TY - GEN A1 - Lisec, Jan T1 - fioRa N2 - R package providing a wrapper for the python module 'FIORA' as well as a 'shiny'-App to facilitate data processing and visualization. 'FIORA' allows to predict Mass-Spectra based on the SMILES code of chemical compounds. It is described in the Nature Communications article by Nowatzky et al. (2025). KW - Mass Spectrometry PY - 2025 UR - https://github.com/cran/fiora/ PB - GitHub CY - San Francisco AN - OPUS4-64663 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Nowatzky, Yannek T1 - Fiora: Source Data for Training and Testing N2 - This repository contains source data for training and testing the Fiora model (see GitHub and DOI: 10.5281/zenodo.14651774). As part of the Fiora study (Nowatzky et al., 2025), which introduces a GNN-based fragmentation algorithm for simulating MS/MS spectra, this dataset enables the reproduction of the study’s findings and the training of new spectral prediction models. KW - Bioinformatics KW - Mass spectrometry KW - Machine Learning PY - 2025 DO - https://doi.org/10.5281/zenodo.14782249 PB - Zenodo CY - Geneva AN - OPUS4-64587 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan A1 - Sommerfeld, Thomas A1 - Riedel, Juliane A1 - Mauch, Tatjana A1 - Koch, Matthias T1 - CRM BAM-B003 eCerto data file N2 - Data file (RData) containing measurement data recorded during the production process of the Certified Reference Material BAM-B003 containing per- and polyfluoroalkyl substances (PFAS) in textiles. The data can be most conveniently openend using the Shiny-App eCerto which is accessible at https://www.bam.de/eCerto. KW - Certified reference material KW - Mass spectrometry KW - PFAS PY - 2025 DO - https://doi.org/10.5281/zenodo.15907581 PB - Zenodo CY - Geneva AN - OPUS4-64544 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Döring, Sarah T1 - Sequence of Mus Musculus monoclonal IgG2c anti-CCMV Immunoglobulin N2 - We report the full-length nucleotide and amino acid sequences of the light (κ) and heavy chain of the IgG2c anti-CCMV monoclonal antibody (hybridoma clone BAM-CCMV-29-81), generated against Cowpea Chlorotic Mottle Virus (CCMV). Sequencing of hybridoma clone was performed using a cost-effective Sanger-based workflow that includes DNA-level subclass determination and peptide mass fingerprint confirmation. The κ-chain sequence was assigned to IGKV4-6101 / IGKJ101, while the heavy chain was assigned to IGHV2-601 / IGHD1-101 / IGHJ3*01 with IgG2c constant regions from the NOD strain. Both chains were validated against RNA Illumina sequencing, confirming 100% identity. The sequences are available in GenBank under accession numbers PX123807 (κ-chain) and PX123808 (heavy chain). KW - Antibody Sequencing KW - BAM-CCMV-29-81 KW - anti-CCMV-antibody PY - 2025 UR - https://www.ncbi.nlm.nih.gov/nuccore/PX123807 UR - https://www.ncbi.nlm.nih.gov/nuccore/PX123808 PB - National Library of Medicine CY - Bethesda AN - OPUS4-63968 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Deumer, J. A1 - Andresen, Elina T1 - SAXS data of bipyramidal LiYF4 nanoparticles N2 - SAXS data of bipyramidal LiYF4 nanoparticles synthesized by the Federal Institute for Materials Research and Testing (BAM) and measured by the Physikalisch-Technische Bundesanstalt (PTB) at the synchrotron facility Bessy II, Berlin, Germany. KW - Reference data set KW - Simulation KW - Reference material KW - Upconversion nanoparticles KW - Particle number concentration KW - SAXS PY - 2024 DO - https://doi.org/10.5281/zenodo.13691409 PB - Zenodo CY - Geneva AN - OPUS4-62134 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Hülagü, Deniz A1 - Tobias, Charlie A1 - Dao, R. A1 - Komarow, P. A1 - Rurack, Knut A1 - Hodoroaba, Vasile-Dan T1 - Dataset accompanying the publication "Towards 3D determination of the surface roughness of core-shell microparticles as a routine quality control procedure by scanning electron microscopy" N2 - This dataset accompanies the following publication: Hülagü, D., Tobias, C., Dao, R., Komarov, P., Rurack, K., Hodoroaba, V.-D., Towards 3D determination of the surface roughness of core-shell microparticles as a routine quality control procedure by scanning electron microscopy. Sci.Rep, 14, 17936 (2024), https://doi.org/10.1038/s41598-024-68797-7. It contains SEM and AFM-in-SEM images of polystyrene (PS) core particles, polystyrene-iron oxide (PS/Fe3O4) core-shell particles, and polystyrene-iron oxide-silica (PS/Fe3O4/SiO2) core-shell-shell particles. Please refer to the publication and its supporting information for more details on the acquisition and contents of the dataset, as well as the GitHub repository at https://github.Com/denizhulagu/roughness-analysis-by-electron-microscopy. The investigated particles were produced at BAM laboratories as previously described in: Hülagü, D. et al. Generalized analysis approach of the profile roughness by electron microscopy with the example of hierarchically grown polystyrene–iron oxide–silica core–shell–shell particles. Adv. Eng. Mater. 24, 2101344, https://doi.org/10.1002/adem.202101344 (2022). Tobias, C., Climent, E., Gawlitza, K. & Rurack, K. Polystyrene microparticles with convergently grown mesoporous silica shells as a promising tool for multiplexed bioanalytical assays. ACS Appl. Mater. Interfaces 13, 207, https://dx.doi.org/10.1021/acsami.0c17940 (2020). KW - Core–shell particles KW - Image analysis KW - Roughness KW - Scanning electron microscopy KW - Atomic force microscopy KW - Tilting KW - Batch analysis PY - 2024 UR - https://zenodo.org/records/11108726 DO - https://doi.org/10.5281/zenodo.11108725 PB - Zenodo CY - Geneva AN - OPUS4-60760 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Kazlagić, Anera A1 - Rosner, M. A1 - Cipriani, A. A1 - Frick, D. A. A1 - Glodny, J. A1 - Hoffmann, E. J. A1 - Hora, J. M. A1 - Irrgeher, J. A1 - Lugli, F. A1 - Magna, T. A1 - Meisel, T. C. A1 - Meixner, A. A1 - Possolo, A. A1 - Pramann, A. A1 - Pribil, M. J. A1 - Prohaska, T. A1 - Retzmann, A. A1 - Rienitz, O. A1 - Rutherford, D. A1 - Paula-Santos, G. M. A1 - Tatzel, M. A1 - Widhalm, S. A1 - Willbold, M. A1 - Zuliani, T. A1 - Vogl, Jochen T1 - Data of the characterisation of conventional 87Sr/86Sr isotope ratios in cement, limestone and slate reference materials based on an interlaboratory comparison study N2 - This dataset represents the electronic supplementary material (ESM) of the publication entitled "Characterisation of conventional 87Sr/86Sr isotope ratios in cement, limestone and slate reference materials based on an interlaboratory comparison study", which is published in Geostandards and Geoanalytical Research under the DOI: 10.1111/GGR.12517. It consists of four files. 'ESM_Data.xlsx' contains all reported data of the participants, a description of the applied analytical procedures, basic calculations, the consensus values, and part of the uncertainty assessment. 'ESM_Figure-S1' displays a schematic on how measurements, sequences and replicates are treated for the uncertainty calculation carried out by PTB. 'ESM_Technical-protocol.pdf' is the technical protocol of the interlaboratory comparison, which has been provided to all participants together with the samples and which contains bedside others the definition of the measurand and guidelines for data assessment and calculations. 'ESM_Reporting-template.xlsx' is the Excel template which has been submitted to all participants for reporting their results within the interlaboratory comparison. Excel files with names of the the structure 'GeoReM_Material_Sr8786_Date.xlsx' represent the Rcon(87Sr/86Sr) data for a specific reference material downloaded from GeoReM at the specified date, e.g. 'GeoReM_IAPSO_Sr8786_20221115.xlsx' contains all Rcon(87Sr/86Sr) data for the IAPSO seawater standard listed in GeoReM until 15 November 2022. KW - Reference data KW - Strontium isotope ratio KW - Interlaboratory comparison KW - Reference material KW - Cement KW - Geological material KW - Value assignment KW - Measurement uncertainty KW - Conventional method PY - 2023 UR - https://doi.org/10.5281/zenodo.7804445 DO - https://doi.org/10.5281/zenodo.7804444 PB - Zenodo CY - Geneva AN - OPUS4-57809 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Sommerfeld, Thomas A1 - Koch, Matthias A1 - Mauch, Tatjana A1 - Jung, Christian A1 - Riedel, Juliane A1 - Lisec, Jan T1 - CRM BAM-A001 eCerto data file N2 - Data file (RData) containing measurement data recorded during the production process of the Certified Reference Material BAM-A001 containing Polycyclic Aromatic Hydrocarbons (PAH) in olive oil. The data can be most conveniently openend using the Shiny-App eCerto which is accessible at https://www.bam.de/eCerto. KW - Certified reference material KW - Mass spectrometry KW - Olive oil KW - Aromatic hydrocarbons KW - Reference data PY - 2023 UR - https://doi.org/10.5281/zenodo.8380870 DO - https://doi.org/10.5281/zenodo.8380869 PB - Zenodo CY - Geneva AN - OPUS4-58488 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan T1 - CorMID - Correct Mass Isotopologue Distribution Vectors N2 - The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN. KW - Mass Spectrometry KW - Software KW - R package KW - Mass Isotopomer Distribution KW - Flux Analysis PY - 2022 UR - https://github.com/cran/CorMID/ PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56442 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan T1 - IsoCor N2 - Despite numerous advantages offered by hyphenation of chromatography and electrokinetic separation methods with multicollector (MC) ICP-MS for isotope analysis, the main limitation of such systems is the decrease in precision and increase in uncertainty due to generation of short transient signals. To minimize this limitation, most authors compare several isotope ratio calculation methods and establish a multi-step data processing routine based on the precision and accuracy of the methods. However, to the best of our knowledge, there is no universal data processing tool available that incorporates all important steps of the treatment of the transient signals. Thus, we introduce a data processing application (App) IsoCor that facilitates automatic calculation of isotope ratios from transient signals and eases selection of the most suitable method. The IsoCor App performs baseline subtraction, peak detection, mass bias correction, isotope ratio calculation and delta calculation. The feasibility and reliability of the App was proven by reproducing the results from isotope analysis of three elements (neodymium, mercury and sulfur) measured on-line via hyphenated systems. The IsoCor App provides trackability of the results to ensure quality control of the analysis. KW - Shiny-App KW - ICP-MS KW - Software PY - 2022 UR - https://github.com/cran/IsoCor/ PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56307 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -