A5002845809- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Peptidase Inhibition and Analysis
- Histone Deacetylase Inhibitors Research
- Biomedical and Engineering Education
- Protein Degradation and Inhibitors
- Machine Learning in Bioinformatics
- Monoclonal and Polyclonal Antibodies Research
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- S100 Proteins and Annexins
- Biosensors and Analytical Detection
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- vaccines and immunoinformatics approaches
- Advanced Biosensing Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Cancer, Hypoxia, and Metabolism
- Advanced biosensing and bioanalysis techniques
- Epigenetics and DNA Methylation
Technical University of Munich
2020-2024
Abstract Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs immune-oncology. Still, identification of non-tryptic peptides presents substantial computational challenges. To address these, we synthesized analyzed >300,000 multi-modal LC-MS/MS within ProteomeTools project representing HLA class I & II ligands products proteases AspN LysN. The resulting data enabled training a single model using...
Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding extent and time- dose-response characteristics drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands PTMs in cells to shed light on target engagement drug mechanism action. Examples range from detecting DNA damage chemotherapeutics, identifying drug-specific PTM...
ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop expand ProteomicsDB. The major focus over the last two years was improving findability, accessibility, interoperability reusability (FAIR) of data as well its implementation. For purpose, release new application programming interface (API) that provides systematic access essentially all in Second, open-source user...
Abstract Machine learning (ML) and deep (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used various applications, ranging from data‐independent acquisition (DIA) data analysis to data‐driven rescoring search engine results. Here, we present Oktoberfest, an open source Python package our spectral library generation pipeline originally only available online via ProteomicsDB. Oktoberfest is...
The prediction of fragment ion intensities and retention time peptides has gained significant attention over the past few years. However, progress shown in accurate such properties focused primarily on unlabeled peptides. Tandem mass tags (TMT) are chemical peptide labels that coupled to free amine groups usually after protein digestion enable multiplexed analysis multiple samples bottom-up spectrometry. It is a standard workflow proteomics ranging from single-cell high-throughput...
Abstract Recent developments in machine-learning (ML) and deep-learning (DL) have immense potential for applications proteomics, such as generating spectral libraries, improving peptide identification, optimizing targeted acquisition modes. Although new ML/DL models various properties are frequently published, the rate at which these adopted by community is slow, mostly due to technical challenges. We believe that, make better use of state-of-the-art models, more attention should be spent on...
Abstract Isobaric labeling increases the throughput of proteomics by enabling parallel identification and quantification peptides proteins. Over past decades, a variety isobaric tags have been developed allowing multiplexed analysis up to 18 samples. However, experiments utilizing such often exhibit reduced rates thus show decreased analytical depth. Re‐scoring has shown rescue otherwise missed identifications but was not yet systematically applied on isobarically labeled data. Because iTRAQ...
The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers' meeting was held from January 13th to 17th in Nyborg, Denmark. Among the participants were scientists as well developers working field of computational mass spectrometry (MS) and proteomics. 4-day program split between introductory keynote lectures parallel hackathon sessions. During latter, developed bioinformatics tools resources addressing outstanding needs community. hackathons allowed less...
Abstract HDAC drugs have entered the pharmacopoeia in 2000s. However, some enigmatic phenotypes suggest off-target engagement. Here, we developed a chemical proteomics assay using three promiscuous chemotypes and quantitative mass spectrometry that deployed to establish target landscape of 53 drugs. The results highlight 14 direct targets, including 9 out 11 human zinc-dependent HDACs, question reported selectivity widely-used molecules, notably for HDAC6, delineate how composition complexes...
The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to 20th, 2023, in Congressi Stefano Franscin at Monte Verità Ticino, Switzerland. participants were scientists and developers working computational mass spectrometry (MS), metabolomics, proteomics. 5-day program split between introductory keynote lectures parallel hackathon sessions focusing on "Artificial Intelligence proteomics" stimulate future directions the MS-driven...