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 - 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 - 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 - 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 - TY - GEN A1 - Lisec, Jan T1 - ABID N2 - 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 - Software KW - Antibody KW - MALDI PY - 2022 UR - https://github.com/BAMresearch/ABID PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56192 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 -