A5087874713- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Metabolomics and Mass Spectrometry Studies
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Fungal and yeast genetics research
- Glycosylation and Glycoproteins Research
- Microbial Metabolic Engineering and Bioproduction
- Monoclonal and Polyclonal Antibodies Research
- Neonatal and fetal brain pathology
- Genomics and Phylogenetic Studies
- Signaling Pathways in Disease
- Enzyme Structure and Function
- Genetics, Aging, and Longevity in Model Organisms
- Mitochondrial Function and Pathology
- Bacteriophages and microbial interactions
- Microtubule and mitosis dynamics
- Trypanosoma species research and implications
- Malaria Research and Control
- Gene Regulatory Network Analysis
- Viral Infectious Diseases and Gene Expression in Insects
- Bacterial Identification and Susceptibility Testing
University of Basel
2016-2025
Goethe University Frankfurt
2024
Jena University Hospital
2014-2024
Boston Medical Center
2024
Columbia University Irving Medical Center
2024
Boston University
2024
Helmholtz-Zentrum Berlin für Materialien und Energie
2023
Ludwig-Maximilians-Universität München
2023
Urologische Klinik München
2023
Gates Foundation
2019-2022
The generation of mathematical models biological processes, the simulation these processes under different conditions, and comparison integration multiple data sets are explicit goals systems biology that require knowledge absolute quantity system's components. To date, systematic estimates cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description proteome commonly used human cell line in two functional states, interphase mitosis. We show...
Abstract Stable isotope labelling in combination with mass spectrometry has emerged as a powerful tool to identify and relatively quantify thousands of proteins within complex protein mixtures. Here we describe novel method, termed isotope‐coded label (ICPL), which is capable high‐throughput quantitative proteome profiling on global scale. Since ICPL based stable tagging at the frequent free amino groups isolated intact proteins, it applicable any sample, including extracts from tissues or...
Simply Mycoplasma The bacterium pneumoniae , a human pathogen, has genome of reduced size and is one the simplest organisms that can reproduce outside host cells. As such, it represents an excellent model organism in which to attempt systems-level understanding its biological organization. Now three papers provide comprehensive quantitative analysis proteome, metabolic network, transcriptome M. (see Perspective by Ochman Raghavan ). Anticipating what might be possible future for more complex...
Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and extracellular accessibility for pharmacological intervention. However, information about the cell protein repertoire (the surfaceome) individual cells is only sparsely available. Here, we applied Surface Capture (CSC) technology 41 human 31 mouse types generate a mass-spectrometry derived Protein Atlas (CSPA) providing surfaceome snapshots at high resolution. The CSPA presented in form...
The complete and specific proteolytic cleavage of protein samples into peptides is crucial for the success every shotgun LC-MS/MS experiment. In particular, popular peptide-based label-free targeted mass spectrometry approaches rely on efficient generation fully cleaved to ensure accurate sensitive quantification. contrast previous studies, we globally quantitatively assessed efficiency different digestion strategies using a yeast cell lysate, quantification, statistical analysis. Digestion...
Comprehensive characterization of a proteome is fundamental goal in proteomics. To achieve saturation coverage or specific subproteome via tandem mass spectrometric identification tryptic protein sample digests, proteomics data sets are growing dramatically size and heterogeneity. The trend toward very large integrated poses so far unsolved challenges to control the uncertainty identifications going beyond well established confidence measures for peptide-spectrum matches. We present MAYU,...
Abstract Label‐free quantification of high mass resolution LC‐MS data has emerged as a promising technology for proteome analysis. Computational methods are required the accurate extraction peptide signals from and tracking these features across measurements different samples. We present here an open source software tool, SuperHirn , that comprises set modules to process acquired on spectrometer. The program includes newly developed functionalities analyze such feature quantification,...
Quantitative phosphoproteomics suggests that kinases other than ATM participate in the initial phase of cellular response to DNA double-strand breaks.
Abstract Background On account of physical distancing measures, universities worldwide are strongly affected by SARS-CoV-2 (COVID-19). Thus, the dental school Justus-Liebig-University Giessen (Germany) transferred established “face-to-face” learning to online in spring term 2020. The aim this study was assess students’ and lecturers’ perspectives on implementation due COVID-19, using a questionnaire survey. Methods After period, all students lecturers were asked fill out an containing...
There is a great interest in reliable ways to obtain absolute protein abundances at proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated abundance. Several variants of approach presented, based on either the number spectral counts per or MS1 peak intensities. Equipped with several datasets representing real biological environments, containing high accurately quantified reference proteins, we...
An integrated account of the molecular changes occurring during process cellular aging is crucial towards understanding underlying mechanisms. Here, using novel culturing and computational methods as well latest analytical techniques, we mapped proteome transcriptome replicative lifespan budding yeast. With age, found primarily proteins involved in protein biogenesis to increase relative their transcript levels. Exploiting dynamic nature our data, reconstructed high-level directional...
Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of flux along open reading frames (ORFs) are not fully understood. Combining measurements rate footprinting data, we here inferred translation initiation elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that amino acid composition synthesized proteins is as important determinant parameters related to codon...
Article21 September 2016Open Access Source DataTransparent process Bacterial persistence is an active σS stress response to metabolic flux limitation Jakub Leszek Radzikowski Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands Search for more papers by this author Silke Vedelaar David Siegel Analytical Biochemistry, Research Institute Pharmacy, Álvaro Dario Ortega Alexander Schmidt Biozentrum, Basel, Switzerland...