TY - JOUR A1 - Nowatzky, Yannek A1 - Benner, Philipp A1 - Reinert, K. A1 - Muth, Thilo T1 - Mistle: bringing spectral library predictions to metaproteomics with an efficient search index JF - Bioinformatics N2 - Motivation: Deep learning has moved to the forefront of tandem mass spectrometry-driven proteomics and authentic prediction for peptide fragmentation is more feasible than ever. Still, at this point spectral prediction is mainly used to validate database search results or for confined search spaces. Fully predicted spectral libraries have not yet been efficiently adapted to large search space problems that often occur in metaproteomics or proteogenomics. Results: In this study, we showcase a workflow that uses Prosit for spectral library predictions on two common metaproteomes and implement an indexing and search algorithm, Mistle, to efficiently identify experimental mass spectra within the library. Hence, the workflow emulates a classic protein sequence database search with protein digestion but builds a searchable index from spectral predictions as an in-between step. We compare Mistle to popular search engines, both on a spectral and database search level, and provide evidence that this approach is more accurate than a database search using MSFragger. Mistle outperforms other spectral library search engines in terms of run time and proves to be extremely memory efficient with a 4- to 22-fold decrease in RAM usage. This makes Mistle universally applicable to large search spaces, e.g. covering comprehensive sequence databases of diverse microbiomes. Availability and implementation: Mistle is freely available on GitHub at https://github.com/BAMeScience/Mistle. KW - Mass spectrometry KW - Proteomics KW - Algorithms KW - Metaproteomics PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-579373 DO - https://doi.org/10.1093/bioinformatics/btad376 SN - 1367-4811 VL - 39 IS - 6 SP - 1 EP - 12 PB - Oxford University Press CY - Oxford, Great Britain AN - OPUS4-57937 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Naik, Aakash A1 - Ertural, Christina A1 - Dhamrait, Nidal A1 - Benner, Philipp A1 - George, Janine T1 - A Quantum-Chemical Bonding Database for Solid-State Materials JF - Scientific Data N2 - An in-depth insight into the chemistry and nature of the individual chemical bonds is essential for understanding materials. Bonding analysis is thus expected to provide important features for large-scale data analysis and machine learning of material properties. Such chemical bonding information can be computed using the LOBSTER software package, which post-processes modern density functional theory data by projecting the plane wave-based wave functions onto an atomic orbital basis. With the help of a fully automatic workflow, the VASP and LOBSTER software packages are used to generate the data. We then perform bonding analyses on 1520 compounds (insulators and semiconductors) and provide the results as a database. The projected densities of states and bonding indicators are benchmarked on standard density-functional theory computations and available heuristics, respectively. Lastly, we illustrate the predictive power of bonding descriptors by constructing a machine learning model for phononic properties, which shows an increase in prediction accuracies by 27% (mean absolute errors) compared to a benchmark model differing only by not relying on any quantum-chemical bonding features. KW - Bonding Analysis KW - DFT KW - High-throughput KW - Database KW - Phonons KW - Machine Learning PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-582892 DO - https://doi.org/10.1038/s41597-023-02477-5 VL - 10 IS - 1 SP - 1 EP - 18 AN - OPUS4-58289 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Albakri, Bashar A1 - Turski Silva Diniz, Analice A1 - Benner, Philipp A1 - Muth, Thilo A1 - Nakajima, Shinichi A1 - Favaro, Marco A1 - Kister, Alexander ED - Hillman, Robert T1 - Machine learning-assisted equivalent circuit identification for dielectric spectroscopy of polymers JF - Electrochimica Acta N2 - Polymers have become indispensable across fields of application, and understanding their structure–property relationships and dynamic behaviour is essential for performance optimization. Polymer membranes, particularly ion exchange membranes, play a crucial role in renewable energy conversion technologies, fuel cells, solar energy conversion, and energy storage. In this context, broadband dielectric spectroscopy (BDS) offers a powerful, non-destructive approach to investigate the electrical response and relaxation dynamics of polymers. These properties are investigated by parametrizing the system’s impedance response in terms of a network of circuit elements, i.e. the electrical equivalent circuit (EEC), whose impedance resembles the one of the system under investigation. However, the determination of the EEC from BDS data is challenging due to system complexity, interdependencies of circuit elements, and researcher biases. In this work, we propose a novel approach that incorporates a convolutional neural network (CNN) model to predict the EEC topology. By reducing user bias and enhancing data analysis, this approach aims to make BDS accessible to both experienced users and those with limited expertise. We show that the combination of machine learning and BDS provides valuable insights into the dynamic behaviour of polymer membranes, thus facilitating the design and characterization of tailored polymers for various applications. We also show that our model outperforms state-of-the-art machine learning methods with a top-5 accuracy of around 80% for predicting the circuit topology and a parameter fitting error as low as 0.05%. KW - Polymer membranes KW - Electrochemical impedance spectroscopy KW - Broadband dielectric spectroscopy KW - Deep learning KW - Machine learning KW - Equivalent circuit PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-602138 DO - https://doi.org/10.1016/j.electacta.2024.144474 VL - 496 SP - 1 EP - 13 PB - Elsevier Ltd. AN - OPUS4-60213 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -