomics 75 1454-1462 (2012)
    Trypsin is the most frequently used proteolytic enzyme in mass spectrometry-based proteomics. Beside its good availability, it also offers some major advantages such as an optimal average peptide length of ~. 14 amino acids, and typically the presence of at least two defined positive charges at the N-terminus as well as the C-terminal Arg/Lys, rendering tryptic peptides well suited for CID-based LC-MS/MS. Here, we conducted a systematic study of different types of commercially available trypsin in order to qualitatively and quantitatively compare cleavage specificity, efficiency as well as reproducibility and the potential impact on quantitation and proteome coverage. We present a straightforward strategy applied to complex digests of human platelets, comprising (1) digest controls using a monolithic column HPLC-setup, (2) SCX enrichment of semitryptic/nonspecific peptides, (3) targeted MRM analysis of corresponding full cleavage/missed cleavage peptide pairs as well as (4) LC-MS analyses of complete digests with a three-step data interpretation. Thus, differences in digest performance can be readily assessed, rendering these procedures extremely beneficial to quality control not only the trypsin of choice, but also to effectively compare as well as optimize different digestion conditions and to evaluate the reproducibility of a dedicated digest protocol for all kinds of quantitative proteome studies. © 2011 Elsevier B.V.
    view abstractdoi: 10.1016/j.jprot.2011.11.016
  • 2012 • 50 Unexpected O and O-3 production in the effluent of He/O-2 microplasma jets emanating into ambient air
    Ellerweg, D. and von Keudell, A. and Benedikt, J.
    Plasma Sources Science & Technology 21 034019 (2012)
    Microplasma jets are commonly used to treat samples in ambient air. The effect of admixing air into the effluent may severely affect the composition of the emerging species. Here, the effluent of a He/O-2 microplasma jet has been analyzed in a helium and in an air atmosphere by molecular beam mass spectrometry. First, the composition of the effluent in air was recorded as a function of the distance to determine how fast air admixes into the effluent. Then, the spatial distribution of atomic oxygen and ozone in the effluent was recorded in ambient air and compared with measurements in a helium atmosphere. Additionally, a fluid model of the gas flow with reaction kinetics of reactive oxygen species in the effluent was constructed. In ambient air, the O density declines only slightly faster with distance compared with a helium atmosphere. In contrast, the O-3 density in ambient air increases significantly faster with distance compared with a helium atmosphere. This unexpected behavior cannot be explained by simple recombination reactions of O atoms with O-2 molecules. A reaction scheme involving the reaction of plasma-produced excited O-2* species of unknown identity with ground state O-2 molecules is proposed as a possible explanation for these observations.
    view abstractdoi: 10.1088/0963-0252/21/3/034019
  • 2012 • 49 Direct experimental observation of the aggregation of α-amino acids into 100-200 nm clusters in aqueous solution
    Hagmeyer, D. and Ruesing, J. and Fenske, T. and Klein, H.-W. and Schmuck, C. and Schrader, W. and Piedade, M.E.M.D. and Epple, M.
    RSC Advances 2 4690-4696 (2012)
    Spherical supramolecular aggregates of α-amino acids with a typical diameter of 100-200 nm are formed spontaneously after dissolution in water at a concentration of a few mM, i.e. well below the solubility limit. Their presence was shown by nanoparticle tracking analysis (NTA), atomic force microscopy (AFM), and ESI mass spectrometry (ESI-MS). There is a dynamic equilibrium between the aggregates and dissolved individual molecules which allows them to penetrate through dialysis membranes and filters. The same phenomenon was observed for para-amino salicylic acid and two dipeptides. Thermodynamic considerations suggest an entropy-controlled process. © 2012 The Royal Society of Chemistry.
    view abstractdoi: 10.1039/c2ra01352e
  • 2012 • 48 Proteomic and metabolomic analyses of mitochondrial complex I-deficient mouse model generated by spontaneous B2 short interspersed nuclear element (SINE) insertion into NADH dehydrogenase (ubiquinone) Fe-S protein 4 (Ndufs4) gene
    Leong, D.W. and Komen, J.C. and Hewitt, C.A. and Arnaud, E. and McKenzie, M. and Phipson, B. and Bahlo, M. and Laskowski, A. and Kinkel, S.A. and Davey, G.M. and Heath, W.R. and Voss, A.K. and Zahedi, R.P. and Pitt, J.J. and Chras...
    Journal of Biological Chemistry 287 20652-20663 (2012)
    Eukaryotic cells generate energy in the form of ATP, through a network of mitochondrial complexes and electron carriers known as the oxidative phosphorylation system. In mammals, mitochondrial complex I (CI) is the largest component of this system, comprising 45 different subunits encoded by mitochondrial and nuclear DNA. Humans diagnosed with mutations in the gene NDUFS4, encoding a nuclear DNA-encoded subunit of CI (NADH dehydrogenase ubiquinone Fe-S protein 4), typically suffer from Leigh syndrome, a neurodegenerative disease with onset in infancy or early childhood. Mitochondria from NDUFS4 patients usually lack detectable NDUFS4 protein and show a CI stability/assembly defect. Here, we describe a recessive mouse phenotype caused by the insertion of a transposable element into Ndufs4, identified by a novel combined linkage and expression analysis. Designated Ndufs4fky, the mutation leads to aberrant transcript splicing and absence of NDUFS4 protein in all tissues tested of homozygous mice. Physical and behavioral symptoms displayed by Ndufs4fky/fkymice include temporary fur loss, growth retardation, unsteady gait, and abnormal body posture when suspended by the tail. Analysis of CI in Ndufs4fky/fky mice using blue native PAGE revealed the presence of a faster migrating crippled complex. This crippled CI was shown to lack subunits of the "Nassembly module", which contains the NADH binding site, but contained two assembly factors not present in intact CI. Metabolomic analysis of the blood by tandem mass spectrometry showed increased hydroxyacylcarnitine species, implying that the CI defect leads to an imbalanced NADH/ NAD+ ratio that inhibits mitochondrial fatty acid β-oxidation. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.
    view abstractdoi: 10.1074/jbc.M111.327601
  • 2012 • 47 Solvent-Free catalytic depolymerization of cellulose to water-soluble oligosaccharides
    Meine, N. and Rinaldi, R. and Schüth, F.
    ChemSusChem 5 1449-1454 (2012)
    The use of cellulose is hampered by difficulties with breaking up the biopolymer into soluble products. Herein, we show that the impregnation of cellulosic substrates with catalytic amounts of a strong acid (e.g., H 2SO 4, HCl) is a highly effective strategy for minimizing the contact problem commonly experienced in mechanically assisted, solid-state reactions. Milling the acid-impregnated cellulose fully converts the substrate into water-soluble oligosaccharides within 2a H. In aqueous solution, soluble products are easily hydrolyzed at 130°C in 1a H, leading to 91% conversion of the glucan fraction of α-cellulose into glucose, and 96% of the xylans into xylose. Minor products are glucose dimers (8%), 5-hydroxymethylfurfural (1%) and furfural (4%). Milling practical feedstocks (e.g., wood, sugarcane bagasse, and switchgrass) also results to water-soluble products (oligosaccharides and lignin fragments). The integrated approach (solid-state depolymerization in combination with liquid-phase hydrolysis) could well hold the key to a highly efficient "entry process" in biorefinery schemes. Reactive milling: Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/cssc.201100770
  • 2012 • 46 Sc 2O 3, Er 2O 3, and Y 2O 3 thin films by MOCVD from volatile guanidinate class of rare-earth precursors
    Milanov, A.P. and Xu, K. and Cwik, S. and Parala, H. and De Los Arcos, T. and Becker, H.-W. and Rogalla, D. and Cross, R. and Paul, S. and Devi, A.
    Dalton Transactions 41 13936-13947 (2012)
    Alternative novel precursor chemistries for the vapor phase deposition of rare-earth (RE) oxide thin films were developed by synthesising the homoleptic guanidinate compounds tris(N,N′-diisopropyl-2-dimethylamidoguanidinato)- scandium(iii) [Sc(DPDMG) 3] (1), tris(N,N′-diisopropyl-2- dimethylamidoguanidinato)-erbium(iii), [Er(DPDMG) 3] (2) and tris(N,N′-diisopropyl-2-dimethylamidoguanidinato)-yttrium(iii), [Y(DPDMG) 3] (3). All three compounds are monomeric as revealed by single crystal X-ray diffraction (XRD) analysis, nuclear magnetic resonance (NMR) and electron impact mass spectrometry (EI-MS). The thermal analysis revealed that the compounds are volatile and very stable under evaporation conditions. Therefore the complexes were evaluated as precursors for the growth of Sc 2O 3, Er 2O 3 and Y 2O 3 thin films, respectively, by metal-organic chemical vapor deposition (MOCVD). Uniform Sc 2O 3, Er 2O 3 and Y 2O 3 films on Si(100) substrates with reproducible quality were grown by MOCVD by the combination of the respective guanidinate precursors and oxygen in the temperature range 350-700 °C. The structural, morphological, compositional and electrical properties of the films were investigated in detail. The most relevant film properties are highlighted in relation to the distinct advantages of the novel precursor chemistries in comparison to the commonly used literature known RE precursors. This study shows that compounds 1-3 are very good precursors for MOCVD yielding Sc 2O 3, Er 2O 3 and Y 2O 3 thin films which are stoichiometric and display suitable electrical properties for their potential use as high dielectric constant (high-k) materials. © 2012 The Royal Society of Chemistry.
    view abstractdoi: 10.1039/c2dt31219k
  • 2012 • 45 N-glycoproteomics: Mass spectrometry-based glycosylation site annotation
    Pasing, Y. and Sickmann, A. and Lewandrowski, U.
    Biological Chemistry 393 249-258 (2012)
    Glycosylations are ubiquitous and, in many cases, essential protein modifications. Yet comprehensive and detailed analysis of glycosylations on a proteome-wide scale is a daunting and still unsolved challenge. However, a common workflow has emerged over the last decade for large-scale N-glycosylation site annotation by application of proteomic methodology. Thereby, the qualitative and quantitative assessment of hundreds or thousands of modification sites is enabled. This review presents a short overview about common enrichment techniques and glycosylation site detection for N-glycopeptides, including benefits and challenges of analysis. © 2012 by Walter de Gruyter · Berlin · Boston.
    view abstractdoi: 10.1515/hsz-2011-0245
  • 2012 • 44 Metabolic enzyme diversity in different human thyroid cell lines and their sensitivity to gravitational forces
    Pietsch, J. and Sickmann, A. and Weber, G. and Bauer, J. and Egli, M. and Wildgruber, R. and Infanger, M. and Grimm, D.
    Proteomics 12 2539-2546 (2012)
    Many cancer cells show unique protein expression patterns. We used proteome technology including MS, free flow isoelectric focusing and Western blotting to determine current concentrations of metabolic enzymes in healthy and malignant human thyroid cells. Three different types of human thyroid cells were investigated after they had been cultured under equal conditions. MS revealed high quantities of glycolytic enzymes and moderate quantities of citric acid cycle enzymes in malignant FTC-133 cells with abnormal LDH B-chains, high quantities of glycolytic enzymes and marginal quantities of citric acid cycle enzymes in normal HTU-5 cells, and low quantities of glycolytic enzymes and marginal quantities of citrate cycle enzymes in malignant CGTH-W1 cells with abnormal LDH A-chains. When an alteration of gene expression activity was challenged physically by removing gravity forces, the concentrations of various glycolytic enzymes were changed in normal and malignant thyroid cells. However, the changes varied among the different cell types. Different cellular alignment of the enzymes could be one reason for the cell type-specific behavior as demonstrated by histological analysis of alpha-enolase. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201200070
  • 2012 • 43 ITRAQ analysis of a cell culture model for malignant transformation, including comparison with 2D-PAGE and SILAC
    Pütz, S.M. and Boehm, A.M. and Stiewe, T. and Sickmann, A.
    Journal of Proteome Research 11 2140-2153 (2012)
    To study human cancer development, cell culture models for malignant transformation can be used. In 1999 Hahn and Coworkers introduced such a model system and established herewith a basis for research on human tumorigenesis. Primary human fibroblasts are sequentially transduced with defined genetic elements (hTERT, SV40 ER, and H-Ras V12), resulting in four defined cell lines, whereby the last has a fully transformed phenotype. In order to get a deeper insight into the molecular biology of human tumorigenesis, we compared the proteomes of these four cell lines following a multimethod concept. At the beginning we assumed SILAC and sample fractionation with COFRADIC is the method of choice to analyze the cell culture model for malignant transformation. Here, the compared samples are combined before sample preparation, thus avoiding differences in sample preparation, and using COFRADIC notably reduces sample complexity. Because 2D-PAGE is a standard method for the separation and visualization of closely related proteomes, we decided to analyze and compare the proteomes of these four cell lines in a first approach by differential 2D-PAGE. Surprisingly, we discovered much more unique results with iTRAQ and sample fractionation with SCX than with the combination of 2D-PAGE and SILAC-COFRADIC. Moreover, iTRAQ outperforms the other strategies not only in number of yielded results but also in analysis time. Here, we present the iTRAQ quantification results and compare them with the results of 2D-PAGE and SILAC-COFRADIC. We found changes in the protein level at each transition. Thereby, SV40 has the strongest impact on the proteome. In detail we identified 201 regulated proteins. Beside others, these proteins are involved in cytoskeleton, RNA processing, and cell cycle, such as CDC2, hnRNPs, snRNPs, collagens, and MCM proteins. For example, MCM proteins are up-regulated and collagens are down-regulated due to SV40 ER expression. Furthermore we made the observation that proteins containing the same domain have analogous regulation profiles during malignant transformation. For instance, several proteins containing a CH or LIM domain are down-regulated. Moreover, by this study and the defined cell culture model, changes could be clearly matched to specific steps during tumorigenesis. © 2012 American Chemical Society.
    view abstractdoi: 10.1021/pr200881c
  • 2012 • 42 The Role of Oxygen and Surface Reactions in the Deposition of Silicon Oxide like Films from HMDSO at Atmospheric Pressure
    Reuter, R. and Rugner, K. and Ellerweg, D. and de los Arcos, T. and von Keudell, A. and Benedikt, J.
    Plasma Processes and Polymers 9 1116--1124 (2012)
    The deposition of thin SiO2-like films by means of atmospheric pressure microplasma jets with admixture of hexamethyldisiloxane (HMDSO) and oxygen and the role of surface reactions in film growth are investigated. Two types of microplasma jets, one with a planar electrodes and operated in helium gas and the other one with a coaxial geometry operated in argon, are used to study the deposition process. The growth rate of the film and the carbon-content in the film are measured as a function of the O2 and HMDSO admixture in the planar jet and are compared to mass spectrometry measurements of the consumption of HMDSO. Additionally, the localized nature of the jetsubstrate interaction is utilized to study surface reactions by applying two jets on a rotating substrate. The addition of oxygen into the gas mixture increases HMDSO depletion and the growth rate and results in the deposition of carbon free films. The surface reaction is responsible for the carbon removal from the growing film. Moreover, carbon free films can be deposited even without addition of oxygen, when coaxial jet operated with argon is used for the surface treatment. We hypothesize that ions or excited species (metastables) could be responsible for the observed effect.
    view abstractdoi: 10.1002/ppap.201100146
  • 2012 • 41 Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells
    Sanges, C. and Scheuermann, C. and Zahedi, R.P. and Sickmann, A. and Lamberti, A. and Migliaccio, N. and Baljuls, A. and Marra, M. and Zappavigna, S. and Rapp, U. and Abbruzzese, A. and Caraglia, M. and Arcari, P.
    Cell Death and Disease 3 e276 (2012)
    We identified eukaryotic translation elongation factor 1A (eEF1A) Raf-mediated phosphorylation sites and defined their role in the regulation of eEF1A half-life and of apoptosis of human cancer cells. Mass spectrometry identified in vitro S21 and T88 as phosphorylation sites mediated by B-Raf but not C-Raf on eEF1A1 whereas S21 was phosphorylated on eEF1A2 by both B- and C-Raf. Interestingly, S21 belongs to the first eEF1A GTP/GDP-binding consensus sequence. Phosphorylation of S21 was strongly enhanced when both eEF1A isoforms were preincubated prior the assay with C-Raf, suggesting that the eEF1A isoforms can heterodimerize thus increasing the accessibility of S21 to the phosphate. Overexpression of eEF1A1 in COS 7 cells confirmed the phosphorylation of T88 also in vivo. Compared with wt, in COS 7 cells overexpressed phosphodeficient (A) and phospho-mimicking (D) mutants of eEF1A1 (S21A/D and T88A/D) and of eEF1A2 (S21A/D), resulted less stable and more rapidly proteasome degraded. Transfection of S21 A/D eEF1A mutants in H1355 cells increased apoptosis in comparison with the wt isoforms. It indicates that the blockage of S21 interferes with or even supports C-Raf induced apoptosis rather than cell survival. Raf-mediated regulation of this site could be a crucial mechanism involved in the functional switching of eEF1A between its role in protein biosynthesis and its participation in other cellular processes. © 2012 Macmillan Publishers Limited All rights reserved.
    view abstractdoi: 10.1038/cddis.2012.16
  • 2012 • 40 Human high temperature requirement serine protease A1 (HTRA1) degrades tau protein aggregates
    Tennstaedt, A. and Pöpsel, S. and Truebestein, L. and Hauske, P. and Brockmann, A. and Schmidt, N. and Irle, I. and Saccà, B. and Niemeyer, C.M. and Brandt, R. and Ksiezak-Reding, H. and Tirniceriu, A.L. and Egensperger, R. and ...
    Journal of Biological Chemistry 287 20931-20941 (2012)
    Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.
    view abstractdoi: 10.1074/jbc.M111.316232
  • 2012 • 39 Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)
    Vaudel, M. and Burkhart, J.M. and Radau, S. and Zahedi, R.P. and Martens, L. and Sickmann, A.
    Journal of Proteome Research 11 5072-5080 (2012)
    With the increasing popularity of comparative studies of complex proteomes, reporter ion-based quantification methods such as iTRAQ and TMT have become commonplace in biological studies. Their appeal derives from simple multiplexing and quantification of several samples at reasonable cost. This advantage yet comes with a known shortcoming: precursors of different species can interfere, thus reducing the quantification accuracy. Recently, two methods were brought to the community alleviating the amount of interference via novel experimental design. Before considering setting up a new workflow, tuning the system, optimizing identification and quantification rates, etc. one legitimately asks: is it really worth the effort, time and money? The question is actually not easy to answer since the interference is heavily sample and system dependent. Moreover, there was to date no method allowing the inline estimation of error rates for reporter quantification. We therefore introduce a method called iQuARI to compute false discovery rates for reporter ion based quantification experiments as easily as Target/Decoy FDR for identification. With it, the scientist can accurately estimate the amount of interference in his sample on his system and eventually consider removing shadows subsequently, a task for which reporter ion quantification might not be the solution of choice. © 2012 American Chemical Society.
    view abstractdoi: 10.1021/pr300247u
  • 2012 • 38 ITRAQ data interpretation
    Vaudel, M. and Burkhart, J.M. and Zahedi, R.P. and Martens, L. and Sickmann, A.
    Methods in Molecular Biology 893 501-509 (2012)
    Quantitative proteomic analysis can help elucidating unexplored biological questions; it, however, relies on highly reproducible experiments and reliable data processing. Among the existing strategies, iTRAQ is known as an easy to use method allowing relative comparison of up to eight multiplexed samples. Once the data is acquired it is important that the final protein quantification reflects the actual amounts in the samples. Data interpretation must thus be achieved with a constant focus on quality. Here, we describe a workflow for processing iTRAQ data in user-friendly environments with emphasis on quality control. © 2012 Springer Science+Business Media, LLC.
    view abstractdoi: 10.1007/978-1-61779-885-6_30
  • 2011 • 37 The good, the bad, the ugly: Validating the mass spectrometric analysis of modified peptides
    Beck, F. and Lewandrowski, U. and Wiltfang, M. and Feldmann, I. and Geiger, J. and Sickmann, A. and Zahedi, R.P.
    Proteomics 11 1099-1109 (2011)
    Mass spectrometric characterization of protein modifications is usually based on single peptides. With the advent of large-scale PTM-focussed MS studies, vast amounts of data are generated continuously, providing biologists extremely valuable and virtually never-ending sources for targeted functional research. However, even more than for proteomics in general, appropriate strategies for quality control of the different steps of the analytical strategy are imperative to prevent functional researchers from doing Sisyphos work on false-positive and unconfident PTM assignments. Here, we describe strategies to address the important issue of quality control for PTM analysis on various levels of the analytical pipeline: sample preparation/processing, analysis/identification and finally data interpretation, for qualitative as well as quantitative studies. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000562
  • 2011 • 36 Quality control of nano-LC-MS systems using stable isotope-coded peptides
    Burkhart, J.M. and Premsler, T. and Sickmann, A.
    Proteomics 11 1049-1057 (2011)
    In analytical sciences, there is a general need for quality control to assess whether a product or a process meets defined requirements. Especially in proteomics, which implies analysis of ten thousands of analytes within a complex mixture, quality control to validate LC-MS performance and method setup is inevitable to achieve day-to-day-, inter-system-, as well as inter-user reproducibility. Thus, results deriving from LC-MS analyses can be benchmarked and the need for system maintenance can be revealed. In particular with the advent of label-free quantification of peptides and proteins, which above all depends on highly stable and reproducible LC separations, HPLC performance has to be appropriately monitored throughout the entire analytical procedure to assure quality and validity of the obtained data. Oftentimes, proteolytic digests of standard proteins are used in this context; however, this approach implies some limitations, such as inadequate batch-to-batch reproducibility, limited (if any) dynamic range and compositional inflexibility. Here, we present an alternative strategy of nano-LC-MS/MS quality control based on a mixture of synthetic peptides covering the entire LC-gradient as well as a dynamic range of more than two orders of magnitude. Thus, (i) reproducibility of LC separation, (ii) MS performance (including limit of detection, identification and quantification), as well as (iii) overall nano-LC-MS system performance and reproducibility can be routinely monitored even in highly complex samples. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000604
  • 2011 • 35 Synthesis of active carbon-based catalysts by chemical vapor infiltration for nitrogen oxide conversion
    Busch, M. and Bergmann, U. and Sager, U. and Schmidt, W. and Schmidt, F. and Notthoff, C. and Atakan, B. and Winterer, M.
    Journal of Nanoscience and Nanotechnology 11 7956-7961 (2011)
    Direct reduction of nitrogen oxides is still a challenge. Strong efforts have been made in developing noble and transition metal catalysts on microporous support materials such as active carbons or zeolites. However, the required activation energy and low conversion rates still limit its break-through. Furthermore, infiltration of such microporous matrix materials is commonly performed by wet chemistry routes. Deep infiltration and homogeneous precursor distribution are often challenging due to precursor viscosity or electrostatic shielding and may be inhibited by pore clogging. Gas phase infiltration, as an alternative, can resolve viscosity issues and may contribute to homogeneous infiltration of precursors. In the present work new catalysts based on active carbon substrates were synthesized via chemical vapor infiltration. Iron oxide nano clusters were deposited in the microporous matrix material. Detailed investigation of produced catalysts included nitrogen oxide adsorption, X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Catalytic activity was studied in a recycle flow reactor by time-resolved mass spectrometry at a temperature of 423 K. The infiltrated active carbons showed very homogeneous deposition of iron oxide nano clusters in the range of below 12 to 19 nm, depending on the amount of infiltrated precursor. The specific surface area was not excessively reduced, nor was the pore size distribution changed compared to the original substrate. Catalytic nitrogen oxides conversion was detected at temperatures as low as 423 K. Copyright © 2011 American Scientific Publishers. All rights reserved.
    view abstractdoi: 10.1166/jnn.2011.5074
  • 2011 • 34 Thermo-msf-parser: An open source Java library to parse and visualize Thermo Proteome Discoverer msf files
    Colaert, N. and Barsnes, H. and Vaudel, M. and Helsens, K. and Timmerman, E. and Sickmann, A. and Gevaert, K. and Martens, L.
    Journal of Proteome Research 10 3840-3843 (2011)
    The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode. com. © 2011 American Chemical Society.
    view abstractdoi: 10.1021/pr2005154
  • 2011 • 33 An experimental and kinetic modeling study of methyl formate low-pressure flames
    Dooley, S. and Dryer, F.L. and Yang, B. and Wang, J. and Cool, T.A. and Kasper, T. and Hansen, N.
    Combustion and Flame 158 732-741 (2011)
    The oxidation of methyl formate (CH3OCHO), the simplest methyl ester, is studied in a series of burner-stabilized laminar flames at pressures of 22-30Torr and equivalence ratios (Φ) from 1.0 to 1.8 for flame conditions of 25-35% fuel. Flame structures are determined by quantitative measurements of species mole fractions with flame-sampling molecular-beam synchrotron photoionization mass spectrometry (PIMS). Methyl formate is observed to be converted to methanol, formaldehyde and methane as major intermediate species of mechanistic relevance. Smaller amounts of ethylene and acetylene are also formed from methyl formate oxidation. Reactant, product and major intermediate species profiles are in good agreement with the computations of a recently developed kinetic model for methyl formate oxidation [S. Dooley, M.P. Burke, M. Chaos, Y. Stein, F.L. Dryer, V.P. Zhukov, O. Finch, J.M. Simmie, H.J. Curran, Int. J. Chem. Kinet. 42 (2010) 527-529] which shows that hydrogen abstraction reactions dominate fuel consumption under the tested flame conditions. Radical-radical reactions are shown to be significant in the formation of a number of small concentration intermediates, including the production of ethyl formate (C2H5OCHO), the subsequent decomposition of which is the major source of observed ethylene concentrations. The good agreement of model computations with this set of experimental data provides a further test of the predictive capabilities of the proposed mechanism of methyl formate oxidation. Other salient issues in the development of this model are discussed, including recent controversy regarding the methyl formate decomposition mechanism, and uncertainties in the experimental measurement and modeling of low-pressure flame-sampling experiments. Kinetic model computations show that worst-case disturbances to the measured temperature field, which may be caused by the insertion of the sampling cone into the flame, do not alter mechanistic conclusions provided by the kinetic model. However, such perturbations are shown to be responsible for disparities in species location between measurement and computation. © 2010 The Combustion Institute.
    view abstractdoi: 10.1016/j.combustflame.2010.11.003
  • 2011 • 32 A shock tube with a high-repetition-rate time-of-flight mass spectrometer for investigations of complex reaction systems
    Drrstein, S.H. and Aghsaee, M. and Jerig, L. and Fikri, M. and Schulz, C.
    Review of Scientific Instruments 82 (2011)
    A conventional membrane-type stainless steel shock tube has been coupled to a high-repetition-rate time-of-flight mass spectrometer (HRR-TOF-MS) to be used to study complex reaction systems such as the formation of pollutants in combustion processes or formation of nanoparticles from metal containing organic compounds. Opposed to other TOF-MS shock tubes, our instrument is equipped with a modular sampling unit that allows to sample with or without a skimmer. The skimmer unit can be mounted or removed in less than 10 min. Thus, it is possible to adjust the sampling procedure, namely, the mass flux into the ionization chamber of the HRR-TOF-MS, to the experimental situation imposed by species-specific ionization cross sections and vapor pressures. The whole sampling section was optimized with respect to a minimal distance between the nozzle tip inside the shock tube and the ion source inside the TOF-MS. The design of the apparatus is presented and the influence of the skimmer on the measured spectra is demonstrated by comparing data from both operation modes for conditions typical for chemical kinetics experiments. The well-studied thermal decomposition of acetylene has been used as a test system to validate the new setup against kinetics mechanisms reported in literature. © 2011 American Institute of Physics.
    view abstractdoi: 10.1063/1.3627573
  • 2011 • 31 Catch me if you can: Mass spectrometry-based phosphoproteomics and quantification strategies
    Eyrich, B. and Sickmann, A. and Zahedi, R.P.
    Proteomics 11 554-570 (2011)
    Phosphorylation of proteins is one of the most prominent PTMs and for instance a key regulator of signal transduction. In order to improve our understanding of cellular phosphorylation events, considerable effort has been devoted to improving the analysis of phosphorylation by MS-based proteomics. Different enrichment strategies for phosphorylated peptides/proteins, such as immunoaffinity chromatography (IMAC) or titanium dioxide, have been established and constantly optimized for subsequent MS analysis. Concurrently, specific MS techniques were developed for more confident identification and phosphorylation site localization. In addition, more attention is paid to the LC-MS instrumentation to avoid premature loss of phosphorylated peptides within the analytical system. Despite major advances in all of these fields, the analysis of phosphopeptides still remains far from being routine in proteomics. However, to reveal cellular regulation by phosphorylation events, not only qualitative information about the phosphorylation status of proteins but also, in particular, quantitative information about distinct changes in phosphorylation patterns upon specific stimulation is mandatory. Thus, yielded insights are of outstanding importance for the emerging field of systems biology. In this review, we will give an insight into the historical development of phosphoproteome analysis and discuss its recent progress particularly regarding phosphopeptide quantification and assessment of phosphorylation stoichiometry. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000489
  • 2011 • 30 F-doped Co3O4 photocatalysts for sustainable H 2 generation from water/ethanol
    Gasparotto, A. and Barreca, D. and Bekermann, D. and Devi, A. and Fischer, R.A. and Fornasiero, P. and Gombac, V. and Lebedev, O.I. and MacCato, C. and Montini, T. and Van Tendeloo, G. and Tondello, E.
    Journal of the American Chemical Society 133 19362-19365 (2011)
    p-Type Co3O4 nanostructured films are synthesized by a plasma-assisted process and tested in the photocatalytic production of H 2 from water/ethanol solutions under both near-UV and solar irradiation. It is demonstrated that the introduction of fluorine into p-type Co3O4 results in a remarkable performance improvement with respect to the corresponding undoped oxide, highlighting F-doped Co 3O4 films as highly promising systems for hydrogen generation. Notably, the obtained yields were among the best ever reported for similar semiconductor-based photocatalytic processes. © 2011 American Chemical Society.
    view abstractdoi: 10.1021/ja210078d
  • 2011 • 29 Synthesis of tailored WO3 and WOx (2.9 \< x \< 3) nanoparticles by adjusting the combustion conditions in a H2/O 2/Ar premixed flame reactor
    Gupta, A. and Ifeacho, P. and Schulz, C. and Wiggers, H.
    Proceedings of the Combustion Institute 33 1883-1890 (2011)
    Flame synthesis of WO3 and WOx (2.9 < x < 3) nanoparticles is carried out by adding a dilute concentration of WF6 as precursor in a low-pressure H2/O2/Ar premixed flame reactor. The reactor is equipped with molecular-beam sampling and particle mass spectroscopy (PMS) to determine particle composition and sizes as a function of height above burner. Varying the H2/O2 ratio allowed us to tune the stoichiometry of the product. With a H2/O2 ratio of 0.67 white colored stoichiometric WO3 is formed, whereas the H2/O2 ratio &gt;0.8 yields blue colored non-stoichiometric WOx (2.9 < x < 3) nanoparticles. The size of nanoparticles can be controlled by varying the residence time in the high-temperature zone of the reactor as observed by molecular-beam sampling with subsequent analysis using PMS. Transmission electron microscopy (TEM) images of as-synthesized nanoparticles show that particles are non-agglomerated and have an almost spherical morphology. The X-ray diffraction (XRD) pattern of the as-synthesized material indicates that the powders exhibit poor crystallinity, however, subsequent thermal annealing of the sample in air changes its structure from amorphous to crystalline phase. It is observed that particles with sub-stoichiometric composition (WOx) show higher conductivity compared to the stoichiometric WO3 sample. © 2010 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
    view abstractdoi: 10.1016/j.proci.2010.06.162
  • 2011 • 28 Identification of Eps15 as antigen recognized by the monoclonal antibodies aa2 and ab52 of the wuerzburg hybridoma library against Drosophila brain
    Halder, P. and Chen, Y.-c. and Brauckhoff, J. and Hofbauer, A. and Dabauvalle, M.-C. and Lewandrowski, U. and Winkler, C. and Sickmann, A. and Buchner, E.
    PLoS ONE 6 (2011)
    The Wuerzburg Hybridoma Library against the Drosophilabrain represents a collection of around 200 monoclonal antibodies that bind to specific structures in the Drosophila brain. Here we describe the immunohistochemical staining patterns, the Western blot signals of one- and two-dimensional electrophoretic separation, and the mass spectrometric characterization of the target protein candidates recognized by the monoclonal antibodies aa2 and ab52 from the library. Analysis of a mutant of a candidate gene identified the Drosophila homolog of the Epidermal growth factor receptor Pathway Substrate clone 15 (Eps15) as the antigen for these two antibodies. © 2011 Halder et al.
    view abstractdoi: 10.1371/journal.pone.0029352
  • 2011 • 27 Fuel-structure dependence of benzene formation processes in premixed flames fueled by C6H12 isomers
    Hansen, N. and Kasper, T. and Yang, B. and Cool, T.A. and Li, W. and Westmoreland, P.R. and Oßwald, P. and Kohse-Höinghaus, K.
    Proceedings of the Combustion Institute 33 585-592 (2011)
    The fuel-structure-dependent significance of various benzene formation pathways is analyzed using data from rich (φ = 1.7) flames fueled by four C6H12 isomers: 1-hexene, cyclohexane, methylcyclopentane, and 3,3-dimethyl-1-butene. The isomer-resolved chemical compositions of the four premixed, laminar low-pressure flat flames are determined by flame-sampling molecular-beam mass spectrometry employing single-photon ionization by synchrotron generated vacuum-ultraviolet photons. Isomer-resolving photoionization efficiency curves and quantitative mole fraction profiles reveal the dominant fuel destruction pathways, the influence of different fuel consumption processes on the formation of commonly considered benzene precursors, and the contributions of several routes towards benzene formation. While propargyl and allyl radicals dominate benzene formation in the combustion of 1-hexene, contributions from reactions involving i-C4H5 and C5H5 radicals are revealed in the flames of 3,3-dimethyl-1-butene and methylcyclopentane, respectively. Close to the burner surface, successive dehydrogenation of the fuel is found to be important for the cyclohexane flame and to some smaller extent for the methylcyclopentane flame. © 2010 Published by Elsevier Inc. on behalf of The Combustion Institute. All rights reserved.
    view abstractdoi: 10.1016/j.proci.2010.05.056
  • 2011 • 26 Multiple benzene-formation paths in a fuel-rich cyclohexane flame
    Li, W. and Law, M.E. and Westmoreland, P.R. and Kasper, T. and Hansen, N. and Kohse-Höinghaus, K.
    Combustion and Flame 158 2077-2089 (2011)
    Detailed data and modeling of cyclohexane flames establish that a mixture of pathways contributes to benzene formation and that this mixture changes with stoichiometry. Mole-fraction profiles are mapped for more than 40 species in a fuel-rich, premixed flat flame (φ=2.0, cyclohexane/O2/30% Ar, 30Torr, 50.0cm/s) using molecular-beam mass spectrometry with VUV-photoionization at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The use of a newly constructed set of reactions leads to an excellent simulation of this flame and an earlier stoichiometric flame (M.E. Law et al., Proc. Combust. Inst. 31 (2007) 565-573), permitting analysis of the contributing mechanistic pathways. Under stoichiometric conditions, benzene formation is found to be dominated by stepwise dehydrogenation of the six-membered ring with cyclohexadienyl⇄benzene+H being the final step. This finding is in accordance with recent literature. Dehydrogenation of the six-membered ring is also found to be a dominant benzene-formation route under fuel-rich conditions, at which H2 elimination from 1,3-cyclohexadiene contributes even more than cyclohexadienyl decomposition. Furthermore, at the fuel-rich condition, additional reactions make contributions, including the direct route via 2C3H3⇄benzene and more importantly the H-assisted isomerization of fulvene formed from i-/n-C4H5+C2H2, C3H3+allyl, and C3H3+C3H3. Smaller contributions towards benzene formation arise from C4H3+C2H3, 1,3-C4H6+C2H3, and potentially via n-C4H5+C2H2. This diversity of pathways is shown to result nominally from the temperature and the concentrations of benzene precursors present in the benzene-formation zone, which are ultimately due to the feed stoichiometry. © 2011 The Combustion Institute.
    view abstractdoi: 10.1016/j.combustflame.2011.03.014
  • 2011 • 25 Atom probe tomography characterization of heavily cold drawn pearlitic steel wire
    Lia, Y.J. and Choi, P. and Borchers, C. and Chen, Y.Z. and Goto, S. and Raabe, D. and Kirchheim, R.
    Ultramicroscopy 111 628-632 (2011)
    Atom Probe Tomography (APT) was used to analyze the carbon distribution in a heavily cold drawn pearlitic steel wire with a true strain of 6.02. The carbon concentrations in cementite and ferrite were separately measured by a sub-volume method and compared with the literature data. It is found that the carbon concentration in ferrite saturates with strain. The carbon concentration in cementite decreases with the lamellar thickness, while the carbon atoms segregate at dislocations or cell/grain boundaries in ferrite. The mechanism of cementite decomposition is discussed in terms of the evolution of dislocation structure during severe plastic deformation. © 2010 Elsevier B.V.
    view abstractdoi: 10.1016/j.ultramic.2010.11.010
  • 2011 • 24 Strong cation exchange chromatography for analysis of sialylated glycopeptides
    Lohrig, K. and Sickmann, A. and Lewandrowski, U.
    Methods in Molecular Biology 753 299-308 (2011)
    Glycosylations represent major and essential co- and post-translational modification forms of proteins and facilitate a multitude of functions such as cell-cell interactions as well as protein folding and stability. The analysis of protein glycosylation is still an enormous task due to the vast heterogeneity and multi-tude of different possible carbohydrate structures. The elucidation of glycosylation sites - the attachment points of carbohydrate structures to the polypeptide backbone - is often among the first necessary steps of analysis. Therefore, we here present a simple protocol for charge-based enrichment of sialylated glycopeptides by strong cation exchange chromatography and subsequent analysis of glycosylation sites by mass spectrometry. © Springer Science+Business Media, LLC 2011.
    view abstractdoi: 10.1007/978-1-61779-148-2_20
  • 2011 • 23 A proteomic approach to analysing spheroid formation of two human thyroid cell lines cultured on a random positioning machine
    Pietsch, J. and Sickmann, A. and Weber, G. and Bauer, J. and Egli, M. and Wildgruber, R. and Infanger, M. and Grimm, D.
    Proteomics 11 2095-2104 (2011)
    The human cell lines FTC-133 and CGTH W-1, both derived from patients with thyroid cancer, assemble to form different types of spheroids when cultured on a random positioning machine. In order to obtain a possible explanation for their distinguishable aggregation behaviour under equal culturing conditions, we evaluated a proteomic analysis emphasising cytoskeletal and membrane-associated proteins. For this analysis, we treated the cells by ultrasound, which freed up some of the proteins into the supernatant but left some attached to the cell fragments. Both types of proteins were further separated by free-flow IEF and SDS gel electrophoresis until their identity was determined by MS. The MS data revealed differences between the two cell lines with regard to various structural proteins such as vimentin, tubulins and actin. Interestingly, integrin α-5 chains, myosin-10 and filamin B were only found in FTC-133 cells, while collagen was only detected in CGTH W-1 cells. These analyses suggest that FTC-133 cells express surface proteins that bind fibronectin, strengthening the three-dimensional cell cohesion. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000817
  • 2011 • 22 Phosphoproteome analysis of the platelet plasma membrane
    Premsler, T. and Lewandrowski, U. and Sickmann, A. and Zahedi, R.P.
    Methods in Molecular Biology 728 279-290 (2011)
    Blood platelets are key players standing at the crossroads between physiologically occurring hemostasis and pathologic thrombus formation. As these cellular particles lack a nucleus, intra- and intercellular processes involved in platelet activity and function are almost exclusively regulated on the protein level. In particular, posttranslational protein modification by phosphorylation, which allows for a quick and highly dynamic transduction of cellular signals, is discussed in this context. In addition, since platelet activation and aggregation usually require surface contact with the surrounding tissue, special interest focuses on this contacting region, and hence on the subproteome of the platelet plasma membrane. In this chapter, we present a mass spectrometry-driven approach capable of dealing with the task of platelet plasma membrane proteomics and phosphoproteomics. The outlined protocols include strategies for the isolation and purification of plasma membrane proteins by aqueous two-phase partitioning and subsequent enrichment of phosphopeptides via titanium dioxide chromatography. © 2011 Springer Science+Business Media, LLC.
    view abstractdoi: 10.1007/978-1-61779-068-3_19
  • 2011 • 21 Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins
    Sinha, S. and Lopes, D.H.J. and Du, Z. and Pang, E.S. and Shanmugam, A. and Lomakin, A. and Talbiersky, P. and Tennstaedt, A. and McDaniel, K. and Bakshi, R. and Kuo, P.-Y. and Ehrmann, M. and Benedek, G.B. and Loo, J.A. and Klär...
    Journal of the American Chemical Society 133 16958-16969 (2011)
    Amyloidoses are diseases characterized by abnormal protein folding and self-assembly, for which no cure is available. Inhibition or modulation of abnormal protein self-assembly, therefore, is an attractive strategy for prevention and treatment of amyloidoses. We examined Lys-specific molecular tweezers and discovered a lead compound termed CLR01, which is capable of inhibiting the aggregation and toxicity of multiple amyloidogenic proteins by binding to Lys residues and disrupting hydrophobic and electrostatic interactions important for nucleation, oligomerization, and fibril elongation. Importantly, CLR01 shows no toxicity at concentrations substantially higher than those needed for inhibition. We used amyloid β-protein (Aβ) to further explore the binding site(s) of CLR01 and the impact of its binding on the assembly process. Mass spectrometry and solution-state NMR demonstrated binding of CLR01 to the Lys residues in Aβ at the earliest stages of assembly. The resulting complexes were indistinguishable in size and morphology from Aβ oligomers but were nontoxic and were not recognized by the oligomer-specific antibody A11. Thus, CLR01 binds already at the monomer stage and modulates the assembly reaction into formation of nontoxic structures. The data suggest that molecular tweezers are unique, process-specific inhibitors of aberrant protein aggregation and toxicity, which hold promise for developing disease-modifying therapy for amyloidoses. © 2011 American Chemical Society.
    view abstractdoi: 10.1021/ja206279b
  • 2011 • 20 Composition and topology of the endoplasmic reticulum-mitochondria encounter structure
    Stroud, D.A. and Oeljeklaus, S. and Wiese, S. and Bohnert, M. and Lewandrowski, U. and Sickmann, A. and Guiard, B. and Van Der Laan, M. and Warscheid, B. and Wiedemann, N.
    Journal of Molecular Biology 413 743-750 (2011)
    Eukaryotic cells contain multiple organelles, which are functionally and structurally interconnected. The endoplasmic reticulum-mitochondria encounter structure (ERMES) forms a junction between mitochondria and the endoplasmic reticulum (ER). Four ERMES proteins are known in yeast, the ER-anchored protein Mmm1 and three mitochondria-associated proteins, Mdm10, Mdm12 and Mdm34, with functions related to mitochondrial morphology and protein biogenesis. We mapped the glycosylation sites of ERMES and demonstrate that three asparagine residues in the N terminal domain of Mmm1 are glycosylated. While the glycosylation is dispensable, the cytosolic C terminal domain of Mmm1 that connects to the Mdm proteins is required for Mmm1 function. To analyze the composition of ERMES, we determined the subunits by quantitative mass spectrometry. We identified the calcium-binding GTPase Gem1 as a new ERMES subunit, revealing that ERMES is composed of five genuine subunits. Taken together, ERMES represents a platform that integrates components with functions in formation of ER-mitochondria junctions, maintenance of mitochondrial morphology, protein biogenesis and calcium binding. © 2011 Elsevier Ltd. All rights reserved.
    view abstractdoi: 10.1016/j.jmb.2011.09.012
  • 2011 • 19 Evaluation of homoleptic guanidinate and amidinate complexes of gadolinium and dysprosium for MOCVD of rare-earth nitride thin films
    Thiede, T.B. and Krasnopolski, M. and Milanov, A.P. and De Los Arcos, T. and Ney, A. and Becker, H.-W. and Rogalla, D. and Winter, J. and Devi, A. and Fischer, R.A.
    Chemistry of Materials 23 1430-1440 (2011)
    Metal-organic chemical vapor deposition (MOCVD) of thin films of two representative rare-earth nitrides is reported here for the first time. Four homoleptic, all-nitrogen-coordinated, rare-earth (RE) complexes were evaluated as precursors for the respective nitride thin film materials. Two guanidinato complexes [RE{(iPrN)2C(NMe2)}3] [RE = Gd (1), Dy (2)] and two amidinato complexes [RE{(iPrN) 2CMe}3] [RE = Gd (3), Dy (4)] were compared and used either as single source precursors or together with ammonia for MOCVD of gadolinium nitride (GdN) and dysprosium nitride (DyN), respectively. The thermal properties of the precursors were studied and the fragmentation patterns were characterized by high-resolution electron impact-mass spectrometry (HR EI-MS). The obtained nitride films were investigated using a series of techniques, including X-ray diffraction (XRD), scanning electron microscopy (SEM), nuclear reaction analysis (NRA), Rutherford backscattering (RBS), and X-ray photoelectron spectroscopy (XPS). The films contain preferentially oriented grains of fcc-GdN and DyN and are contaminated with small amounts of carbon and oxygen (significantly below 10 at.-% in the best cases). The temperature-dependent magnetic properties of the films, as measured using a superconducting quantum interference device (SQUID), suggest the existence of small ferromagnetic grains of the rare-earth nitrides that exhibit superparamagnetism. Despite the chemical and structural similarity of the guanidinato and amidinato complexes (1-4), a distinctly different behavior as MOCVD precursors was found for 1 and 2, compared with that for 3 and 4. While the guanidinates operate well as single-source precursors (SSPs), the amidinates are not suited at all as SSPs, but give very good nitride films when used in the presence of ammonia. This characteristic behavior was correlated with the different fragmentation mechanisms, as revealed by EI-MS. © 2011 American Chemical Society.
    view abstractdoi: 10.1021/cm102840v
  • 2011 • 18 SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
    Vaudel, M. and Barsnes, H. and Berven, F.S. and Sickmann, A. and Martens, L.
    Proteomics 11 996-999 (2011)
    The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI, for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000595
  • 2011 • 17 Peptide identification quality control
    Vaudel, M. and Burkhart, J.M. and Sickmann, A. and Martens, L. and Zahedi, R.P.
    Proteomics 11 2105-2114 (2011)
    Identification of large proteomics data sets is routinely performed using sophisticated software tools called search engines. Yet despite the importance of the identification process, its configuration and execution is often performed according to established lab habits, and is mostly unsupervised by detailed quality control. In order to establish easily obtainable quality control criteria that can be broadly applied to the identification process, we here introduce several simple quality control methods. An unbiased quality control of identification parameters will be conducted using target/decoy searches providing significant improvement over identification standards. MASCOT identifications were for instance increased by 13% at a constant level of confidence. The target/decoy approach can however not be universally applied. We therefore also quality control the application of this strategy itself, providing useful and intuitive metrics for evaluating the precision and robustness of the obtained false discovery rate. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/pmic.201000704
  • 2010 • 16 The synthesis of highly loaded Cu/Al2O3 and Cu/Zno/Al2O3 catalysts by the two-step CVD of Cu IIdiethylamino-2-propoxide in a fluidized-bed reactor
    Becker, M. and D'Alnoncourt, R.N. and Kähler, K. and Sekulic, J. and Fischer, R.A. and Muhler, M.
    Chemical Vapor Deposition 16 85-92 (2010)
    Highly loaded copper catalysts supported on alumina are synthesized applying the cyclic two-step CVD of the precursor copper(II)diethylamino-2- propoxide in a fluidized-bed reactor. Copper/zinc oxide/alumina composites are synthesized by either the CVD of the precursor bis[bis (trimethylsilyl) amido]zinc on Cu/Al2O3, or the CVD of the Cu precursor on Zn-pretreated alumina, impregnating with diethyl zinc in addition. The composites are extensively characterized by atomic absorption spectroscopy (AAS), elemental analysis (EA), mass spectrometry (MS), N2 physisorption, N2O reactive frontal chromatography (RFC), and X-ray diffraction (XRD). The Cu and ZnO nanoparticles originating from the efficient two-step procedure, consisting of adsorption and subsequent decomposition of the adsorbed species in two separated steps, are highly dispersed, X-ray amorphous, and, in the case of the Cu-containing catalysts, have high specific Cu surface areas. The catalytic activities are determined both in methanol synthesis, to judge the contact between the deposited Cu and ZnO nanoparticles, and in the steam reforming of methanol (SRM) to probe the stability of the Cu particles. The turn-over frequencies (TOF) in methanol synthesis of these Cu/ZnO/Al 2O3 catalysts are higher than that of a commercial ternary catalyst. The varied sequence of the CVD of Cu and ZnO on alumina leads to catalysts with similar activities in the case of similar specific Cu areas. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    view abstractdoi: 10.1002/cvde.200906808
  • 2010 • 15 Comparison of bismuth emitting liquid metal ion sources
    Bischoff, L. and Pilz, W. and Mazarov, P. and Wieck, A.D.
    Applied Physics A: Materials Science and Processing 99 145-150 (2010)
    Four different liquid metal ion sources (LMIS), working with pure Bi as well as with Bi containing alloys (Au13Bi87, Ga 38Bi62, Ga35Bi60Li5) were investigated with respect to the emission behavior as a function of current and temperature, the mass spectra and the energy distribution of the individual ion species. Additionally, for the pure Bi-LMIS the sputtering rates for Bi ions and clusters on Si, SiO2 and Ge substrates were compared with that of Ga projectile ions using a mass separating focused ion beam system. © Springer-Verlag 2010.
    view abstractdoi: 10.1007/s00339-010-5597-0
  • 2010 • 14 Synthesis and catalytic properties of metal nanoparticles: Size, shape, support, composition, and oxidation state effects
    Cuenya, B.R.
    Thin Solid Films 518 3127-3150 (2010)
    Exciting new opportunities are emerging in the field of catalysis based on nanotechnology approaches. A new understanding and mastery of catalysis could have broad societal impacts, since about 80% of the processes in the chemical industry depend on catalysts to work efficiently. Efforts in surface science have led to the discovery of new heterogeneous catalysts, however, until recently the only way to develop new or improved catalysts was by empirical testing in trial-and-error experiments. This time-consuming and costly procedure is now rapidly being replaced by rational design methods that utilize fundamental knowledge of catalysts at the nanoscale. The advent of nanoscience and nanotechnology is providing the ability to create controlled structures and geometries to investigate and optimize a broad range of catalytic processes. As a result, researchers are obtaining fundamental insight into key features that influence the activity, selectivity, and lifetime of nanocatalysts. This review article examines several new findings as well as current challenges in the field of nanoparticle based catalysis, including the role played by the particle structure and morphology (size and shape), its chemical composition and oxidation state, and the effect of the cluster support. © 2010 Elsevier B.V. All rights reserved.
    view abstractdoi: 10.1016/j.tsf.2010.01.018
  • 2010 • 13 Characterization of a novel interaction between vasodilator-stimulated phosphoprotein and abelson interactor 1 in human platelets: A concerted computational and experimental approach
    Dittrich, M. and Strassberger, V. and Fackler, M. and Tas, P. and Lewandrowski, U. and Sickmann, A. and Walter, U. and Dandekar, T. and Birschmann, I.
    Arteriosclerosis, Thrombosis, and Vascular Biology 30 843-850 (2010)
    Objective: The goal of this study was systematic profiling of vasodilator-stimulated phosphoprotein (VASP)-Ena/VASP homology 1 (EVH1) interactors in human platelets using a combined in silico and in vitro approach. Methods and results: Exploiting the information of the comprehensive proteome catalogue in the PlateletWeb database (http://plateletweb.bioapps.biozentrum. uni-wuerzburg.de/PlateletWeb.php), we performed a motif search of all sequences and identified potential target sites of class I EVH1 domains in human platelet proteins. Performing affinity purification with VASP-EVH1 domain and the lysates of platelets, we examined complex partners by mass spectrometry. Combining the results of both analyses, we identified Abelson interactor 1 (Abi-1) as a novel EVH1 domain-specific interaction partner of VASP in human platelets and investigated this interaction by yeast 2-hybrid mutational studies and immunoprecipitation. Immunofluorescence microscopy indicated colocalization of both proteins at the lamellipodia of spread human platelets, suggesting a role in reorganizing the cytoskeleton during spreading. Conclusion: The combination of experimental and computational interactome research has emerged as a valuable tool for the analysis of protein-protein interaction networks and facilitates the discovery and characterization of novel interactions as detailed here for Abi-1 and VASP in human platelets. System biological approaches can be expected to play an important role in basic and clinical platelet research, as they offer the potential to analyze signal transduction beyond the scope of established pathways. © 2010 American Heart Association, Inc.
    view abstractdoi: 10.1161/ATVBAHA.109.200683
  • 2010 • 12 Characterization of the effluent of a He/O-2 microscale atmospheric pressure plasma jet by quantitative molecular beam mass spectrometry
    Ellerweg, D. and Benedikt, J. and von Keudell, A. and Knake, N. and Schulz-von der Gathen, V.
    New Journal of Physics 12 013021 (2010)
    The effluent of a microscale atmospheric pressure plasma jet (mu-APPJ) operated in helium with a small admixture of molecular oxygen (< 1.6%) has been analyzed by means of two independent diagnostics, quantitative molecular beam mass spectrometry (MBMS) and two-photon absorption laser-induced fluorescence spectroscopy (TALIF). The atomic oxygen density, the ozone density and the depletion of molecular oxygen have been measured by MBMS and the atomic oxygen density has been validated by TALIF. Absolute atomic oxygen densities in the effluent up to 4.7x10(15) cm(-3) could be measured with a very good agreement between both diagnostics. In addition, ozone densities in the effluent up to 1.4x10(15) cm(-3) and an O-2 depletion up to 10% could be measured by MBMS. The atomic oxygen density shows a maximum value at an O-2 admixture of 0.6%, whereas the ozone density continues to increase toward higher O-2 admixtures. With increasing distance from the jet, the atomic oxygen density decreases but is still detectable at a distance of 30 mm. The ozone density increases with distance, saturating at a distance of 40 mm. By applying higher powers to the mu-APPJ, the atomic oxygen density increases linearly whereas the ozone density exhibits a maximum.
    view abstractdoi: 10.1088/1367-2630/12/1/013021
  • 2010 • 11 ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
    Helsens, K. and Colaert, N. and Barsnes, H. and Muth, T. and Flikka, K. and Staes, A. and Timmerman, E. and Wortelkamp, S. and Sickmann, A. and Vandekerckhove, J. and Gevaert, K. and Martens, L.
    Proteomics 10 1261-1264 (2010)
    MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms-lims (http://genesis.UGent.be/ms-lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/pmic.200900409
  • 2010 • 10 Quantitative visualization of colloidal and intracellular gold nanoparticles by confocal microscopy
    Klein, S. and Petersen, S. and Taylor, U. and Rath, D. and Barcikowski, S.
    Journal of Biomedical Optics 15 (2010)
    Gold nanoparticles (AuNPs) have the potential to become a versatile biomarker. For further use of AuNPs labeled with functionalized molecules, their visualization in biological systems by routine laboratory tools such as light microscopy is crucial. However, the size far below the diffraction limit affords specialized parameters for microscopical detection, which stimulated the current study, aimed to determine from which size onward AuNPs, either in dispersion or cell-associated, can be reliably detected by standard confocal microscopy. First, gold colloids of size-restricted fractions are examined in dispersion. At a minimum particle size of 60 nm, detection appears to be reliable. Particle counts in dilution series confirm these results by revealing single particle detection of 60-nm colloids. Second, AuNPs are visualized and quantified in cells, which interestingly cause a phase shift in the reflection of AuNPs. Gold mass spectroscopy confirms the number of AuNPs counted microscopically inside cells. Furthermore, it demonstrates for the first time a very high diffusion rate of 15-nm particles into the cells. In conclusion, the results back the suitability of confocal microscopy for the quantitative tracking of colloidal and intracellular gold nanoparticles sized 60 nm. © 2010 Society of Photo-Optical Instrumentation Engineers.
    view abstractdoi: 10.1117/1.3461170
  • 2010 • 9 Biofuel combustion chemistry: From ethanol to biodiesel
    Kohse-Höinghaus, K. and Oßwald, P. and Cool, T.A. and Kasper, T. and Hansen, N. and Qi, F. and Westbrook, C.K. and Westmoreland, P.R.
    Angewandte Chemie - International Edition 49 3572-3597 (2010)
    Biofuels, such as bio-ethanol, bio-butanol, and biodiesel, are of increasing interest as alternatives to petroleum-based transportation fuels because they offer the long-term promise of fuel-source regenerability and reduced climatic impact. Current discussions emphasize the processes to make such alternative fuels and fuel additives, the compatibility of these substances with current fuel-delivery infrastructure and engine performance, and the competition between biofuel and food production. However, the combustion chemistry of the compounds that constitute typical biofuels, including alcohols, ethers, and esters, has not received similar public attention. Herein we highlight some characteristic aspects of the chemical pathways in the combustion of prototypical representatives of potential biofuels. The discussion focuses on the decomposition and oxidation mechanisms and the formation of undesired, harmful, or toxic emissions, with an emphasis on transportation fuels. New insights into the vastly diverse and complex chemical reaction networks of biofuel combustion are enabled by recent experimental investigations and complementary combustion modeling. Understanding key elements of this chemistry is an important step towards the intelligent selection of next-generation alternative fuels. © 2010 Wiley-VCH Verlag GmbH & Co. KCaA.
    view abstractdoi: 10.1002/anie.200905335
  • 2010 • 8 Development and evaluation of a fluorescence microplate assay for quantification of heparins and other sulfated carbohydrates
    Lühn, S. and Schrader, T. and Sun, W. and Alban, S.
    Journal of Pharmaceutical and Biomedical Analysis 52 1-8 (2010)
    Due to their complex composition, quantification of heparins is difficult. On the one hand there are many biological tests, which only indirectly detect effects of the antithrombin-binding material. On the other hand direct quantitative methods are available but they are often insensitive, challenging, time-consuming or expensive. The aim of this study was to develop a sensitive, rapid, simple as well as inexpensive direct quantification assay suitable for routine analysis. Based on Polymer-H, a novel heparin complexing, fluorescent labeled synthetic polymer (λ(ex) 320 nm, λ(em) 510 nm), a microplate assay was developed and optimized. The specificity of the assay was evaluated by structure-assay response relationships studies using structurally defined glucan sulfates, heparins, and other natural and synthetic sulfated carbohydrates. The fluorescence intensity of Polymer-H (7.5 μg/ml) showed to be concentration-dependently amplified by heparins as well as by other sulfated carbohydrates. The best sensitivity, accuracy and linearity were observed in a range from 0.63 to 5.0 μg/ml heparins. No differences in the fluorescence between various heparins were observed, so that only one calibration curve is needed. In addition, all types of carbohydrates with a degree of sulfation (DS) &gt; ∼1.2 and a Mr &gt; 3000 can be quantified as well. By own calibration curves also other sulfated carbohydrates like fondaparinux or other glycosaminoglycans (DS &gt; 0.4) can be determined. © 2009 Elsevier B.V. All rights reserved.
    view abstractdoi: 10.1016/j.jpba.2009.12.014
  • 2010 • 7 XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results
    Muth, T. and Vaudel, M. and Barsnes, H. and Martens, L. and Sickmann, A.
    Proteomics 10 1522-1524 (2010)
    Identification of proteins by MS plays an important role in proteomics. A crucial step concerns the identification of peptides from MS/MS spectra. The X!Tandem Project (http://www.thegpm.org/tandem) supplies an open-source search engine for this purpose. In this study, we present an open-source Java library called XTandem Parser that parses X!Tandem XML result files into an easily accessible and fully functional object model (http://xtandem-parser.googlecode. com). In addition, a graphical user interface is provided that functions as a usage example and an end-user visualization tool. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/pmic.200900759
  • 2010 • 6 Identification of a Protein Kinase C-dependent phosphorylation site involved in sensitization of TRPV4 channel
    Peng, H. and Lewandrowski, U. and Müller, B. and Sickmann, A. and Walz, G. and Wegierski, T.
    Biochemical and Biophysical Research Communications 391 1721-1725 (2010)
    Transient Receptor Potential (TRP) proteins are non-selective cation channels performing diverse cellular functions. TRPV1 and TRPV4, two calcium-permeable channels of the vanilloid subfamily of TRP proteins, are activated by various physical and chemical stimuli, including noxious heat and mechanical stress, respectively. These channels are also required for exaggerated sensation of painful stimuli, condition referred to as hyperalgesia, which is frequently associated with inflammation. Phosphorylation of TRPV1, involving Protein Kinase C (PKC) and Protein Kinase A (PKA), appears to be the predominant mechanism for channel sensitization and development of heat hyperalgesia. PKC and PKA pathways have also been implicated in the sensitization of TRPV4, but the respective phosphorylation sites remain unknown. Using mass spectrometry, we report now that TRPV4 is phosphorylated on serine 824 by the PKC-activating phorbol 12-myristate 13-acetate. This phosphorylation is prevented by a PKC inhibitor, confirming the involvement of PKC. Ser824, located in the carboxy-terminal cytosolic tail of TRPV4, is also phosphorylated after activation of the PKA pathway by forskolin, albeit less potently. Substitution of Ser824 with aspartic acid, mimicking phosphorylation at this site, increased TRPV4-mediated calcium influx in resting and in stimulated cells, underlining the importance of this residue in TRPV4 regulation. Thus PKC, and possibly PKA, phosphorylate TRPV4 at Ser824 leading to the enhancement of TRPV4 channel function. Our findings suggest an important role of this phosphorylation in TRPV4 sensitization and the development of hyperalgesia. © 2009 Elsevier Inc. All rights reserved.
    view abstractdoi: 10.1016/j.bbrc.2009.12.140
  • 2010 • 5 Application of free-flow IEF to identify protein candidates changing under microgravity conditions
    Pietsch, J. and Kussian, R. and Sickmann, A. and Bauer, J. and Weber, G. and Nissum, M. and Westphal, K. and Egli, M. and Grosse, J. and Schönberger, J. and Wildgruber, R. and Infanger, M. and Grimm, D.
    Proteomics 10 904-913 (2010)
    Using antibody-related methods, we recently found that human thyroid cells express various proteins differently depending on whether they are cultured under normal gravity (1g) or simulated microgravity (s-μg). In this study, we performed proteome analysis in order to identify more gravity-sensitive thyroid proteins. Cells cultured under 1g or s-μg conditions were sonicated. Proteins released into the supernatant and those remaining in the cell fragments were fractionated by free-flow IEF. The fractions obtained were further separated by SDS-gel electrophoresis. Selected gel pieces were excised and their proteins were determined by MS. A total of 235 different proteins were found. Out of 235 proteins, 37 appeared to be first identifications in human thyroid cells. Comparing SDS gel lanes of equally numbered free-flow IEF fractions revealed similar patterns with a number of identical bands if proteins of a distinct cell line had been applied, irrespective of whether the cells had been cultured under 1g or s-μg. Most of the identical band pairs contained identical proteins. However, the concentrations of some types of proteins were different within the two pieces of gel. Proteins that concentrated differently in such pieces of gel are considered as candidates for further investigations of gravitational sensitivity. © 2009 WILEY-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/pmic.200900226
  • 2010 • 4 Peptide and protein quantification: A map of the minefield
    Vaudel, M. and Sickmann, A. and Martens, L.
    Proteomics 10 650-670 (2010)
    The increasing popularity of gel-free proteomics technologies has created a strong demand for compatible quantitative analysis methods. As a result, a plethora of different techniques has been proposed to perform gel-free quantitative analysis of proteomics samples. Each of these methods comes with certain strengths and shortcomings, and they often are dedicated to a specific purpose. This review will present a brief overview of the main methods, organized by their underlying concepts, and will discuss the issues they raise with a focus on data processing. Finally, we will list the available software that can help with the data processing from quantitative experiments. We hope that this review will thus enable researchers to find the most appropriate method available for their research objectives, and can also serve as a basis for creating a reliable data processing strategy.
    view abstractdoi: 10.1002/pmic.200900481
  • 2010 • 3 First on-line analysis of petroleum from single inclusion using ultrafast laser ablation
    Volk, H. and Fuentes, D. and Fuerbach, A. and Miese, C. and Koehler, W. and Bärsch, N. and Barcikowski, S.
    Organic Geochemistry 41 74-77 (2010)
    For many years, geochemical analysis of petroleum from single inclusions has been a challenging objective for fluid inclusion studies. In this study, individual petroleum inclusions have been selectively opened and analysed, for the first time, by coupling an on-line femtosecond laser with a gas chromatograph-mass spectrometer (GC-MS). GC-MS chromatograms show straight chained, branched and cyclic alkanes and aromatic hydrocarbons with carbon numbers ranging from 4 (iso-butane) to 19 (pristane). The distribution of these compounds is similar to that observed by on-line bulk crushing, and pyrolysis artefacts such as alkenes and ketones were not detected. Hydrocarbons with higher carbon numbers appear to have remained in the extraction chamber, a limitation that may be overcome by improvements to the inlet system. This pilot study proves that ultrashort laser pulses can be used to liberate unaltered oil from individual inclusions, thereby creating exciting opportunities for further research aimed at determining the nature of different hydrocarbon palaeo-fluids trapped within single minerals. © 2009 Elsevier Ltd.
    view abstractdoi: 10.1016/j.orggeochem.2009.05.006
  • 2010 • 2 Inactivation of bacteria and biomolecules by low-pressure plasma discharges
    Von Keudell, A. and Awakowicz, P. and Benedikt, J. and Raballand, V. and Yanguas-Gil, A. and Opretzka, J. and Flötgen, C. and Reuter, R. and Byelykh, L. and Halfmann, H. and Stapelmann, K. and Denis, B. and Wunderlich, J. and Mur...
    Plasma Processes and Polymers 7 327-352 (2010)
    (Figure Presented) The inactivation of bacteria and biomolecules using plasma discharges were investigated within the European project BIODECON. The goal of the project was to identify and isolate inactivation mechanisms by combining dedicated beam experiments with especially designed plasma reactors. The plasma reactors are based on a fully computer-controlled, low-pressure inductively-coupled plasma (ICP). Four of these reactors were built and distributed among the consortium, thereby ensuring comparability of the results between the teams. Based on this combined effort, the role of UV light, of chemical sputtering (i.e. the combined impact of neutrals and ions), and of thermal effects on bacteria such as Bacillus atrophaeus, Aspergillus niger, as well as on biomolecules such as LPS, Lipid A, BSA and prions have been evaluated. The particle fluxes emerging from the plasmas are quantified by using mass spectrometry, Langmuir probe measurements, retarding field measurements and optical emission spectroscopy. The effects of the plasma on the biological systems are evaluated using atomic force microscopy, ellipsometry, electrophoresis, specially-designed western blot tests, and animal models. A quantitative analysis of the plasma discharges and the thorough study of their effect on biological systems led to the identification of the different mechanisms operating during the decontamination process. Our results confirm the role of UV in the 200-2 50 nm range for the inactivation of microorganisms and a large variability of results observed between different strains of the same species. Moreover, we also demonstrate the role of chemical sputtering corresponding to the synergism between ion bombardment of a surface with the simultaneous reaction of active species such as O, O2 or H. Finally, we show that plasma processes can be efficient against different micro-organisms, bacteria and fungi, pyrogens, model proteins and prions. The effect of matrices is described, and consequences for any future industrial implementation are discussed. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA.
    view abstractdoi: 10.1002/ppap.200900121
  • 2010 • 1 Gas-phase synthesis of gradient catalyst libraries consisting of nanoparticles supported on high surface area porous substrates
    Xia, W. and Mei, B. and Muhler, M.
    Nanoscience and Nanotechnology Letters 2 1-6 (2010)
    Despite the advances in high throughput experimentation in recent years the synthesis of realistic catalyst libraries especially gradient catalyst libraries remains as a challenge in material science. Recently, we have developed a method for the synthesis of gradient catalyst libraries consisting of nanoparticles supported on high surface area porous substrates. Chemical vapor deposition (CVD) was employed as a gas-phase method for the synthesis. The method made use of the lateral concentration profile of the precursor-loaded carrier gas stream during CVD, resulting in concentration profile of the deposits on porous substrates. In this report, high surface area materials of both powders (e.g., silica) and bulk composites (e.g., hierarchical carbon structures) were successfully employed as substrates for the deposition of single metal or bimetallic catalyst libraries. The synthesis was achieved by controlling the flow behavior of the effluent precursor stream. The resulting effusion cone led to a radial deposition gradient on the substrate. Different from thin film-type model catalyst libraries, the obtained catalysts can be tested under realistic reaction conditions. Methanol oxidation was studied as a test reaction using scanning mass spectrometry. Copyright © 2010 American Scientific Publishers.
    view abstractdoi: 10.1166/nnl.2010.1046