A5048212783- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Endoplasmic Reticulum Stress and Disease
- Metabolomics and Mass Spectrometry Studies
- Autophagy in Disease and Therapy
- Cellular transport and secretion
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Advanced Biosensing Techniques and Applications
- Toxin Mechanisms and Immunotoxins
- Viral Infectious Diseases and Gene Expression in Insects
- Immunotherapy and Immune Responses
- Chemical Synthesis and Analysis
- Advanced MRI Techniques and Applications
- Plant-Microbe Interactions and Immunity
- Bacterial Genetics and Biotechnology
- Plant Pathogenic Bacteria Studies
- Immune Cell Function and Interaction
- Analytical Chemistry and Sensors
- Diatoms and Algae Research
- Scientific Computing and Data Management
- Ubiquitin and proteasome pathways
- HIV Research and Treatment
- Extracellular vesicles in disease
- Gene Regulatory Network Analysis
Max Planck Institute of Biochemistry
2018-2025
DKFZ-ZMBH Alliance
2019
Heidelberg University
2014-2019
Max Planck Institute for Medical Research
2016
Heidelberg University
2014
Abstract In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making efficient analysis a principal challenge. A plethora different computational tools can process the MS data to derive peptide and protein identification quantification. However, during last years there has been dramatic progress in computer science, including collaboration that have transformed research industry. To leverage these advances, we develop...
Article5 December 2019Open Access ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast Jasmin A Schäfer DKFZ-ZMBH Alliance and CellNetworks Cluster Excellence, Center for Molecular Biology Heidelberg University (ZMBH), Heidelberg, Germany Search more papers by this author Julia P Schessner Peter W Bircham Takuma Tsuji Research Institute Diseases Old Age, Juntendo Graduate School Medicine, Tokyo, Japan Charlotta Funaya Electron Microscopy Core Facility,...
The centrosome provides an intracellular anchor for the cytoskeleton, regulating cell division, migration, and cilia formation. We used spatial proteomics to elucidate protein interaction networks at of human induced pluripotent stem cell-derived neural cells (NSCs) neurons. Centrosome-associated proteins were largely type-specific, with hubs involved in RNA dynamics. Analysis neurodevelopmental disease cohorts identified a significant overrepresentation NSC variants patients periventricular...
During initiation of antiviral and antitumor T cell–mediated immune responses, dendritic cells (DCs) cross-present exogenous antigens on major histocompatibility complex (MHC) class I molecules. Cross-presentation relies the unusual “leakiness” endocytic compartments in DCs, whereby internalized proteins escape into cytosol for proteasome-mediated generation MHC I–binding peptides. Given that type 1 conventional DCs excel at cross-presentation, we searched cell type–specific effectors...
Recent advances in mass spectrometry-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks bioinformatics pipeline. Although peptide identification is already scalable, most label-free quantification (LFQ) algorithms scale quadratic or cubic with sample numbers, may even preclude analysis large-scale data. Here we introduce directLFQ, a ratio-based approach for normalization and calculation protein intensities. It...
Cells release diverse types of extracellular vesicles (EVs), which transfer complex signals to surrounding cells. Specific markers distinguish different EVs (e.g. exosomes, ectosomes, enveloped viruses like HIV) are still lacking. We have developed a proteomic profiling approach for characterizing EV subtype composition and applied it human Jurkat T generated an interactive database define groups proteins with similar profiles, suggesting in EVs. Biochemical validation confirmed the presence...
Misfolded proteins in the endoplasmic reticulum (ER) activate unfolded protein response (UPR), which enhances folding to restore homeostasis. Additional pathways respond ER stress, but how they help counteract misfolding is incompletely understood. Here, we develop a titratable system for induction of stress yeast enable genetic screen factors that augment resistance independently UPR. We identify proteasome biogenesis regulator Rpn4 and show it cooperates with abundance increases during...
ABSTRACT In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making their efficient analysis a principal challenge. There is plethora different computational tools that process the MS data and derive peptide protein identification quantification. During last decade, there has been dramatic progress in computer science software engineering, including collaboration have transformed research industry. To leverage these...
Production of indigoidine can be enhanced by swapping a synthetic T domain into the NRPS IndC.
The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we enhance the performance DOMs through data-independent acquisition (DIA) mass spectrometry. DIA-DOMs achieve twice depth our previous workflow in same spectrometry runtime, substantially improve precision reproducibility. We leverage this gain to establish flexible map formats scaling from high-throughput analyses extra-deep...
Abstract The Perseus software provides a comprehensive framework for the statistical analysis of large‐scale quantitative proteomics data, also in combination with other omics dimensions. Rapid developments technology and ever‐growing diversity biological studies increasingly require flexibility to incorporate computational methods designed by user. Here, we present new functionality integrate self‐made plugins written C#, R, or Python. user‐written codes will be fully integrated into data...
Sophisticated techniques are available for systematic studies of yeast cell biology. However, it remains challenging to investigate protein subcellular localization changes on a proteome-wide scale. Here, we apply Dynamic Organellar Maps (DOMs) by label-free mass spectrometry detect native, untagged proteins during endoplasmic reticulum (ER) stress. We find that hundreds shift between cellular compartments. For example, show numerous secretory pathway accumulate in the ER, thus defining...
An arsenal of effector proteins is injected by bacterial pathogens into the host cell or its vicinity to increase virulence. The commonly used top-down approaches inferring toxic mechanism individual from host's phenotype are often impeded multiple targets different effectors as well their pleiotropic effects. Here we describe our bottom-up approach, showing that type III AvrRxo1 plant an authentic phosphotransferase produces two novel metabolites phosphorylating nicotinamide/nicotinic acid...
Abstract Eukaryotic cells are highly compartmentalized and protein subcellular localization critically influences function. Identification of the localizations proteins their translocation events upon perturbation has mostly been confined to targeted studies or laborious microscopy‐based methods. Here we describe a systematic mass spectrometry‐based method for spatial proteomics. The approach uses simple fractionation profiling two applications: Firstly it can be used infer on proteome‐wide...
Abstract During initiation of antiviral and antitumour T cell-mediated immune responses, dendritic cells (DCs) cross-present exogenous antigens on MHC class I. Cross-presentation relies the unique ‘leakiness’ endocytic compartments in DCs, whereby internalised proteins escape into cytosol for proteasome-mediated generation I-binding peptides. Given that type 1 conventional DCs excel at cross-presentation, we searched cell-type specific effectors escape. We devised an assay suitable genetic...
Time-resolved cell culture assays circumvent the need to set arbitrary end-points and reveal dynamics of quality controlled experiments. However, they lead generation large data sets, which can represent a complexity barrier their use. We therefore developed Time-Resolved Cell Culture Assay (TReCCA) Analyser program perform standard assay analyses efficiently make sophisticated in-depth easily available. The functions include normalising averaging, as well smoothing slope calculation,...
ABSTRACT Recent advances in mass spectrometry (MS)-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks bioinformatics pipeline. Whereas peptide identification is already scalable, most label-free quantification (LFQ) algorithms scale quadratic or cubic with sample numbers, may even preclude analysis large-scale data. Here we introduce directLFQ, a ratiobased approach for normalization and calculation protein...
ABSTRACT ER-phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER-phagy can occur macroautophagic microautophagic mechanisms. While dedicated machinery for macro-ER-phagy has been discovered, molecules mechanisms mediating micro-ER-phagy remain unknown. Here, we first show that in yeast involves conversion stacked cisternal into multilamellar whorls during uptake lysosomes. Second, identify...
ABSTRACT The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we have drastically enhanced the performance DOMs through data-independent acquisition (DIA) mass spectrometry (MS). DIA-DOMs achieve twice depth our previous workflow in same MS runtime, substantially improve precision reproducibility. We leveraged this gain to establish flexible map formats scaling from rapid...