A5019411472- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Glycosylation and Glycoproteins Research
- Gut microbiota and health
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Probiotics and Fermented Foods
- Peptidase Inhibition and Analysis
- Protein Degradation and Inhibitors
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Forest Biomass Utilization and Management
- Vehicle Routing Optimization Methods
- Monoclonal and Polyclonal Antibodies Research
- Malaria Research and Control
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Analytical Chemistry and Chromatography
- Urban and Freight Transport Logistics
- Chemical Synthesis and Analysis
- Machine Learning in Bioinformatics
Leibniz-Institute for Food Systems Biology at the Technical University of Munich
2015-2024
Technische Universität Dresden
2020
Technical University of Munich
2010-2018
Newcastle University
2011
Universität Greifswald
2008-2011
Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the spectrum 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration phosphoproteomic...
Article18 February 2019Open Access Transparent process A deep proteome and transcriptome abundance atlas of 29 healthy human tissues Dongxue Wang orcid.org/0000-0002-4402-0690 Chair Proteomics Bioanalytics, Technische Universität München, Freising, Germany Search for more papers by this author Basak Eraslan Computational Biology, Department Informatics, Technical University Munich, Garching bei Biochemistry, Quantitative Biosciences Gene Center, Ludwig Maximilian Universität, Thomas Wieland...
Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological technical heterogeneity in experiments further add to there are strong differences opinion regarding conceptual validity protein FDR no consensus methodology for determination. There also limitations inherent widely used classic target–decoy strategy that particularly show lead...
The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms cancer in general and vitro drug action particular. It model system tissue types genetic diversity human cancers has been extensively molecularly characterized. Here, we present quantitative proteome kinome profile covering, total, 10,350 proteins (including 375 protein kinases) including core 5,578 that were consistently quantified across all types. Bioinformatic analysis revealed strong...
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...
ABSTRACT In its natural habitats, Bacillus subtilis is exposed to changing osmolarity, necessitating adaptive stress responses. Transcriptomic and proteomic approaches can provide a picture of the dynamic changes occurring in salt-stressed B. cultures because these studies an unbiased view cells coping with high salinity. We applied whole-genome microarray technology metabolic labeling, combined state-of-the-art techniques, global time-resolved physiological response severe sudden osmotic...
The post-translational modification of proteins with N-acetylglucosamine (O-GlcNAc) is involved in the regulation a wide variety cellular processes and associated number chronic diseases. Despite its emerging biological significance, systematic identification O-GlcNAc still challenging. In present study, we demonstrate significantly improved protein enrichment procedure, which exploits metabolic labeling cells by azide-modified GlcNAc copper-mediated Click chemistry for purification modified...
N-Linked protein glycosylation is one of the most prevalent post-translational modifications and involved in essential cellular functions such as cell-cell interactions recognition well chronic diseases. In this study, we explored stable isotope labeled carbonyl-reactive tandem mass tags (glyco-TMTs) a novel approach for quantification N-linked glycans. Glyco-TMTs bearing hydrazide- aminooxy-functionalized groups were compared glycan reducing end derivatization efficiency merits. Aminooxy...
One of the limiting factors in determining sensitivity tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is duty cycle ion injection system. As a consequence, only fraction generated fragment beam collected by analyzer. Here we describe method utilizing postfragmentation mobility peptide ions conjunction with time synchronized leading to substantially improved and concomitant improvement up 10-fold for bottom-up proteomic experiments. This...
Citrullination is a posttranslational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss positive charge may cause structural or functional alterations, and while the has been linked to several diseases, including rheumatoid arthritis (RA) cancer, its physiological pathophysiological roles remain largely unclear. In part, this owing limitations available methodology robustly enrich, detect, localize modification. As result, only few...
Article18 February 2019Open Access Transparent process Quantification and discovery of sequence determinants protein-per-mRNA amount in 29 human tissues Basak Eraslan Computational Biology, Department Informatics, Technical University Munich, Garching, Germany Graduate School Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Search for more papers by this author Dongxue Wang orcid.org/0000-0002-4402-0690 Chair Proteomics Bioanalytics, Freising, Mirjana Gusic Institute...
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic prognostic value. One main challenge that molecular identity such potential biomarkers mostly remains unknown. We introduce generic method removes this issue by systematically identifying embedded MALDI matrix using combination bottom-up top-down proteomics. The analyses ten human lead to identification...
The attachment of N-acetylglucosamine to serine or threonine residues (O-GlcNAc) is a post-translational modification on nuclear and cytoplasmic proteins with emerging roles in numerous cellular processes, such as signal transduction, transcription, translation. It further presumed that O-GlcNAc can exhibit site-specific, dynamic possibly functional interplay phosphorylation. are commonly identified by tandem mass spectrometry following some form biochemical enrichment. In the present study,...
The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification the protein targets a necessary step before MS identification. biotin-streptavidin system widely used this process, but harsh denaturing conditions also release natively biotinylated non-selectively bound proteins. A cleavable linker strategy promising approach for solving problem. Though several linkers have been developed tested, efficient, easily...
The identification of new biomarkers for preneoplastic pancreatic lesions (PanINs, IPMNs) and early ductal adenocarcinoma (PDAC) is crucial due to the diseasés high mortality rate upon late detection. To address this task we used novel technique matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on genetically engineered mouse models (GEM) cancer. Various GEM were analyzed with MALDI IMS investigate peptide/protein-expression pattern precursor in comparison...
The Gram-positive bacterium Staphylococcus aureus is a serious human pathogen causing wide variety of diseases, and its increasing resistance toward all available antibiotics makes further investigation absolutely essential. We examined the membrane proteome exponentially growing cells S. COL because this subproteome plays major role in virulence host. In general, an analysis proteins impeded by their hydrophobic nature as well high abundance many cytosolic proteins. implementation three...
The coupling of atmospheric pressure ionization (API) sources like electrospray (ESI) to vacuum based applications mass spectrometry (MS) or ion beam deposition (IBD) is done by differential pumping, starting with a capillary pinhole inlet. Because its low transfer efficiency the inlet represents major bottleneck for these applications. Here we present nano-ESI interface optimized exploit hydrodynamic drag background gas collimation and reduction space charge repulsion. Up limit 40 nA...
Background & aims The causes of gastrointestinal complaints in irritable bowel syndrome (IBS) remain poorly understood. Altered nerve function has emerged as an important pathogenic factor IBS mucosal biopsy supernatants consistently activate enteric and sensory neurons. We investigated the neurally active molecular components such from patients with quiescent ulcerative colitis (UC). Method Effects 7 healthy controls (HC), 20 12 UC on human guinea pig submucous neurons were studied...