TY - JOUR A1 - Schiebenhoefer, H. A1 - Schallert, K. A1 - Renard, B. Y. A1 - Trappe, K. A1 - Schmid, E. A1 - Benndorf, D. A1 - Riedel, K. A1 - Muth, Thilo A1 - Fuchs, S. T1 - A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane JF - Nature Protocols N2 - Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow. KW - Bioinformatics KW - Protocol KW - Microbial proteomics KW - Software KW - Mass spectrometry KW - Metaproteomics PY - 2020 DO - https://doi.org/10.1038/s41596-020-0368-7 SN - 1750-2799 VL - 15 IS - 10 SP - 3212 EP - 3239 PB - Nature Publishing Group AN - OPUS4-51335 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Bui, M. A1 - Hoffmann, K. F. A1 - Braun, T. A1 - Riedel, S. A1 - Heinekamp, Christian A1 - Scheurell, K. A1 - Scholz, G. A1 - Stawski, Tomasz A1 - Emmerling, Franziska T1 - An Amorphous Teflate Doped Aluminium Chlorofluoride: A Solid Lewis-Superacid for the Dehydrofluorination of Fluoroalkanes JF - ChemCatChem N2 - Ananion-dopedaluminiumchlorofluoride AlCl0.1F2.8(OTeF5)0.1(ACF-teflate) was synthesized.The material contains pentafluor-oorthotellurate(teflate)groups, which mimic fluoride ions electronically, but are sterically more demanding. They are embedded into the amorphous structure. The latter was studied by PDF analysis, EXAFS data and MAS NMR spectroscopy. The mesoporous powder is a Lewis superacid, and ATR-IR spectra of adsorbed CD3CN reveal a blue-shift of the adsorption band by73 cm-1, which is larger than the shift for SbF5. Remarkably,ACF-teflate catalyzes dehydrofluorination reactions of mono-fluoroalkanes to yield olefins in C6D6. In these cases,no Friedel-Crafts products were formed. KW - Aluminium fluorides KW - Aluminium teflates KW - C-F bond activation KW - Lewis superacids KW - Silanes PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-572290 DO - https://doi.org/10.1002/cctc.202300350 SN - 1867-3880 SP - 1 EP - 7 PB - Wiley VHC-Verlag AN - OPUS4-57229 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Westwood, S. A1 - Martos, G. A1 - Josephs, R. A1 - Choteau, T. A1 - Wielgosz, R. A1 - Davies, S. A1 - Moawad, M. A1 - Tarrant, G. A1 - Chan, B. A1 - Alamgir, M. A1 - de Rego, E. A1 - Wollinger, W. A1 - Garrido, B. A1 - Fernandes, J. A1 - de Sena, R. A1 - Oliveira, R. A1 - Melanson, J. A1 - Bates, J. A1 - Mai Le, P. A1 - Meija, J. A1 - Quan, C. A1 - Huang, T. A1 - Zhang, W. A1 - Ma, R. A1 - Zhang, S. A1 - Hao, Y. A1 - He, Y. A1 - Song, S. A1 - Wang, H. A1 - Su, F. A1 - Zhang, T. A1 - Li, H. A1 - Lam, W. A1 - Wong, W. A1 - Fung, W. A1 - Philipp, Rosemarie A1 - Dorgerloh, Ute A1 - Meyer, Klas A1 - Piechotta, Christian A1 - Riedel, Juliane A1 - Westphalen, Tanja A1 - Giannikopoulou, P. A1 - Alexopoulos, Ch. A1 - Kakoulides, E. A1 - Kitamaki, Y. A1 - Yamazaki, T. A1 - Shimizu, Y. A1 - Kuroe, M. A1 - Numata, M. A1 - Pérez-Castorena, A. A1 - Balderas-Escamilla, M. A1 - Garcia-Escalante, J. A1 - Krylov, A. A1 - Mikheeva, A. A1 - Beliakov, M. A1 - Palagina, M. A1 - Tkachenko, I. A1 - Spirin, S. A1 - Smirnov, V. A1 - Tang Lin, T. A1 - Pui Sze, C. A1 - Juan, W. A1 - Lingkai, W. A1 - Ting, L. A1 - Quinde, L. A1 - Yizhao, C. A1 - Lay Peng, S. A1 - Fernandes-Whaley, M. A1 - Prevoo-Franzsen, D. A1 - Quinn, L. A1 - Nhlapo, N. A1 - Mkhize, D. A1 - Marajh, D. A1 - Chamane, S. A1 - Ahn, S. A1 - Choi, K. A1 - Lee, S. A1 - Han, J. A1 - Baek, S. A1 - Kim, B. A1 - Marbumrung, S. A1 - Jongmesuk, P. A1 - Shearman, K. A1 - Boonyakong, C. A1 - Bilsel, M. A1 - Gündüz, S. A1 - Ün, I. A1 - Yilmaz, H. A1 - Bilsel, G. A1 - Gökçen, T. A1 - Clarkson, C. A1 - Warren, J. A1 - Achtar, E. T1 - Mass fraction assignment of Bisphenol-A high purity material JF - Metrologia N2 - The CCQM-K148.a comparison was coordinated by the BIPM on behalf of the CCQM Organic Analysis Working Group for NMIs and DIs which provide measurement services in organic analysis under the CIPM MRA. It was undertaken as a "Track A" comparison within the OAWG strategic plan. CCQM-K148.a demonstrates capabilities for assigning the mass fraction content of a solid organic compound having moderate molecular complexity, where the compound has a molar mass in the range (75 - 500) g/mol and is non-polar (pKow < −2), when present as the primary organic component in a neat organic solid and where the mass fraction content of the primary component in the material is in excess of 950 mg/g. Participants were required to report the mass fraction of Bisphenol A present in one supplied unit of the comparison material. Participants using a mass balance method for the assignment were also required to report their assignments of the impurity components present in the material. Methods used by the seventeen participating NMIs or DIs were predominantly based on either stand-alone mass balance (summation of impurities) or qNMR approaches, or the combination of data obtained using both methods. The results obtained using thermal methods based on freezing-point depression methods were also reported by a limited number of participants. There was excellent agreement between assignments obtained using all three approaches to assign the BPA content. The assignment of the values for the mass fraction content of BPA consistent with the KCRV was achieved by most of the comparison participants with an associated relative standard uncertainty in the assigned value in the range (0.1 - 0.5)%. KW - Bisphenol-A KW - Purity assessment KW - Interlaboratory key comparison KW - Metrology PY - 2021 DO - https://doi.org/10.1088/0026-1394/58/1A/08015 VL - 58 IS - 1A SP - 08015 PB - IOP Publishing AN - OPUS4-54188 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kidangan, R. T. A1 - Unnikrishnakurup, Sreedhar A1 - P. Vengara, N. A1 - Balasubramaniam, Krishnan A1 - Rajagopal, P. A1 - Phani Prabhakar, K. V. A1 - Padmanabham, G. A1 - Riedel, F. A1 - Puschmann, M. T1 - Online monitoring of cold metal transfer (CMT) process using infrared thermography JF - Quantitative Infrared Thermography Journal N2 - Online (passive) thermographic inspection of overlap joints of aluminium and zinc coated steel sheets made by cold metal Transfer weld brazing process was explored. Different experimental Trials were conducted for demonstrating the feasibility of thermographic inspection to detect the porosities, improper weld bead and to differentiate the pre weld temperature. The whole process was monitored using infrared cameras in different wavelength region. Image analysis algorithms were developed to reconstruct the thermal images that contain the signatures of the weld defects and to extract the pre weld temperature and ist evolution with distance from the centre of the weld torch. Post-weld radiography lends strong Support to the observations. KW - Infrared thermography KW - Dissimilar joints KW - Online monitoring KW - Cold metal transfer process PY - 2016 DO - https://doi.org/10.1080/17686733.2016.1229330 SN - 1768-6733 SN - 2116-7176 VL - 14 IS - 1 SP - 68 EP - 78 PB - Taylor & Francis AN - OPUS4-38910 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Hofmann, J. A1 - Riedel, Jens A1 - Beck, S. A1 - Pagel, K. A1 - Linscheid, M. W. T1 - Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility JF - European Journal of Mass Spectrometry N2 - Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence. KW - Ion mobility KW - Collision-induced dissociation KW - Mass spectrometry KW - Oligonucleotide KW - Fragmentation KW - Tandem-MS PY - 2018 DO - https://doi.org/10.1177/1469066717746896 SN - 1469-0667 SN - 1751-6838 VL - 24 IS - 2 SP - 225 EP - 230 PB - Sage AN - OPUS4-44429 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Schwaar, Timm A1 - Springer, A. A1 - Grabarics, M. A1 - Riedel, Jens A1 - Beck, S. A1 - Pagel, K. A1 - Linscheid, M. W. T1 - Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes JF - Journal of Mass Spectrometry N2 - DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences – bearing mismatch positions and abasic sites of complementary DNA 15-mers – were investigated to unravel general trends in their stability in the gas phase. Single stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid. KW - Oligonucleotide fragmentation KW - Locked nucleic acids KW - Collision induced dissociation (CID) KW - Double strands KW - Ion mobility spectrometry PY - 2019 DO - https://doi.org/10.1002/jms.4344 VL - 54 IS - 5 SP - 402 EP - 411 PB - Wiley AN - OPUS4-47485 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -