A5027856560- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Ubiquitin and proteasome pathways
- Metabolomics and Mass Spectrometry Studies
- Phagocytosis and Immune Regulation
- Endoplasmic Reticulum Stress and Disease
- Autophagy in Disease and Therapy
- Analytical Chemistry and Chromatography
- Immune cells in cancer
- Sirtuins and Resveratrol in Medicine
- Protein purification and stability
- Chromatography in Natural Products
- Alzheimer's disease research and treatments
- Plant Gene Expression Analysis
- Mitochondrial Function and Pathology
- Biotin and Related Studies
- Nuclear Structure and Function
- Amyotrophic Lateral Sclerosis Research
- Wnt/β-catenin signaling in development and cancer
- Immunotherapy and Immune Responses
- Glycosylation and Glycoproteins Research
- Plant Molecular Biology Research
- Parkinson's Disease Mechanisms and Treatments
- Cellular transport and secretion
- RNA and protein synthesis mechanisms
ETH Zurich
2014-2022
Max Planck Institute of Biochemistry
2011-2017
Max Planck Society
2014
Utrecht University
2007-2012
Netherlands Metabolomics Centre
2011
Cancer Genomics Centre
2009
University College Dublin
2006
How proteomes take the heat Living organisms are very sensitive to temperature, and much of this is attributed its effect on structure function proteins. Leuenberger et al. explored thermostability a proteome-wide scale in bacteria, yeast, human cells by using combination limited proteolysis mass spectrometry (see Perspective Vogel). Their results suggest that temperature-induced cell death caused loss subset proteins with key functions. The study also provides insight into molecular...
Stable isotope labeling is at present one of the most powerful methods in quantitative proteomics. has been performed both protein as well peptide level using either metabolic or chemical labeling. Here, we a straightforward and cost-effective triplex quantification method that based on stable dimethyl level. Herein, all proteolytic peptides are chemically labeled their alpha- epsilon-amino groups. We use three different isotopomers formaldehyde to enable parallel analysis samples. These...
In proteomics, a digested cell lysate is often too complex for direct comprehensive mass spectrometric analysis. To reduce complexity, several peptide separation techniques have been introduced including very successful two-dimensional liquid chromatography (2D-LC) approaches. Here, we assess the potential of zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC) as first dimension analysis mixtures. We show that ZIC-HILIC dramatically dependent on buffer pH in range from 3...
Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal exact sites phosphorylation, be quantitative, and not cost-prohibitive. The latter is often an issue as typically several milligrams (stable isotope-labeled) starting protein material are required to enable detection low abundance phosphotyrosine peptides. Here, we adopted refined a peptidecentric immunoaffinity purification approach...
•Dynamic structural proteomic screens detect functional changes at high resolution•Detect enzyme activity, phosphorylation, and molecular interactions in situ•Generate new hypotheses increase proteomics coverage•Enabled discovery of a regulatory mechanism glucose uptake E. coli Biological processes are regulated by intermolecular chemical modifications that do not affect protein levels, thus escaping detection classical screens. We demonstrate here global readout based on limited...
The complexity of peptide mixtures that are analyzed in proteomics necessitates fractionation by multidimensional separation approaches prior to mass spectrometric analysis. In this work, we introduce and evaluate hydrophilic interaction liquid chromatography (HILIC) based strategies for the complex mixtures. two zwitterionic HILIC materials (ZIC-HILIC ZIC-cHILIC) chosen work differ spatial orientation positive negative charged groups. Online experiments revealed a pH-independent resolving...
Down syndrome (DS) is mostly caused by a trisomy of the entire Chromosome 21 (Trisomy 21, T21). Here, we use SWATH mass spectrometry to quantify protein abundance and turnover in fibroblasts from monozygotic twin pair discordant for T21, profile expression 11 unrelated DS individuals matched controls. The integration steady-state proteomic data indicates that protein-specific degradation members stoichiometric complexes major determinant T21 gene dosage outcome, both within between...
Histone deacetylases have central functions in regulating stress defenses and development plants. However, the knowledge about deacetylase is largely limited to histones, although these enzymes were found diverse subcellular compartments. In this study, we determined proteome-wide signatures of RPD3/HDA1 class histone Arabidopsis Relative quantification changes lysine acetylation levels was on a scale after treatment leaves with inhibitors apicidin trichostatin A. We identified 91 new...
During interphase, the nuclear envelope (NE) serves as a selective barrier between cytosol and nucleoplasm. When vertebrate cells enter mitosis, NE is dismantled in process of breakdown (NEBD). Disassembly pore complexes (NPCs) key aspect NEBD, required for permeabilization formation cytoplasmic mitotic spindle. Here, we show that both CDK1 polo-like kinase 1 (PLK1) support NPC disintegration by hyperphosphorylation Nup98, gatekeeper nucleoporin, Nup53, central nucleoporin linking inner...
Cells secrete a large number of proteins to communicate with their surroundings. Furthermore, plasma membrane and intracellular can be released into the extracellular space by regulated or non-regulated processes. Here, we profiled supernatant 11 cell lines that are representative different stages breast cancer development specifically capturing N-glycosylated peptides using N-glyco FASP technology. For accurate quantification developed super-SILAC mix from several labeled used it as an...
Abstract The posttranslational regulation of proteins by lysine (Lys) acetylation has recently emerged to occur not only on histones, but also organellar in plants and animals. In particular, the catalytic activities metabolic enzymes have been shown be regulated Lys acetylation. Arabidopsis (Arabidopsis thaliana) genome encodes two predicted sirtuin-type deacetylases, which Silent Information Regulator2 homolog (SRT2) contains a presequence for mitochondrial targeting. Here, we investigated...
The role of fibroblast growth factor-2 (FGF-2) in maintaining undifferentiated human embryonic stem cells (hESC) was investigated using a targeted phosphoproteomics approach to specifically profile tyrosine phosphorylation events following FGF-2 stimulation. A cumulative total number 735 unique sites on 430 proteins were identified, by far the largest inventory date for hESC. Early signaling stimulated hESC quantitatively monitored stable isotope dimethyl labeling, resulting temporal...
Abstract Post-translational protein modification controls the function of Tau as a scaffold linking variety molecular partners. This is most studied in context microtubules, where regulates their stability well distribution cellular components to defined compartments. However, also located cell nucleus; and found protect DNA. Quantitative assessment nucleus when compared cytosol may elucidate how subcellular regulated. We undertook an unbiased approach by combing bimolecular fluorescent...
Parkinson's disease (PD) is a neurological disorder characterized by the progressive accumulation of neuronal α-synuclein (αSyn) inclusions called Lewy bodies. It believed that bodies spread throughout nervous system due to cell-to-cell propagation αSyn via cycles secretion and uptake. Here, we investigated internalization intracellular exogenous αSyn, two key steps body pathogenesis, amplification spreading. We found stable fibrils substantially accumulate in different cell lines upon...