TY - JOUR A1 - Sajulga, R. A1 - Easterly, C. A1 - Riffle, M. A1 - Mesuere, B. A1 - Muth, Thilo A1 - Mehta, S. A1 - Kumar, P. A1 - Johnson, J. A1 - Gruening, B. A1 - Schiebenhoefer, H. A1 - Kolmeder, C. A1 - Fuchs, S. A1 - Nunn, B. A1 - Rudney, J. A1 - Griffin, T. A1 - Jagtap, P. T1 - Survey of metaproteomics software tools for functional microbiome analysis N2 - To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform. KW - Bioinformatics KW - Metaproteomics KW - Mass spectrometry PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516358 DO - https://doi.org/10.1371/journal.pone.0241503 SP - e0241503 AN - OPUS4-51635 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Vogl, Jochen T1 - The triple-isotope calibration approach: a universal and standard-free calibration approach for obtaining absolute isotope ratios of multi-isotopic elements N2 - The theory of a new calibration approach for obtaining absolute isotope ratios of multi-isotopic elements without the use of any standard has been developed. The calibration approach basically uses the difference in the instrumental isotope fractionation of two different types of mass spectrometers, leading to two different fractionation lines in a three-isotope diagram. When measuring the same sample with both mass spectrometers, the different fractionation lines have one point in common: this is the ‘true’ logarithmized isotope ratio pair of the sample. Thus, the intersection of both fractionation lines provides us with the absolute isotope ratios of the sample. This theory has been tested in practice by measuring Cd and of Pb isotope ratios in the certified reference materials BAM-I012 and NIST SRM981 by thermal ionization mass spectrometry and by inductively coupled plasma mass spectrometry while varying the ionization conditions for both mass spectrometers. With this experiment, the theory could be verified, and absolute isotope ratios were obtained, which were metrologically compatible with the certified isotope ratios. The so-obtained absolute isotope ratios are biased by − 0.5% in average, which should be improved with further developments of the method. This calibration approach is universal, as it can be applied to all elements with three or more isotopes and it is not limited to the type of mass spectrometers applied; it can be applied as well to secondary ion mass spectrometry or others. Additionally, this approach provides information on the fractionation process itself via the triple-isotope fractionation exponent θ. KW - Triple isotope fractionation KW - Absolute isotope ratio KW - Mass spectrometry KW - Calibration KW - Uncertainty PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516364 DO - https://doi.org/10.1007/s00216-020-03050-4 VL - 413 IS - 3 SP - 821 EP - 826 PB - Springer Verlag AN - OPUS4-51636 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Pramann, A. A1 - Vogl, Jochen A1 - Rienitz, O. T1 - The Uncertainty Paradox: Molar Mass of Enriched Versus Natural Silicon Used in the XRCD Method N2 - The X-ray crystal density method uses silicon spheres highly enriched in 28Si as a primary method for the dissemination of the SI base unit kilogram yielding smallest possible uncertainties associated with the mass m within a few parts in 10-8. This study compares different available and newly developed analytical methods and their results for the determination of the molar mass M of silicon highly enriched in 28Si (Me) and of silicon (Mx) with an almost natural isotopic distribution. While for Me relative uncertainties urel(Me) in the lower 10-9 range are obtained routinely, it was not possible to fall below a value of urel(Mx) < 4 x 10-6 in the case of natural silicon, which is approximately three orders of magnitude larger. The application of the state-of the-art isotope ratio mass spectrometry accompanied with sophisticated thoroughly investigated methods suggests an intrinsic cause for the large uncertainty associated with the molar mass of natural silicon compared to the enriched material. KW - silicon KW - Molar mass KW - Isotope ratios KW - SI KW - Kilogram KW - Mole KW - XRCD method PY - 2020 DO - https://doi.org/10.1007/s12647-020-00408-y VL - 35 SP - 499 EP - 510 PB - Springer Verlag AN - OPUS4-51637 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Reichel, V. E. A1 - Matuszak, J. A1 - Bente, Klaas A1 - Heil, T. A1 - Kraupner, A. A1 - Dutz, S. A1 - Cicha, I. A1 - Faivre, D. T1 - Magnetite-Arginine Nanoparticles as a Multifunctional Biomedical Tool N2 - Iron oxide nanoparticles are a promising platform for biomedical applications, both in terms of diagnostics and therapeutics. In addition, arginine-rich polypeptides are known to penetrate across cell membranes. Here, we thus introduce a system based on magnetite nanoparticles and the polypeptide poly-l-arginine (polyR-Fe3O4). We show that the hybrid nanoparticles exhibit a low cytotoxicity that is comparable to Resovist®, a commercially available drug. PolyR-Fe3O4 particles perform very well in diagnostic applications, such as magnetic particle imaging (1.7 and 1.35 higher signal respectively for the 3rd and 11th harmonic when compared to Resovist®), or as contrast agents for magnetic resonance imaging (R2/R1 ratio of 17 as compared to 11 at 0.94 T for Resovist®). Moreover, these novel particles can also be used for therapeutic purposes such as hyperthermia, achieving a specific heating power ratio of 208 W/g as compared to 83 W/g for Feridex®, another commercially available product. Therefore, we envision such materials to play a role in the future theranostic applications, where the arginine ability to deliver cargo into the cell can be coupled to the magnetite imaging properties and cancer fighting activity. KW - Iron oxide KW - Nanoparticle KW - Theranostics KW - MRI KW - Hyperthermia PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-515993 DO - https://doi.org/10.3390/nano10102014 VL - 10 IS - 10 SP - 2014 PB - MDPI AN - OPUS4-51599 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Goedecke, Caroline A1 - Dittmann, Daniel A1 - Eisentraut, Paul A1 - Wiesner, Yosri A1 - Schartel, Bernhard A1 - Klack, Patrick A1 - Braun, Ulrike T1 - Evaluation of thermoanalytical methods equipped with evolved gas analysis for the detection of microplastic in environmental samples N2 - Microplastic particles are currently detected in almost all environmental compartments. The results of detection vary widely, as a multitude of very different methods are used with very different requirements for analytical validity. In this work four thermoanalytical methods are compared and their advantages and limitations are discussed. One of them is thermal extraction-desorption gas chromatography mass spectrometry (TED-GC/MS), an analysis method for microplastic detection that has become established in recent years. In addition, thermogravimetric analysis coupled with Fourier-transform infrared spectroscopy (TGA-FTIR) and mass spectrometry (TGA-MS) were applied, two methods that are less common in this field but are still used in other research areas. Finally, microscale combustion calorimeter (MCC) was applied, a method not yet used for microplastic detection. The presented results are taken from a recently published interlaboratory comparison test by Becker et al. (2020). Here a reference material consisting of suspended matter and specified added polymer masses was examined, and only the results of the recoveries were presented. In the present paper, however, the results for the individual polymers are discussed in detail and individual perspectives for all instruments are shown. It was found that TED-GC/MS is the most suitable method for samples with unknown matrix and unknown, variable kinds and contents of microplastic. TGA-FTIR is a robust method for samples with known matrix and with defined kinds of microplastic. TGA-MS may offer a solution for the detection of PVC particles in the future. MCC can be used as a very fast and simple screening method for the identification of a potential microplastic load of standard polymers in unknown samples. KW - Microplastic KW - TED-GC/MS KW - TGA-MS KW - TGA-FTIR KW - MCC KW - Thermal analysis PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516687 DO - https://doi.org/10.1016/j.jaap.2020.104961 VL - 152 SP - 104961 PB - Elsevier B.V. AN - OPUS4-51668 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Gornushkin, Igor B. A1 - Sennikov, P. A1 - Kornev, R. A1 - Ermakov, A. A1 - Shkrunin, V. A1 - Polyakov, V. T1 - Laser induced dielectric breakdown for synthesis of chlorofluorosilanes N2 - Tetrafluorosilane (SF4) and tetrachlorosilane (SiCl4) plasmas have been widely used as a source of either F or Cl for etching silicon or as a source of silicon for deposition of Si-based materials. Using different combinations of F and Cl in molecules of chlorofluorosilane SiFxCly adds additional flexibility in realization of these processes. Direct synthesis of SiFxCl4-x (x=1, 2, 3) from SiF4 and SiCl4 is thermodynamically forbidden under standard conditions. This restriction is removed in low-temperature plasmas studied in this work: a laser induced dielectric breakdown (LIDB) plasma and steady-state inductively-coupled plasma (ICP). The plasmas differ in many respects including energy content, temperature, and electron density that lead to different ionization/excitation states of plasma species, which are observed from plasma optical emission spectra. IR spectroscopy and mass-spectrometry confirm the formation of three chlorofluorosilanes, SiF3Cl, SiF2Cl2, and SiFCl3 that constitute ~60% in products of LIDB plasma and split 50/50 between SiF3Cl, SiFCl3 and SiF2Cl2. Experimental observations are verified by equilibrium static calculations via the minimization of Gibbs free energy and by dynamic calculations via the chemical-hydrodynamic plasma model of a spherically expanding plasma plume. The both types of calculations qualitatively agree with the results of spectroscopic analysis and reproduce dominant presence of SiF2Cl2 as the temperature of the gas approaches the room temperature. KW - Chemical-hydrodynamic modeling KW - Chlorofluorosilanes KW - Laser induced dielectric breakdown KW - Inductively coupled plasma KW - Equilibrium chemical modeling PY - 2020 DO - https://doi.org/10.1016/j.jfluchem.2020.109692 VL - 241 SP - 109692 PB - Elsevier B.V. AN - OPUS4-51646 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Beckmann, Jörg T1 - Novel Technique for On-Line Monitoring of the Curing Process of Fiber Reinforced Polymer Composites N2 - A specially designed experimental set up has been integrated into a commercially available FT IR Spectrometer for ATR experiments on Epoxy Systems. Representative data of far infrared spectra measured during the curing process at different temperatures of an epoxy system will be presented in dependency of the curing situation. The experiments and the selected set up are discussed to demonstrate its potential for future monitoring and ageing control applications during a manufacturing process of polymer composites. T2 - 45. International Confercene on infrared, milimeter and terahertz waves CY - Online meeting DA - 08.11.2020 KW - Far-infrared spectroscopy KW - Curing Monitoring PY - 2020 UR - https://live-irmmwthz.pantheonsite.io/technical-program AN - OPUS4-51649 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Kruschwitz, Sabine T1 - Evaluation of Advanced NDT-Methods for Measurement of Fibre Orientation in Concrete N2 - Integration of fibre reinforcement in high-performance cementitious materials has become widely applied in many fields of construction. One of the most investigated advantages of steel fibre reinforced concrete (FRC) is the deceleration of crack growth and hence it’s improved sustainability due to e.g. decrease of permeability of concrete by aggressive substances. Additional benefits are associated with the structural properties of FRC, where fibres can significantly increase the ductility and the tensile strength of concrete. In some applications, such as tunnel linings or industrial slabs, it is even possible to entirely replace the conventional reinforcement, leading to significant logistical and environmental benefits. Fibre reinforcement can, however, have critical disadvantages and even hinder the performance of concrete, since it can induce an anisotropic material behaviour of the mixture if the fibres are not appropriately oriented. For a safe use of FRC in the future, reliable non-destructive methods need to be identified to assess the fibres’ orientation in hardened concrete. In this study, ultrasonic material testing, electrical impedance testing, and X-ray computer tomography have been investigated for this purpose using specially produced samples with biased or random fibre orientations. This paper demonstrates the capabilities of each of these NDT techniques for fibre orientation measurements and draws conclusions based on these results about the most promising areas for future research and development using these techniques. T2 - fib2020 Shanghai CY - Online meeting DA - 22.11.2020 KW - Ultrasonic testing KW - Steel fibre reinforced concrete (FRC) KW - Fibre orientation KW - X-ray computed tomography (CT) KW - Electrical impedance PY - 2020 AN - OPUS4-51651 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Schade, U. T1 - Etalon Effects in THz Film Measurements N2 - Etalon effects in THz transmittance spectra, either taken in time-domain or frequency-domain, often hamper or even hinder the interpretation of film properties. In this paper we discuss the transferability and applicability of spectroscopic methods usually employed in the near and mid infrared spectral range and exemplarily present the application field. T2 - 45. International Confercene on infrared, milimeter and terahertz waves CY - Online meeting DA - 08.11.2020 KW - Far-infrared spectroscopy KW - Etalon Effects PY - 2020 UR - https://live-irmmwthz.pantheonsite.io/technical-program AN - OPUS4-51652 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Bayerlein, Bernd T1 - Focused ion beam techniques beyond the ordinary - Methodological developments within ADVENT N2 - This poster presents the focused ion beam preparation methodologies developed within the framework of the EU funded EURAMET project ADVENT (Advanced Energy-Saving Technology). It summarises the key breakthroughs achieved for various in situ investigation techniques, e.g. in situ experiments at the Synchrotron facility BESSY II (IR-SNOM and XRS), TEM and SMM instrumentation. The created experimental devices from diverse thin-film semiconductor materials paved the way to dynamic structural studies bearing the potential to determine nanoscale correlations between strain and electric fields and, moreover, for the fundamental development of new in situ capabilities. N2 - Dieses Poster zeigt die FIB Präparationstechniquen, die im Rahmen des EU-finanzierten EURAMET-Projekts ADVENT (Advanced Energy Saving Technology) entwickelt wurden. Es fasst die wichtigsten Errungenschaften zusammen, die für verschiedene in situ Untersuchungstechniken erzielt wurden, z.B. situ-Experimente in dem Synchrotronring BESSY II (IR-SNOM und XRS), in situ TEM Experimente und für die SMM Technik. Die experimentellen Probenstrukturen, die aus verschiedenen Dünnschicht-Halbleitermaterialien erzeugt wurden, ebneten den Weg für dynamische Strukturstudien, die das Potenzial haben, nanoskalige Korrelationen zwischen Dehnung und elektrischen Feldern zu bestimmen und darüber hinaus neue in situ Messmethoden zu entwickeln. T2 - Final Meeting CY - Online Meeting DA - 30.06.2020 KW - FIB KW - Sample preparation KW - In situ KW - TEM KW - AFM PY - 2020 AN - OPUS4-51606 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -