TY - JOUR A1 - Bekemeier, Simon A1 - Caldeira Rêgo, C. R. A1 - Mai, H. L. A1 - Sikia, Ujjal A1 - Waseda, O. A1 - Apel, M. A1 - Arendt, F. A1 - Aschemann, A. A1 - Bayerlein, Bernd A1 - Courant, R. A1 - Dziwis, G. A1 - Fuchs, F. A1 - Giese, U. A1 - Junghanns, K. A1 - Kamal, M. A1 - Koschmieder, L. A1 - Leineweber, S. A1 - Luger, M. A1 - Lukas, M. A1 - Maas, J. A1 - Mertens, J. A1 - Mieller, Björn A1 - Overmeyer, L. A1 - Pirch, N. A1 - Reimann, J. A1 - Schröck, S. A1 - Schulze, P. A1 - Schuster, J. A1 - Seidel, A. A1 - Shchyglo, O. A1 - Sierka, M. A1 - Silze, F. A1 - Stier, S. A1 - Tegeler, M. A1 - Unger, Jörg F. A1 - Weber, M. A1 - Hickel, Tilmann A1 - Schaarschmidt, J. T1 - Advancing Digital Transformation in Material Science: The Role of Workflows Within the MaterialDigital Initiative N2 - The MaterialDigital initiative represents a major driver toward the digitalization of material science. Next to providing a prototypical infrastructure required for building a shared data space and working on semantic interoperability of data, a core focus area of the Platform MaterialDigital (PMD) is the utilization of workflows to encapsulate data processing and simulation steps in accordance with findable, accessible, interoperable, and reusable principles. In collaboration with the funded projects of the initiative, the workflow working group strives to establish shared standards, enhancing the interoperability and reusability of scientific data processing steps. Central to this effort is the Workflow Store, a pivotal tool for disseminating workflows with the community, facilitating the exchange and replication of scientific methodologies. This article discusses the inherent challenges of adapting workflow concepts, providing the perspective on developing and using workflows in the respective domain of the various funded projects. Additionally, it introduces the Workflow Store’s role within the initiative and outlines a future roadmap for the PMD workflow group, aiming to further refine and expand the role of scientific workflows as a means to advance digital transformation and foster collaborative research within material science. KW - Digitalisation KW - FAIR principles KW - MaterialDigital KW - Scientific workflows KW - Semantic interoperability PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-624088 DO - https://doi.org/10.1002/adem.202402149 SN - 1527-2648 IS - 2402149 SP - 1 EP - 25 PB - Wiley-VCH GmbH AN - OPUS4-62408 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - 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 - Reed, B. P. A1 - Cant, D.J.H. A1 - Spencer, J. A1 - Carmona-Carmona, A. J. A1 - Bushell, A. A1 - Herrara-Gómez, A. A1 - Kurokawa, A. A1 - Thissen, A. A1 - Thomas, A.G. A1 - Britton, A.J. A1 - Bernasik, A. A1 - Fuchs, A. A1 - Baddorf, A. P. A1 - Bock, B. A1 - Thellacker, B. A1 - Cheng, B. A1 - Castner, D.G. A1 - Morgan, D.J. A1 - Valley, D. A1 - Willneff, E.A. A1 - Smith, E.F. A1 - Nolot, E. A1 - Xie, F. A1 - Zorn, G. A1 - Smith, G.C. A1 - Yasukufu, H. A1 - Fenton, J. L. A1 - Chen, J. A1 - Counsell, J..D.P. A1 - Radnik, Jörg A1 - Gaskell, K.J. A1 - Artyushkova, K. A1 - Yang, L. A1 - Zhang, L. A1 - Eguchi, M. A1 - Walker, M. A1 - Hajdyla, M. A1 - Marzec, M.M. A1 - Linford, M.R. A1 - Kubota, N. A1 - Cartazar-Martínez, O. A1 - Dietrich, P. A1 - Satoh, R. A1 - Schroeder, S.L.M. A1 - Avval, T.G. A1 - Nagatomi, T. A1 - Fernandez, V. A1 - Lake, W. A1 - Azuma, Y. A1 - Yoshikawa, Y. A1 - Shard, A.G. T1 - Versailles Project on Advanced Materials and Standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene N2 - We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration. KW - X-ray photoelectron spectroscopy KW - Transmission function KW - Intensity scale calibration KW - Reference spectra KW - Low-density polyethylene (LDPE) PY - 2020 DO - https://doi.org/10.1116/6.0000577 VL - 38 IS - 6 SP - 063208 AN - OPUS4-51655 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Reed, B. P. A1 - Cant, D.J.H. A1 - Spencer, S.J. A1 - Carmona-Carmona, A. J. A1 - Bushell, A. A1 - Herrara-Gómez, A. A1 - Kurokawa, A. A1 - Thissen, A. A1 - Thomas, A.G. A1 - Britton, A.J. A1 - Bernasik, A. A1 - Fuchs, A. A1 - Baddorf, A.P. A1 - Bock, B. A1 - Thellacker, B. A1 - Cheng, B. A1 - Castner, D.G. A1 - Morgan, D.J. A1 - Valley, D. A1 - Willneff, E.A. A1 - Smith, E.P. A1 - Nolot, E. A1 - Xie, F. A1 - Zorn, G. A1 - Smith, G.C. A1 - Yasukufu, H. A1 - Fenton, J.L. A1 - Chen, J. A1 - Counsell, J.D.P. A1 - Radnik, Jörg A1 - Gaskell, K.J. A1 - Artyushkova, K. A1 - Yang, L. A1 - Zhang, L. A1 - Eguchi, M. A1 - Walker, M. A1 - Hajdyla, M. A1 - Marzec, M.M. A1 - Linford, M.R. A1 - Kubota, N. A1 - Cortazar-Martinez, O. A1 - Dietrich, P. A1 - Satoh, R. A1 - Schroeder, S.L.M. A1 - Avval, T.G. A1 - Nagatomi, T. A1 - Fernandez, V. A1 - Lake, W. A1 - Azuma, Y. A1 - Yoshikawa, Y. A1 - Compean-Gonzalez, C.L. A1 - Ceccone, G. A1 - Shard, A.G. T1 - ERRATUM: “Versailles project on advanced materials and standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene” [J. Vac. Sci. Technol. A 38, 063208 (2020)] N2 - The lead authors failed to name two collaborators as co-authors. The authors listed should include: Miss Claudia L. Compean-Gonzalez (ORCID: 0000-0002-2367-8450) and Dr. Giacomo Ceccone (ORCID: 0000-0003-4637-0771). These co-authors participated in VAMAS project A27, provided data that were analyzed and presented in this publication (and supporting information), and reviewed the manuscript before submission. KW - X-ray photoelectron spectroscopy KW - Transmission function KW - Low-density polyethylene PY - 2021 DO - https://doi.org/10.1116/6.0000907 VL - 39 IS - 2 SP - 027001 PB - American Vacuum Society AN - OPUS4-52380 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Altmann, Korinna A1 - Heymann, S. A1 - Braun, U. A1 - Bannick, C.-G. A1 - Heller, C. A1 - Fuchs, M. A1 - Scheid, C. A1 - Abusafia, A. A1 - Steinmetz, H. A1 - Ricking, M. A1 - Kerndorff, A. T1 - Untersuchungsverfahren von Mikroplastikgehalten im Wasser für Praxis und Wissenschaft N2 - Zielsetzung des vom Bundesministerium für Bildung und Forschung geförderten Projektes RUSEKU war es, repräsentative Untersuchungsstrategien für die Detektion von Mikroplastik mittels TED GC/MS in wässerigen Medien zu ermitteln. Dabei wurden verschiedene Probenahmekonzepte und – verfahren für unterschiedliche Fallgestaltungen und Fragestellungen untersucht, sowie neue Filtersysteme entwickelt. Bei der Detektion der Partikel lag der Fokus auf der Anwendung und Weiterentwicklung der ThermoExtraktion/Desorption-Gaschromatographie-Massenspektrometrie (TED-GC/MS) zur Bestimmung von Mikroplastikgehalten. Anwendung fanden die Methoden bei der Beprobung von Flaschenwasser, Waschmaschinenabläufen, dem urbanen Abwassersystem der Stadt Kaiserslautern, sowie in Oberflächengewässer. KW - Mikroplastik KW - TED-GC/MS KW - Mikroplastik-Analytik KW - Probennahme PY - 2021 VL - 14. Jahrgang IS - 3 SP - 147 EP - 152 PB - Deutschen Vereinigung für Wasserwirtschaft, Abwasser und Abfall CY - Hennef AN - OPUS4-52260 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - 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 - Heller, C. A1 - Altmann, Korinna A1 - Braun, U. A1 - Kerndorff, A. A1 - Bannick, C.-G. A1 - Fuchs, M. A1 - Thamsen, P. U. T1 - Garment ageing in a laundry care process under household‐like conditions N2 - This study reflects typical consumer textile washing behaviour while taking into account existing standards in the household appliance and garment industries. Two garments were washed repeatedly with artificial dirt and detergent 30 times. The collected washing water was separated using fractional filtration. Textile physical tests were used to follow property changes of the garments, the microplastic release is determined using thermoextraction/desorbtion–gas chromatography/mass spectrometry and the total organic carbon was measured as a sum parameter for the organic bonded carbon. This article shows the importance of a reality‐based approach when investigating microplastics of textile origin in the laundry care process. Deposits of detergent and dirt on the textiles were detected. The total mass of sieve residues was much higher than the release of synthetic polymers. The cotton content of the garments causes a much higher fibre release than synthetic fibres. Both will lead to false results by purely gravimetric analysis because nonpolymer fibres will be included microplastic mass. The results cannot be generalised only by the main polymer type, knowledge of the textile construction must be included for final evaluation. KW - Fibre release KW - Microplastics KW - TED-GC/MS KW - Washing machine PY - 2023 DO - https://doi.org/10.1002/appl.202200086 SP - 1 EP - 8 PB - Wiley online library AN - OPUS4-56976 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kasper, J. A1 - Herrmanns, M.I. A1 - Bantz, C. A1 - Utech, S. A1 - Koshkina, Olga A1 - Maskos, Michael A1 - Brochhausen, C. A1 - Pohl, C. A1 - Fuchs, S. A1 - Unger, R. E. A1 - Kirkpatrick, C.J. T1 - Flotillin-involved uptake of silica nanoparticles and responses of an alveolar-capillary barrier in vitro N2 - Drug and gene delivery via nanoparticles across biological barriers such as the alveolar-capillary barrier of the lung constitutes an interesting and increasingly relevant field in nanomedicine. Nevertheless, potential hazardous effects of nanoparticles (NPs) as well as their cellular and systemic fate should be thoroughly examined. Hence, this study was designed to evaluate the effects of amorphous silica NPs (Sicastar) and (poly)organosiloxane NPs (AmOrSil) on the viability and the inflammatory response as well as on the cellular uptake mechanisms and fate in cells of the alveolar barrier. For this purpose, the alveolar epithelial cell line (NCI H441) and microvascular endothelial cell line (ISO-HAS-1) were used in an experimental set up resembling the alveolar-capillary barrier of the lung. In terms of IL-8 and sICAM Sicastar resulted in harmful effects at higher concentrations (60 µg/ml) in conventional monocultures but not in the coculture, whereas AmOrSil showed no significant effects. Immunofluorescence counterstaining of endosomal structures in NP-incubated cells showed no evidence for a clathrin- or caveolae-mediated uptake mechanism. However, NPs were enclosed in flotillin-1 and -2 marked vesicles in both cell types. Flotillins appear to play a role in cellular uptake or trafficking mechanisms of NPs and are discussed as indicators for clathrin- or caveolae-independent uptake mechanisms. In addition, we examined the transport of NPs across this in vitro model of the alveolar-capillary barrier forming a tight barrier with a transepithelial electrical resistance of 560 ± 8 Ω cm². H441 in coculture with endothelial cells took up much less NPs compared to monocultures. Moreover, coculturing prevented the transport of NP from the epithelial compartment to the endothelial layer on the bottom of the filter insert. This supports the relevance of coculture models, which favour a differentiated and polarised epithelial layer as in vitro test systems for nanoparticle uptake. KW - Silica nanoparticles KW - Alveolar-capillary barrier KW - NP uptake KW - NP-transport KW - Endocytosis KW - Flotillin-1/-2-dependent uptake/trafficking PY - 2013 DO - https://doi.org/10.1016/j.ejpb.2012.10.011 SN - 0939-6411 SN - 1873-3441 VL - 84 IS - 2 SP - 275 EP - 287 PB - Elsevier B.V. CY - Amsterdam AN - OPUS4-28841 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -