A5047691340- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Ubiquitin and proteasome pathways
- Cancer Genomics and Diagnostics
- Histone Deacetylase Inhibitors Research
- Cancer Cells and Metastasis
- Metabolomics and Mass Spectrometry Studies
- Protein Degradation and Inhibitors
- Immune cells in cancer
- Single-cell and spatial transcriptomics
- Immune responses and vaccinations
- Immunodeficiency and Autoimmune Disorders
- Drug Transport and Resistance Mechanisms
- Extracellular vesicles in disease
- Ferroptosis and cancer prognosis
- Psoriasis: Treatment and Pathogenesis
- Biotin and Related Studies
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- HIV Research and Treatment
- interferon and immune responses
- Chronic Lymphocytic Leukemia Research
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
Heidelberg University
2020-2022
German Cancer Research Center
2019-2022
University Hospital Heidelberg
2020-2021
GlaxoSmithKline (Germany)
2018-2021
European Molecular Biology Laboratory
2020
Method16 January 2020Open Access Source DataTransparent process Automated sample preparation with SP3 for low-input clinical proteomics Torsten Müller German Cancer Research Center (DKFZ), Heidelberg, Germany Medical Faculty, Heidelberg University, Search more papers by this author Mathias Kalxdorf EMBL, Rémi Longuespée Department of Clinical Pharmacology and Pharmacoepidemiology, Daniel N Kazdal orcid.org/0000-0001-8187-3281 Institute Pathology, Albrecht Stenzinger Jeroen Krijgsveld...
Abstract Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands proteins, however it notoriously suffers from high rates missing values, thus prohibiting consistent protein across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly workflow that combines identification with low value similar to data-independent acquisition. Specifically, uses ion information for a...
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival, identity. As such, it is prominent target for pharmacological intervention. relatively low abundance of this subproteome conjunction with challenging extractability solubility still hampers its comprehensive analysis. Here, we combined chemical glycoprotein-tagging strategy mass spectrometry to enable analysis the cell-surface glycoproteome. To benchmark workflow provide guidance line...
As key cells of the immune system, macrophages coordinate activation and regulation response. Macrophages present a complex phenotype that can vary from homeostatic, proinflammatory, profibrotic to anti-inflammatory phenotypes. The factors drive differentiation monocyte macrophage largely define resultant phenotype, as has been shown by differences found in M-CSF- GM-CSF-derived macrophages. We explored alternative inflammatory mediators could be used for vitro human monocytes into IFN-γ is...
Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing patient-derived CRC models to decipher distinct subpopulations based on their transcriptional profiles. Cell type-specific expression modules stem-like, transit amplifying-like, differentiated cells resemble differentiation states normal intestinal epithelial cells. Strikingly, identified differ in proliferative...
Summary High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety sources, including fresh frozen tissue, FFPE or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on liquid handling robot automated (autoSP3) tissue lysates 96-well format, performing unbiased protein purification digestion, delivering peptides that can be directly analyzed by LCMS....
Abstract Label-free proteomics by data-dependent acquisition (DDA) enables the unbiased quantification of thousands proteins, however it notoriously suffers from high rates missing values, thus prohibiting consistent protein across large sample cohorts. To solve this, we here present IceR, an efficient and user-friendly workflow that combines identification DDA with low value similar to DIA. Specifically, IceR uses ion current information in data for a hybrid peptide propagation (PIP)...
Studying biological processes at a molecular level and monitoring drug-target interactions is established for simple cell systems but challenging in vivo. We introduce apply methodology proteome-wide thermal stability measurements to characterize organ physiology activity of many fundamental across tissues, such as energy metabolism protein homeostasis. This method, termed tissue proteome profiling (tissue-TPP), also enabled target off-target identification occupancy tissues derived from...
Abstract Adverse drug reactions (ADRs) contribute significantly to late-stage attrition in discovery due their unpredictability and enigmatic underlying mechanisms. Here we applied mass spectrometry-based proteomics assess the effects of 46 approved or retracted drugs with various levels concerns for drug-induced liver injury annotated mitochondrial mechanisms, along 8 tool compounds, on secretome a hepatocyte model. We observed distinct clusters non-canonical secretion, intracellular...
Abstract Tumor progression in colorectal cancer (CRC) is driven by a subpopulation of cells with tumor-initiating cell (TIC) activity. In the past, bulk experiments provided strong evidence for functional heterogeneity CRC TIC compartment distinct types TICs driving progression. However, these retrospective direct assignment states to individual functionally relevant has not been possible. We here asked whether can be assigned specific subpopulations. Therefore, 4,663 single-cell profiles...
Abstract Ependymal tumors (EPNs) account for ~10% of all pediatric brain tumors. Supratentorial EPN characterized by RELA fusions (ST-EPN-RELA) and posterior fossa group A (PF-EPN-A) form the two most frequent molecular groups, both which are associated with poor prognosis only limited therapeutic options available. Since EPNs have a relatively low mutational burden, identification characterization tumor-associated pathways processes is critical importance to inform potential targets....
Abstract INTRODUCTION: Atypical teratoid/rhabdoid tumors (ATRT) represent frequent brain in infants. In recent years, large-scale landscaping efforts on the epigenome and transcriptome of these have unravelled a high degree heterogeneity three major molecular subgroups, termed ATRT-TYR, ATRT-SHH,ATRT-MYC, been identified. The ATRT-proteome, turn, still represents largely unchartered territory. METHODS: We performed peptide-based screening approach to characterize proteome 40 ATRTs six ATRT...