TY - JOUR A1 - Van Den Bossche, T. A1 - Kunath, B. A1 - Schallert, K. A1 - Schäpe, S. A1 - Abraham, P. E. A1 - Armengaud, J. A1 - Arntzen, M. Ø. A1 - Bassignani, A. A1 - Benndorf, D. A1 - Fuchs, S. A1 - Giannone, R. J. A1 - Griffin, T. J. A1 - Hagen, L. H. A1 - Halder, R. A1 - Henry, C. A1 - Hettich, R. L. A1 - Heyer, R. A1 - Jagtap, P. A1 - Jehmlich, N. A1 - Jensen, M. A1 - Juste, C. A1 - Kleiner, M. A1 - Langella, O. A1 - Lehmann, T. A1 - Leith, E. A1 - May, P. A1 - Mesuere, B. A1 - Miotello, G. A1 - Peters, S. L. A1 - Pible, O. A1 - Queiros, P. T. A1 - Reichl, U. A1 - Renard, B. Y. A1 - Schiebenhoefer, H. A1 - Sczyrba, A. A1 - Tanca, A. A1 - Trappe, K. A1 - Trezzi, J.-P. A1 - Uzzau, S. A1 - Verschaffelt, P. A1 - von Bergen, M. A1 - Wilmes, P. A1 - Wolf, M. A1 - Martens, L. A1 - Muth, Thilo T1 - Critical Assessment of MetaProteome Investigation (CAMPI): A multi-laboratory comparison of established workflows N2 - Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments. KW - Metaproteomics KW - Mass spectrometry KW - Data science KW - Benchmarking KW - Bioinformatics PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-541220 DO - https://doi.org/10.1038/s41467-021-27542-8 SN - 2041-1723 VL - 12 SP - 1 EP - 15 PB - Nature Publishing Group CY - London AN - OPUS4-54122 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Anzt, H. A1 - Bach, F. A1 - Druskat, S. A1 - Löffler, F. A1 - Loewe, A. A1 - Renard, B. Y. A1 - Seemann, G. A1 - Struck, A. A1 - Achhammer, E. A1 - Aggarwal, P. A1 - Appel, F. A1 - Bader, M. A1 - Brusch, L. A1 - Busse, C. A1 - Chourdakis, G. A1 - Dabrowski, P. W. A1 - Ebert, P. A1 - Flemisch, B. A1 - Friedl, S. A1 - Fritzsch, B. A1 - Funk, M. D. A1 - Gast, V. A1 - Goth, F. A1 - Grad, J. A1 - Hegewald, J. A1 - Hermann, S. A1 - Hohmann, F. A1 - Janosch, S. A1 - Kutra, D. A1 - Linxweiler, J. A1 - Muth, Thilo A1 - Peters-Kottig, W. A1 - Rack, F. A1 - Raters, F. H. C. A1 - Rave, S. A1 - Reina, G. A1 - Reißig, M. A1 - Ropinski, T. A1 - Schaarschmidt, J. A1 - Seibold, H. A1 - Thiele, J. P. A1 - Uekermann, B. A1 - Unger, S. A1 - Weeber, R. T1 - An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action N2 - Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. KW - Research Software KW - Sustainable Software Development KW - Academic Software KW - Software Infrastructure KW - Software Training KW - Software Licensing PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-522029 DO - https://doi.org/10.12688/f1000research.23224.2 VL - 9 SP - 1 EP - 35 AN - OPUS4-52202 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Buckle, T. A1 - van der Wal, S. A1 - van Malderen, S. A1 - Müller, Larissa A1 - Kuil, J. A1 - van Unen, V. A1 - Peters, R. A1 - van Bemmel, M. A1 - McDonnell, L. A1 - Velders, A. A1 - Koning, F. A1 - Vanhaeke, F. A1 - van Leeuwen, F. T1 - Hybrid imaging labels: providing the link between mass spectrometry-based molecular pathology and theranostics N2 - Development of theranostic concepts that include inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) imaging can be hindered by the lack of a direct comparison to more standardly used methods for in vitro and in vivo evaluation; e.g. fluorescence or nuclear medicine. In this study a bimodal (or rather, hybrid) tracer that contains both a fluorescent dye and a chelate was used to evaluate the existence of a direct link between mass spectrometry (MS) and in vitro and in vivo molecular imaging findings using fluorescence and radioisotopes. At the same time, the hybrid label was used to determine whether the use of a single isotope label would allow for MS-based diagnostics. KW - Imaging KW - Laser Ablation ICP-MS KW - Diagnostics PY - 2017 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-396813 DO - https://doi.org/10.7150/thno.17484 VL - 7 IS - 3 SP - 624 EP - 633 PB - IvySpring AN - OPUS4-39681 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Mielke, Johannes A1 - Hanke, F. A1 - Peters, M.V. A1 - Hecht, S. A1 - Persson, M. A1 - Grill, L. T1 - Adatoms underneath single porphyrin molecules on Au(111) N2 - The adsorption of porphyrin derivatives on a Au(111) surface was studied by scanning tunneling microscopy and spectroscopy at low temperatures in combination with density functional theory calculations. Different molecular appearances were found and could be assigned to the presence of single gold adatoms bonded by a coordination bond underneath the molecular monolayer, causing a characteristic change of the electronic structure of the molecules. Moreover, this interpretation could be confirmed by manipulation experiments of individual molecules on and off a single gold atom. This study provides a detailed understanding of the role of metal adatoms in surface–molecule bonding and anchoring and of the appearance of single molecules, and it should prove relevant for the imaging of related molecule–metal systems. PY - 2015 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-324144 UR - http://pubs.acs.org/doi/pdf/10.1021/ja510528x DO - https://doi.org/10.1021/ja510528x SN - 0002-7863 SN - 1520-5126 VL - 137 IS - 5 SP - 1844 EP - 1849 PB - American Chemical Society CY - Washington, DC AN - OPUS4-32414 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Peters, R. A1 - Elbers, I. A1 - Undas, A. A1 - Sijtsma, E. A1 - Briffa, S. A1 - Carnell-Morris, P. A1 - Siupa, A. A1 - Yoon, T.-H. A1 - Burr, L. A1 - Schmid, D. A1 - Tentschert, J. A1 - Hachenberger, Y. A1 - Jungnickel, H. A1 - Luch, A. A1 - Meier, F. A1 - Kocic, J. A1 - Kim, J. A1 - Park, B. C. A1 - Hardy, B. A1 - Johnston, C. A1 - Jurkschat, K. A1 - Radnik, Jörg A1 - Hodoroaba, Vasile-Dan A1 - Lynch, I. A1 - Valsami-Jones, E. T1 - Benchmarking the ACEnano toolbox for characterisation of nanoparticle size and concentration by interlaboratory comparisons N2 - ACEnano is an EU-funded project which aims at developing, optimising and validating methods for the detection and characterisation of nanomaterials (NMs) in increasingly complex matrices to improve confidence in the results and support their use in regulation. Within this project, several interlaboratory comparisons (ILCs) for the determination of particle size and concentration have been organised to benchmark existing analytical methods. In this paper the results of a number of these ILCs for the characterisation of NMs are presented and discussed. The results of the analyses of pristine well-defined particles such as 60 nm Au NMs in a simple aqueous suspension showed that laboratories are well capable of determining the sizes of these particles. The analysis of particles in complex matrices or formulations such as consumer products resulted in larger variations in particle sizes within technologies and clear differences in capability between techniques. Sunscreen lotion sample analysis by laboratories using spICP-MS and TEM/SEM identified and confirmed the TiO2 particles as being nanoscale and compliant with the EU definition of an NM for regulatory purposes. In a toothpaste sample orthogonal results by PTA, spICP-MS and TEM/SEM agreed and stated the TiO2 particles as not fitting the EU definition of an NM. In general, from the results of these ILCs we conclude that laboratories are well capable of determining particle sizes of NM, even in fairly complex formulations. KW - Nanomaterials KW - Benchmarking KW - Inter-laboratory comparison KW - ACEnano KW - Characterisation KW - Size KW - Concentration PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-531852 DO - https://doi.org/10.3390/molecules26175315 SN - 1420-3049 VL - 26 IS - 17 SP - 1 EP - 23 PB - MDPI CY - Basel AN - OPUS4-53185 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Peters, R. A1 - Elbers, I. A1 - Undas, A. A1 - Sijtsma, E. A1 - Briffa, S. A1 - Carnell-Morris, P. A1 - Siupa, A. A1 - Yoon, T.-H. A1 - Burr, L. A1 - Schmid, D. A1 - Tentschert, J. A1 - Hachenberger, Y. A1 - Jungnickel, H. A1 - Luch, A. A1 - Meier, F. A1 - Kocic, J. A1 - Kim, J. A1 - Park, B. C. A1 - Hardy, B. A1 - Johnston, C. A1 - Jurkschat, K. A1 - Radnik, Jörg A1 - Hodoroaba, Vasile-Dan A1 - Lynch, I. A1 - Valsami-Jones, E. T1 - Correction: Peters et al. Benchmarking the ACEnano Toolbox for Characterisation of Nanoparticle Size and Concentration by Interlaboratory Comparisons. Molecules 2021, 26, 5315 N2 - This is a corrigendum to the original article "Benchmarking the ACEnano toolbox for characterisation of nanoparticle size and concentration by interlaboratory comparisons" that was published in the journal "Molecules", vol. 26 (2021), no. 17, article 5315. PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-554381 DO - https://doi.org/10.3390/molecules27154849 VL - 27 IS - 4849 SP - 1 EP - 3 PB - MDPI CY - Basel AN - OPUS4-55438 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Mielke, Johannes A1 - Martınez-Blanco, J. A1 - Peters, M. V. A1 - Hecht, S. A1 - Grill, L. T1 - Observing single-atom diffusion at a molecule-metal interface N2 - The dynamics at the interface between a close-packed porphyrin monolayer and Au(111) is investigated by time-dependent scanning tunneling microscopy, detecting the motion of single-interface adatoms in real space. Imaging sequences reveal predominant switching of the molecular appearance in adjacent molecules, pointing to a spatial correlation that is consistent with adatom diffusion from one molecule to the next. In some cases, the number of switching molecules is drastically increased, indicating collective switching events. In addition to the thermally induced motion of adatoms at the interface, also voltage pulses from the microscope tip can induce the process—revealing different yields in agreement with the model of adatom hopping. KW - STM KW - molecular switch KW - single molecule KW - switching dynamics KW - porphyrin KW - Au(111) PY - 2016 UR - http://journals.aps.org/prb/abstract/10.1103/PhysRevB.94.035416 DO - https://doi.org/10.1103/PhysRevB.94.035416 VL - 94 IS - 3 SP - 035416-1 EP - 035416-7 PB - American Physical Society AN - OPUS4-37177 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -