TY - JOUR A1 - Nowatzky, Yannek A1 - Russo, Francesco Friedrich A1 - Lisec, Jan A1 - Kister, Alexander A1 - Reinert, Knut A1 - Muth, Thilo A1 - Benner, Philipp T1 - FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events N2 - Non-targeted metabolomics holds great promise for advancing precision medicine and biomarker discovery. However, identifying compounds from tandem mass spectra remains a challenging task due to the incomplete nature of spectral reference libraries. Augmenting these libraries with simulated mass spectra can provide the necessary references to resolve unmatched spectra, but generating high-quality data is difficult. In this study, we present FIORA, an open-source graph neural network designed to simulate tandem mass spectra. Our main contribution lies in utilizing the molecular neighborhood of bonds to learn breaking patterns and derive fragment ion probabilities. FIORA not only surpasses state-of-the-art fragmentation algorithms, ICEBERG and CFM-ID, in prediction quality, but also facilitates the prediction of additional features, such as retention time and collision cross section. Utilizing GPU acceleration, FIORA enables rapid validation of putative compound annotations and large-scale expansion of spectral reference libraries with high-quality predictions. KW - Metabolomics KW - Machine Learning KW - Mass spectrometry KW - Bioinformatics PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-627585 DO - https://doi.org/10.1038/s41467-025-57422-4 SN - 2041-1723 VL - 16 IS - 1 SP - 1 EP - 17 PB - Springer Science and Business Media LLC AN - OPUS4-62758 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - López-Puertollano, Daniel A1 - Duncan, Hadyn A1 - Abad-Somovilla, Antonio A1 - Abad-Fuentes, Antonio A1 - Rurack, Knut T1 - Competitive cytometry-based immunoassay for patulin determination in apple juice N2 - Patulin is a mycotoxin that is frequently found in apples and apple-derived products. Given the potential harm it can cause to humans, maximum levels for patulin in food have been set worldwide. Conventional methods for the detection of patulin are often time-consuming or lack sensitivity. In this study, a novel cytometry approach based on specific monoclonal antibodies is presented. These high-affinity binders do not target patulin itself, but a stable derivative (adduct) that is rapidly obtained in an aqueous medium at room temperature. To develop the assay, a specific fluorescent competitor was designed and synthesized. After optimizing the assay conditions, including the concentration of the fluorescent competitor and of the antibody bound to polystyrene-silica core–shell microparticles, a detection limit of 0.03 μg L-1 in buffer was achieved. Finally, validation according to Commission Regulation (EU) 2023/2782 demonstrated that apple juice samples spiked with patulin at 25 or 50 μg L-1 (permissible limits set by the EU) were properly scored as non-compliant without any additional treatment other than a simple dilution step in buffer. The developed assay offers several key advantages, including rapid analysis, high sensitivity and specificity, and the potential for multiplexing, making it a promising analytical tool for routine monitoring of patulin contamination in food. KW - Bead-based assay KW - Cytometry KW - Derivatization KW - Mycotoxin KW - Patulin PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-627659 DO - https://doi.org/10.1016/j.microc.2025.113287 SN - 1095-9149 VL - 212 SP - 1 EP - 8 PB - Elsevier B.V. AN - OPUS4-62765 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - López-Puertollano, Daniel A1 - Tobias, Charlie A1 - Bell, Jérémy A1 - Abad-Somovilla, A. A1 - Abad-Fuentes, A. A1 - Rurack, Knut T1 - Superparamagnetic Bead-Based Microfluidic Fluoroimmunoassay Platform for Rapid Ochratoxin A Detection in Flour N2 - Simplification and reduction of time and costs are the primary goals in the development and use of onsite methods in diagnostics and food safety. To facilitate the transition from laboratory techniques to simple, miniaturized devices, we have developed a modular microfluidic platform. This platform integrates a competitive fluorescence immunoassay on the surface of superparamagnetic beads, serving as a complementary technique to traditional cytometry assays. In the first chip module, a fast competitive reaction (5 min) occurs, after which the particles are retained in the second module. This module consists of a PDMS chip and a permanent magnet, allowing only the fluorescent competitor to reach the detection module. Ochratoxin A (OTA) was chosen as the model analyte for device development, using fluorescein-labeled OTA as a competitor. The system efficiently separates particles, with OTA concentration directly correlated to the amount of fluorescent competitor remaining in solution after the competitive reaction. This innovative setup allows to perform rapid measurements with small sample volumes in a short time (10 min), achieving a limit of detection for OTA of 1.2 μg L–1. The system was successfully applied to the accurate determination of OTA in wheat flour spiked at regulatorily relevant concentrations. Using this device, conventional cytometry immunoassays can be seamlessly transformed into user-friendly, miniaturized analytical methods at reduced cost for applications outside of a laboratory directly at the point of need. KW - Bead-based assay KW - Fluorescence KW - Immunoassay KW - Microfluidics KW - mycotoxins PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-638472 DO - https://doi.org/10.1021/acssensors.5c01119 SN - 2379-3694 SP - 1 EP - 10 PB - American Chemical Society CY - Washington, D.C. AN - OPUS4-63847 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Winckelmann, Alexander A1 - Nowak, S. A1 - Richter, Silke A1 - Recknagel, Sebastian A1 - Riedel, Jens A1 - Vogl, Jochen A1 - Panne, Ulrich A1 - Abad Andrade, Carlos Enrique T1 - High-Resolution Atomic Absorption Spectrometry Combined With Machine Learning Data Processing for Isotope Amount Ratio Analysis of Lithium N2 - An alternative method for lithium isotope amount ratio analysis based on a combination of high-resolution atomic absorption spectrometry and spectral data analysis by machine learning (ML) is proposed herein. It is based on the well-known isotope shift of approximately 15 pm for the electronic transition 22P←22S at around the wavelength of 670.8 nm, which can be measured by the state-of-the-art high-resolution continuum source graphite furnace atomic absorption spectrometry. For isotope amount ratio analysis, a scalable tree boosting ML algorithm (XGBoost) was employed and calibrated using a set of samples with 6Li isotope amount fractions, ranging from 0.06 to 0.99 mol mol–1, previously determined by a multicollector inductively coupled plasma mass spectrometer (MC-ICP-MS). The calibration ML model was validated with two certified reference materials (LSVEC and IRMM-016). The procedure was applied toward the isotope amount ratio determination of a set of stock chemicals (Li2CO3, LiNO3, LiCl, and LiOH) and a BAM candidate reference material NMC111 (LiNi1/3Mn1/3Co1/3O2), a Li-battery cathode material. The results of these determinations were compared with those obtained by MC-ICP-MS and found to be metrologically comparable and compatible. The residual bias was −1.8‰, and the precision obtained ranged from 1.9 to 6.2‰. This precision was sufficient to resolve naturally occurring variations, as demonstrated for samples ranging from approximately −3 to +15‰. To assess its suitability to technical applications, the NMC111 cathode candidate reference material was analyzed using high-resolution continuum source atomic absorption spectrometry with and without matrix purification. The results obtained were metrologically compatible with each other. KW - Lithium KW - Isotope KW - Machine learning KW - Algorithms KW - Reference material KW - AAS KW - Atomic Absorption Spectrometry PY - 2021 DO - https://doi.org/10.1021/acs.analchem.1c00206 SN - 1520-6882 VL - 93 IS - 29 SP - 10022 EP - 10030 PB - American Chemical Society CY - Washington, DC, USA AN - OPUS4-53028 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Sun, Yijuan A1 - Gawlitza, Kornelia A1 - Valderrey, Virginia A1 - Bell, Jérémy A1 - Rurack, Knut T1 - Polymerizable BODIPY probe crosslinker for the molecularly imprinted polymer-based detection of organic carboxylates via fluorescence N2 - This contribution reports the development of a polymerizable BODIPY-type fluorescent probe targeting small-molecule carboxylates for incorporation into molecularly imprinted polymers (MIPs). The design of the probe crosslinker includes a urea recognition site p-conjugated to the 3-position of the BODIPY core and two methacrylate moieties. Titration experiments with a carboxylate-expressing antibiotic, levofloxacin (LEVO), showed a blue shift of the absorption band as well as a broadening and decrease in emission, attributed to hydrogen bonding between the probe’s urea group and the carboxylate group of the antibiotic. Using this probe crosslinker, core–shell particles with a silica core and a thin MIP shell were prepared for the detection of LEVO. The MIP exhibited highly selective recognition of LEVO, with an imprinting factor of 18.1 compared to the non-imprinted polymer. Transmission electron microscopy confirmed the core–shell structure and spectroscopic studies revealed that the receptor’s positioning leads to a unique perturbation of the polymethinic character of the BODIPY chromophore, entailing the favourable responses. These features are fully preserved in the MIP, whereas no such response was observed for competitors such as ampicillin. The sensory particles allowed to detect LEVO down to submicromolar concentrations in dioxane. We have developed here for the first time a BODIPY probe for organic carboxylates and incorporated it into polymers using the imprinting technique, paving the way for BODIPY-type fluorescent MIP sensors. KW - Fluorescence KW - BODIPY probe KW - Molecularly Imprinted Polymers KW - Sensor Materials KW - Dyes KW - Water analysis KW - Advanced materials PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-598629 DO - https://doi.org/10.1039/D3MA00476G SP - 1 EP - 11 PB - Royal Society of Chemistry (RSC) AN - OPUS4-59862 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Verhassel, Alejandra A1 - Kimani, Martha Wamaitha A1 - Gidwani, Kamlesh A1 - Sandholm, Jouko A1 - Gawlitza, Kornelia A1 - Rurack, Knut A1 - Härkönen, Pirkko T1 - Detection of Tn-antigen in breast and prostate cancer models by VVL-labeled red dye-doped nanoparticles N2 - Aim: Fluorescence detection of breast and prostate cancer cells expressing Tn-antigen, a tumor marker, with Vicia villosa lectin (VVL)-labeled nanoparticles. Materials & methods: Breast and prostate cancer cells engineered to express high levels of Tn-antigen and non-engineered controls were incubated with VVL-labeled or unlabeled red dye-doped silica-coated polystyrene nanoparticles. The binding to cells was studied with flow cytometry, confocal microscopy, and electron microscopy. Results: Flow cytometry showed that the binding of VVL-labeled nanoparticles was significantly higher to Tn-antigen-expressing cancer cells than controls. Confocal microscopy demonstrated that particles bound to the cell surface. According to the correlative light and electron microscopy the particles bound mostly as aggregates. Conclusion: VVL-labeled nanoparticles could provide a new tool for the detection of Tn-antigen-expressing breast and prostate cancer cells. KW - Breast cancer cells KW - Fluorescence detection KW - Lectin labeling KW - Prostate cancer cells KW - Silica-coated polystyrene nanoparticles KW - Tn-antigen KW - VVL PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-613451 DO - https://doi.org/10.1080/17435889.2024.2405454 SN - 1743-5889 VL - 19 SP - 2463 EP - 2478 PB - Taylor & Francis CY - London AN - OPUS4-61345 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Morcillo, Dalia A1 - Winckelmann, Alexander A1 - Frick, Daniel A. A1 - Jacobsen, Lars A1 - Seger, Tino A1 - Florek, Stefan A1 - Richter, Silke A1 - Vogl, Jochen A1 - Recknagel, Sebastian A1 - Panne, Ulrich A1 - Abad Andrade, Carlos Enrique T1 - Lithium isotope ratio analysis of geological samples using atomic absorption spectrometry with improved spectral resolution N2 - This study introduces an improved spectrometric method with enhanced precision to determine isotope ratios in geological samples without chromatographic separation. Firstly, the improvement is achieved by increasing the spectral resolution of the spectrometer applied in well-known high-resolution continuum source atomic absorption spectrometry (HR-CS-AAS). The resulting resolving power and linear dispersion of the upgraded setup, which is denoted in the following as HR+CS-AAS, is well adapted to the line widths of the Li isotope components we investigated. Secondly, our proposed method combines optical absorption spectrometry with machine learning data analysis using an extreme gradient boosting algorithm (XGBoost). This method was applied to analyze certified geological reference materials with δLSVEC(7Li/6Li) (hereafter δ7Li) values ranging from −0.5 ‰ to 4.5 ‰. With a pixel related optical resolving power of λ/∆λ ≈ 780 000, we obtain precisions in δ7Li measurements from 1.0 ‰ to 2.5 ‰. The method is validated by comparing the results with multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), confirming its metrological compatibility. This work presents a fast, robust, and reliable method for δ7Li measurement in geological samples. KW - Isotope KW - High-resolution continuum source atomic absorption spectroscopy KW - Lithium KW - Machine learning KW - Echelle spectrometer PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-611807 DO - https://doi.org/10.1016/j.sab.2024.107013 VL - 220 SP - 1 EP - 5 PB - Elsevier BV AN - OPUS4-61180 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Pauli, Jutta A1 - Ramírez, A. A1 - Crasselt, C. A1 - Schmidt, W. A1 - Resch-Genger, Ute T1 - Utilizing optical spectroscopy and 2',7'-difluorofluorescein to characterize the early stages of cement hydration N2 - The increasingly sophisticated nature of modern, more environmentally friendly cementitious binders requires a better understanding and control particularly of the complex, dynamic processes involved in the early phase of cement hydration. In-situ monitoring of properties of a constantly changing system over a defined period of time calls for simple, sensitive, fast, and preferably also non-invasive methods like optical spectroscopy KW - Flourescence KW - Optical probe KW - Sensor KW - Dye KW - Flourescin KW - Photophysics KW - PH KW - Quantum yield KW - Quality assurance KW - Mechanism KW - Cement KW - Concrete KW - Building material KW - Hydration KW - Process monitoring PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-537176 DO - https://doi.org/10.1088/2050-6120/ac2da0 SN - 2050-6120 VL - 10 IS - 1 SP - 2 EP - 13 PB - IOP Science AN - OPUS4-53717 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Yanbaeva, M. A1 - Soyka, J. A1 - Holthoff, J. M. A1 - Rietsch, P. A1 - Engelage, E. A1 - Ruff, A. A1 - Resch-Genger, Ute A1 - Weiss, R. A1 - Eigler, S. A1 - Huber, S. M. T1 - Dimethylene-Cyclopropanide Units as Building Blocks for Fluorescence Dyes N2 - Many organic dyes are fluorescent in solution. In the solid state, however, quenching processes often dominate, hampering material science applications such as light filters, light-emitting devices, or coding tags. We show that the dimethylene-cyclopropanides caffold can be used to form two structurally different types of chromophores, which feature fluorescence quantum yields up to 0.66 in dimethyl sulfoxide and 0.53 in solids. The increased fluorescence in the solid state for compounds bearing malonate substituents instead of dicyanomethide ones is rationalized by the induced twist between the planes of the cyclopropanide core and a pyridine ligand. KW - Fluorescence KW - Dye KW - Sensor KW - Quantum yield KW - Spectroscopy KW - Photophysics KW - Synthesis KW - Solvatochromism PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-614931 DO - https://doi.org/10.1002/chem.202402476 VL - 30 IS - 56 SP - 1 EP - 7 PB - Chemistry - A European Journal AN - OPUS4-61493 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Abram, Sarah-Luise A1 - Tavernaro, Isabella A1 - Resch-Genger, Ute A1 - Johnston, L. J. A1 - Zou, S. T1 - Nanoscale reference and test materials for the validation of characterization methods for engineered nanomaterials — current state, limitations, and needs N2 - The rational design of engineered nanomaterials (NMs) with improved functionality and their increasing industrial application requires reliable, validated, and ultimately standardized characterization methods for their application-relevant, physicochemical key properties such as size, size distribution, shape, or surface chemistry. This calls for nanoscale (certified) reference materials (CRMs; RMs) and well-characterized reference test materials (RTMs) termed also quality control (QC) samples, assessed, e.g., in interlaboratory comparisons, for the validation and standardization of commonly used characterization methods. Thereby, increasing concerns regarding potential risks of NMs are also addressed and the road for safe and sustainable-by-design concepts for the development of new functional NMs and their use as nanomedicines is paved. With this respect, we will provide an overview of relevant international standardization and regulatory activities, definitions, and recommendations on characterization methods and review currently available organic or inorganic nanoscale CRMs, RMs, and RTMs, including their characterization or certification. In addition, we will highlight typical applications to streamline the regulatory approval process and improve manufacturability including the special challenges imposed by the colloidal nature and sometimes limited stability of NMs. Subsequently, we will critically assess the limitations of currently available nanoscale RMs and RTMs and address the gaps to be filled in the future such as the availability of NMs that come with reference data on properties other than commonly addressed particle size, such as surface chemistry or particle number concentration, or more closely resemble commercially available formulations or address application-relevant matrices. KW - Nano KW - Particle KW - Silica KW - Quality assurance KW - Reference material KW - Review KW - Surface chemistry KW - Size KW - Shape KW - Particle number concentration KW - Lipid nanoparticles KW - Metal nanoparticles KW - Liposomes PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-625746 DO - https://doi.org/10.1007/s00216-024-05719-6 SN - 1618-2650 SP - 1 EP - 21 PB - Springer AN - OPUS4-62574 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -