A5045600739- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Genomics and Chromatin Dynamics
- Microtubule and mitosis dynamics
- Ubiquitin and proteasome pathways
- Metabolomics and Mass Spectrometry Studies
- Protein Degradation and Inhibitors
- Nuclear Structure and Function
- Advanced Biosensing Techniques and Applications
- Analytical Chemistry and Chromatography
- Chromatin Remodeling and Cancer
- DNA Repair Mechanisms
- Mitochondrial Function and Pathology
- Autophagy in Disease and Therapy
- Enzyme Structure and Function
- Microfluidic and Capillary Electrophoresis Applications
- Cellular transport and secretion
- Cell death mechanisms and regulation
- Machine Learning in Bioinformatics
- Muscle Physiology and Disorders
- Advanced biosensing and bioanalysis techniques
- Histone Deacetylase Inhibitors Research
- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- PARP inhibition in cancer therapy
Vienna Biocenter
2018-2025
Research Institute of Molecular Pathology
2009-2025
Austrian Academy of Sciences
2010-2019
Institute of Molecular Biotechnology
2009-2019
University of Vienna
2010
Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate the identity composition of these complexes is incompletely understood. Using gene tagging bacterial artificial chromosomes, localization, tandem-affinity purification-mass spectrometry, MitoCheck consortium has analyzed about 100 human complexes, many which had not or only been characterized. This work led to...
The timing and localization of events during mitosis are controlled by the regulated phosphorylation proteins mitotic kinases, which include Aurora A, B, Nek2 (never in kinase 2), Plk1 (Polo-like 1), cyclin-dependent complex Cdk1/cyclin B. Although kinases can have overlapping subcellular localizations, each appears to phosphorylate its substrates on distinct sites. To gain insight into relative importance local sequence context selectivity, identify previously unknown these five explore...
Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare number samples without additional labeling effort. Here, we present bioinformatics approach that significantly improves label-free results. We employ Percolator assess quality quantified peptides. This allows extract accurate reliable quantitative results based on false discovery rate. Benchmarking our previously published public shows it...
Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally functioning as a suppressor autophagy. We performed structure-function analysis in complex with caspase-9, HTRA2, SMAC, LC3B, which are critical autophagy proteins. Cryo–electron microscopy structures showed that forms megadalton crescent shape arcs around spacious cavity containing receptor sites...
Analysis of the phosphorylation mitotic protein complexes suggests that specific members relay regulatory signals to these molecular machines.
Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) anion-exchange (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue are well-retained in AEX. However, peptides with one or phosphate groups not separated from multiple Asp Glu residues, interfering...
Capitalizing on the massive increase in sample concentrations which are produced by extremely low elution volumes, nanoliquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS) is currently one of most sensitive analytical technologies for comprehensive characterization complex protein samples. However, despite tremendous technological improvements made production and packing monodisperse spherical particles nanoflow high-pressure liquid chromatography...
Sample carryover is a significant problem that occurs in high-performance liquid chromatography (HPLC) analysis. Carryover effects cannot be tolerated any chromatography−mass spectroscopy (HPLC-MS) separation system, and proteomics analysis must performed system with virtually no carryover. Several procedures have been tested for effective fast removal of interfering peptides proteins originating from previous analyses the HPLC system. We developed optimized cleaning method eliminating...
Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, small molecule inhibitors PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity substrates limited. Here we present results proteome-wide analysis PLK1-regulated phosphorylation sites human cells. We compared HeLa cells that were or not treated with PLK1-inhibitor BI 4834, by labeling peptides via methyl...
Metal oxide affinity chromatography (MOAC) has become a prominent method to enrich phosphopeptides prior their analysis by liquid chromatography−mass spectrometry. To overcome limitations in material design, we have previously reported the use of nanocasting as means generate metal spheres with tailored properties. Here, report on application two oxides, tin dioxide (stannia) and titanium (titania), for HeLa phosphoproteome. In combination nanoflow LC−MS/MS linear ion trap-Fourier transform...
ABSTRACT Sirtuin 2 (SIRT2) is an NAD-dependent deacetylase known to regulate microtubule dynamics and cell cycle progression. SIRT2 has also been implicated in the pathology of cancer, neurodegenerative diseases progeria. Here, we show that depletion or overexpression causes nuclear envelope reassembly defects. We link this phenotype recently identified regulator ANKLE2. ANKLE2 acetylation at K302 phosphorylation S662 are dynamically regulated throughout by essential for normal reassembly....
The HOP2–MND1 heterodimer is essential for meiotic homologous recombination in plants and other eukaryotes promotes the repair of DNA double-strand breaks. We investigated conformational flexibility HOP2–MND1, important understanding mechanistic details heterodimer, with chemical cross-linking combination mass spectrometry (XL–MS). final XL–MS workflow encompassed use complementary cross-linkers, quenching, digestion, size exclusion enrichment, HCD-based LC–MS/MS detection prior to data...
Signaling networks regulate cellular responses to external stimuli through post-translational modifications such as protein phosphorylation. Phosphoproteomics facilitate the large-scale identification of kinase substrates. Yet, characterization critical connections within these and respective kinases remain major analytical challenge. To address this problem, we present a novel approach for direct substrates using chemical genetics in combination with quantitative phosphoproteomics....
Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) data sets. Here show be used to infer additional peptide-spectrum matches quality label-free quantitative sets also containing only tens MS runs. We analyzed four well-known public benchmark represent different experimental settings using counting peak...
The development of the neuromuscular synapse depends on signaling processes that involve protein phosphorylation as a crucial regulatory event. Muscle-specific kinase (MuSK) is key molecule at whose activity required for formation mature and functional synapse. However, cascade downstream MuSK regulation different components are still poorly understood. In this study we used quantitative phosphoproteomics approach to events their temporal MuSK. We identified total 10,183 phosphopeptides,...
Summary Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. BIRC6 is an exceptionally large, multidomain IAP that inhibits its targets by means atypical ubiquitin ligase activity in addition, functions as inhibitor autophagy depleting LC3B. Little known the mechanisms which interacts with fulfills these two roles. Here, we determined cryo-EM structure alone complex mitochondrial proteins, HTRA2 SMAC. We show antiparallel...