A5063574912- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Mitochondrial Function and Pathology
- Biotin and Related Studies
- Protein Structure and Dynamics
- Gene expression and cancer classification
- Fungal and yeast genetics research
- Cell death mechanisms and regulation
- interferon and immune responses
- Heat shock proteins research
- Single-cell and spatial transcriptomics
- Erythrocyte Function and Pathophysiology
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Immune Response and Inflammation
- Advanced Biosensing Techniques and Applications
- Metabolism and Genetic Disorders
- Microbial Natural Products and Biosynthesis
- Genetic Mapping and Diversity in Plants and Animals
Max Planck Institute of Biochemistry
2019-2024
ETH Zurich
2017-2022
University of Zurich
2018-2019
Life Science Zurich
2018-2019
German Cancer Research Center
2017
Heidelberg University
2017
Machine learning and in particular deep (DL) are increasingly important mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention time, ion mobility fragment intensities of a peptide just from amino acid sequence with good accuracy. However, is very rapidly developing field new neural network architectures frequently appearing, which challenging to incorporate for proteomics researchers. Here we introduce AlphaPeptDeep, modular Python framework built on PyTorch...
The recent revolution in computational protein structure prediction provides folding models for entire proteomes, which can now be integrated with large-scale experimental data. Mass spectrometry (MS)-based proteomics has identified and quantified tens of thousands posttranslational modifications (PTMs), most them uncertain functional relevance. In this study, we determine the structural context these PTMs investigate how information leveraged to pinpoint potential regulatory sites. Our...
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited proteomic depth, throughput, robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated complete dimethyl labeling bulk or single-cell samples, without losing depth. Lys-N digestion enables five-plex quantification MS1 MS2 level. Because channels are...
Cellular functions are mediated by protein-protein interactions, and mapping the interactome provides fundamental insights into biological systems. Affinity purification coupled to mass spectrometry is an ideal tool for such mapping, but it has been difficult identify low copy number complexes, membrane complexes that disrupted protein tagging. As a result, our current knowledge of far from complete, assessing reliability reported interactions challenging. Here we develop sensitive...
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...
Article14 January 2019Open Access Transparent process Complex-centric proteome profiling by SEC-SWATH-MS Moritz Heusel Department of Biology, Institute Molecular Systems ETH Zurich, Switzerland PhD Program in and Translational Biomedicine the Competence Center Personalized Medicine UZH/ETH, Search for more papers this author Isabell Bludau orcid.org/0000-0002-2601-238X Life Science Zurich Graduate School, University George Rosenberger orcid.org/0000-0002-1655-6789 Robin Hafen Computer...
Abstract Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power data independent acquisition (DIA) regards to sensitivity single run analysis and completeness not yet been explored. Here, we develop sensitive workflow combining antibody-based enrichment...
To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that coding genome. Various processes create multiple distinct but related proteins per gene - so-called proteoforms expand capacity cell. Evaluating from classical bottom-up proteomics datasets, where peptides instead intact are measured, has remained difficult. Here we present COPF, tool for COrrelation-based ProteoForm assessment data. It leverages concept peptide correlation...
Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes affects activity and/or function and is thus great interest for biological research. Here, we describe implementation an integrated technique to quantify cell-state-specific changes in physical arrangement protein...
Abstract Tumor necrosis factor (TNF) is one of the few cytokines successfully targeted by therapies against inflammatory diseases. However, blocking this well studied and pleiotropic ligand can cause dramatic side-effects. Here, we reason that a systems-level proteomic analysis TNF signaling could dissect its diverse functions offer base for developing more therapies. Therefore, combine phosphoproteomics time course experiments with subcellular localization kinase inhibitor to identify...
Mitochondria are essential organelles whose dysfunction causes human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondrial fitness depends on versatile proteomes specialized to meet diverse requirements. Increasing evidence suggests phosphorylation may play an important role regulating functions and pathophysiology. Building recent advances mass spectrometry (MS)-based proteomics, we here quantitatively profile tissue along with their matching...
ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints improved segmentation. clearly outperforms widely used state-of-the art methods, provides fully automated cell content ploidy, additionally computes homologous recombination deficiency scores.
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...
Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, undergo changes in their abundance, subunit composition, or state modification. Understanding function biological systems requires global strategies capture this contextual information. Methods based on cofractionation paired with mass spectrometry have demonstrated capability for deep insight, but scope studies using approach has been limited by large measurement time per sample...
ABSTRACT Data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments a predefined precursor m/z range. Although these selection windows collectively cover the entire range, overall only few percent all incoming ions are sampled. Making use correlation molecular weight ion mobility in trapped device (timsTOF Pro), we here devise novel scan mode that samples up to 100% peptide current. We extend an established...