TY - JOUR A1 - Zia, Ghezal Ahmad Jan A1 - Hanke, Thomas A1 - Skrotzki, Birgit A1 - Völker, Christoph A1 - Bayerlein, Bernd T1 - Enhancing Reproducibility in Precipitate Analysis: A FAIR Approach with Automated Dark-Field Transmission Electron Microscope Image Processing JF - Integrating Materials and Manufacturing Innovation N2 - AbstractHigh-strength aluminum alloys used in aerospace and automotive applications obtain their strength through precipitation hardening. Achieving the desired mechanical properties requires precise control over the nanometer-sized precipitates. However, the microstructure of these alloys changes over time due to aging, leading to a deterioration in strength. Typically, the size, number, and distribution of precipitates for a quantitative assessment of microstructural changes are determined by manual analysis, which is subjective and time-consuming. In our work, we introduce a progressive and automatable approach that enables a more efficient, objective, and reproducible analysis of precipitates. The method involves several sequential steps using an image repository containing dark-field transmission electron microscopy (DF-TEM) images depicting various aging states of an aluminum alloy. During the process, precipitation contours are generated and quantitatively evaluated, and the results are comprehensibly transferred into semantic data structures. The use and deployment of Jupyter Notebooks, along with the beneficial implementation of Semantic Web technologies, significantly enhances the reproducibility and comparability of the findings. This work serves as an exemplar of FAIR image and research data management. KW - Industrial and Manufacturing Engineering KW - General Materials Science KW - Automated image analysis KW - FAIR research data management KW - Reproducibility KW - microstructural changes PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-593905 DO - https://doi.org/10.1007/s40192-023-00331-5 SN - 2193-9772 SP - 1 EP - 15 PB - Springer Science and Business Media LLC CY - Heidelberg AN - OPUS4-59390 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Bayerlein, Bernd A1 - Schilling, Markus A1 - Birkholz, Henk A1 - Jung, Matthias A1 - Waitelonis, Jörg A1 - Mädler, Lutz A1 - Sack, Harald T1 - PMD Core Ontology: Achieving semantic interoperability in materials science JF - Materials and Design N2 - Knowledge representation in the Materials Science and Engineering (MSE) domain is a vast and multi-faceted challenge: Overlap, ambiguity, and inconsistency in terminology are common. Invariant (consistent) and variant (context-specific) knowledge are difficult to align cross-domain. Generic top-level semantic terminology often is too abstract, while MSE domain terminology often is too specific. In this paper, an approach how to maintain a comprehensive MSE-centric terminology composing a mid-level ontology–the Platform MaterialDigital Core Ontology (PMDco)–via MSE community-based curation procedures is presented. The illustrated findings show how the PMDco bridges semantic gaps between high-level, MSE-specific, and other science domain semantics. Additionally, it demonstrates how the PMDco lowers development and integration thresholds. Moreover, the research highlights how to fuel it with real-world data sources ranging from manually conducted experiments and simulations with continuously automated industrial applications. KW - Ontology KW - Materials science and engineering KW - Knowledge representation KW - Reproducibility KW - Semantic interoperability KW - Semantic data integration PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-592948 DO - https://doi.org/10.1016/j.matdes.2023.112603 SN - 0264-1275 VL - 237 SP - 1 EP - 12 PB - Elsevier CY - Amsterdam AN - OPUS4-59294 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Becker, Roland A1 - Sporkert, F. A1 - Lô, I. A1 - Baumgartner, M. T1 - The determination of ethyl glucuronide in hair: Experiences from nine consecutive interlaboratory comparison rounds JF - Forensic Science International N2 - The increasing request for hair ethyl glucuronide (HEtG) in alcohol consumption monitoring according to cut-off levels set by the Society of Hair Testing (SoHT) has triggered a proficiency testing program based on interlaboratory comparisons (ILC). Here, the outcome of nine consecutive ILC rounds organised by the SoHT on the determination of HEtG between 2011 and 2017 is summarised regarding interlaboratory reproducibility and the influence of procedural variants. Test samples prepared from cut hair (1 mm) with authentic (in-vivo incorporated) and soaked (in-vitro incorporated) HEtG concentrations up to 80 pg/mg were provided for 27–35 participating laboratories. Laboratory results were evaluated according to ISO 5725-5 and provided robust averages and relative reproducibility standard deviations typically between 20 and 35% in reasonable accordance with the prediction of the Horwitz model. Evaluation of results regarding the analytical techniques revealed no significant differences between gas and liquid chromatographic methods In contrast, a detailed evaluation of different sample preparations revealed significantly higher average values in case when pulverised hair is tested compared to cut hair. This observation was reinforced over the different ILC rounds and can be attributed to the increased acceptance and routine of hair pulverisation among laboratories. Further, the reproducibility standard deviations among laboratories performing pulverisation were on average in very good agreement with the prediction of the Horwitz model. Use of sonication showed no effect on the HEtG extraction yield. KW - Ethyl glucuronide KW - Interlaboratory comparison KW - Proficiency testing KW - Society of hair testing KW - Reproducibility KW - Pulverization PY - 2018 DO - https://doi.org/10.1016/j.forsciint.2018.04.025 SN - 0379-0738 SN - 1872-6283 VL - 288 SP - 67 EP - 71 PB - Elsevier AN - OPUS4-44881 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tscheuschner, Georg A1 - Schwaar, Timm A1 - Weller, Michael G. T1 - Fast Confirmation of Antibody Identity by MALDI-TOF MS Fingerprints JF - Antibodies N2 - Thousands of antibodies for diagnostic and other analytical purposes are on the market. However, it is often difficult to identify duplicates, reagent changes, and to assign the correct original publications to an antibody. This slows down scientific progress and might even be a cause of irreproducible research and a waste of resources. Recently, activities were started to suggest the sole use of recombinant antibodies in combination with the open communication of their sequence. In this case, such uncertainties should be eliminated. Unfortunately, this approach seems to be rather a long-term vision since the development and manufacturing of recombinant antibodies remain quite expensive in the foreseeable future. Nearly all commercial antibody suppliers also may be reluctant to publish the sequence of their antibodies, since they fear counterfeiting. De novo sequencing of antibodies is also not feasible today for a reagent user without access to the hybridoma clone. Nevertheless, it seems to be crucial for any scientist to have the opportunity to identify an antibody undoubtedly to guarantee the traceability of any research activity using antibodies from a third party as a tool. For this purpose, we developed a method for the identification of antibodies based on a MALDI-TOF MS fingerprint. To circumvent lengthy denaturation, reduction, alkylation, and enzymatic digestion steps, the fragmentation was performed with a simple formic acid hydrolysis step. Eighty-nine unknown monoclonal antibodies were used for this study to examine the feasibility of this approach. Although the molecular assignment of peaks was rarely possible, antibodies could be easily recognized in a blinded test, simply from their mass-spectral fingerprint. A general protocol is given, which could be used without any optimization to generate fingerprints for a database. We want to propose that, in most scientific projects relying critically on antibody reagents, such a fingerprint should be established to prove and document the identity of the used antibodies, as well as to assign a specific reagent to a datasheet of a commercial supplier, public database record, or antibody ID. KW - Reproducibility KW - Quality Control KW - Traceability KW - Diagnostics KW - Hybridoma KW - Monoclonal Antibody KW - Recombinant Antibody PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-506611 DO - https://doi.org/10.3390/antib9020008 SN - 2310-287X VL - 9 IS - 2 SP - 1 EP - 17 PB - MDPI CY - Basel AN - OPUS4-50661 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tscheuschner, Georg A1 - Kaiser, Melanie N. A1 - Lisec, Jan A1 - Beslic, D. A1 - Muth, Thilo A1 - Krüger, M. A1 - Mages, H. W. A1 - Dorner, B. G. A1 - Knospe, J. A1 - Schenk, J. A. A1 - Sellrie, F. A1 - Weller, Michael G. T1 - MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour JF - Antibodies N2 - During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 60 min and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 degrees C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context. KW - Reproducibility KW - Quality control KW - Traceability KW - Peptides KW - Peptide mass fingerprinting KW - Monoclonal antibody KW - Recombinant antibody KW - Identity KW - Antibody identification KW - Sequencing KW - Light chain KW - Mass spectrometry KW - Software KW - Open science KW - Library KW - COVID-19 KW - Corona virus KW - Sequence coverage KW - NIST-mAb 8671 KW - Reference material KW - RBD KW - Spike protein KW - Nucleocapsid KW - Cleavage KW - Tryptic digest KW - MALDI KW - DHAP KW - 2,5-dihydroxyacetophenone KW - Github KW - Zenodo KW - ABID PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-547347 DO - https://doi.org/10.3390/antib11020027 VL - 11 IS - 2 SP - 1 EP - 22 PB - MDPI CY - Basel AN - OPUS4-54734 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -