Torsten Müller

Torsten Müller
Universität Heidelberg · German Cancer Research Centre (DKFZ)

Master of Sc., Biotechnology - Biomedical Science and Technology

About

31
Publications
6,641
Reads
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893
Citations
Additional affiliations
June 2016 - present
German Cancer Research Center
Position
  • PhD Student
September 2015 - March 2016
ETH Zurich
Position
  • Intern
Description
  • Master Thesis Project
April 2014 - August 2014
University of Bonn - Institute of Biochmistry and Molecular Biology
Position
  • Research Associate
Education
September 2014 - February 2016
Hochschule Mannheim
Field of study
  • Biotechnology with focus on Biomedical Sciences and Technology
September 2009 - February 2014
Fachhochschule Bingen
Field of study
  • Biotechnics
August 1999 - March 2008
Gymnasium auf der Karthause
Field of study
  • Biology, English, Civics and Economics

Publications

Publications (31)
Article
INTRODUCTION: The majority of pediatric ependymoma (EPN) comprise either supratentorial EPN characterized by ZFTA-fusions (ST-EPN-ZFTA) or posterior fossa group A EPN (PF-EPN-A), for both of which only limited therapeutic options are available. Because pediatric EPNs have a relatively low mutational burden, identification and characterization of tu...
Article
INTRODUCTION: Atypical teratoid/rhabdoid tumors (ATRT) represent frequent brain tumors in infants. In recent years, large-scale landscaping efforts on the epigenome and transcriptome of these tumors have unravelled a high degree of heterogeneity and three major molecular subgroups, termed ATRT-TYR, ATRT-SHH,ATRT-MYC, have been identified. The ATRT-...
Article
Full-text available
Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficie...
Article
Full-text available
Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit ampl...
Article
Clinically translatable large animal models have become indispensable for cardiovascular research, clinically relevant proof of concept studies and for novel therapeutic interventions. In particular, the pig has emerged as an essential cardiovascular disease model, because its heart, circulatory system, and blood supply are anatomically and functio...
Article
Full-text available
Ependymal tumors (EPNs) account for ~10% of all pediatric brain tumors. Supratentorial EPN characterized by RELA fusions (ST-EPN-RELA) and posterior fossa EPN group A (PF-EPN-A) form the two most frequent molecular groups, both of which are associated with poor prognosis and for which only limited therapeutic options are available. Since pediatric...
Preprint
Full-text available
Label-free proteomics by data-dependent acquisition (DDA) enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR, an efficient and user-friendly quantification w...
Article
To date, the effects of specific modification types and sites on protein lifetime have not been systematically illustrated. Here, we describe a proteomic method, DeltaSILAC, to quantitatively assess the impact of site-specific phosphorylation on the turnover of thousands of proteins in live cells. Based on the accurate and reproducible mass spectro...
Conference Paper
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 of the CRC TIC compartment with distinct types of TICs driving CRC progression. However, in these retrospective experiments direct assignmen...
Preprint
Full-text available
Post-translational modifications such as phosphorylation can have profound effects on the physicochemical and biological properties of proteins. However, high-throughput and systematic approaches have not yet been developed to assess the effects of specific modification types and sites on protein lifetime, which represents a key parameter for under...
Article
Full-text available
Abstract High‐throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh‐frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single‐pot solid‐phase‐enhanced sample preparation (SP3) on a liquid handling robot for automated proc...
Thesis
The genetic information of all life is encoded within DNA molecules that are translated into functional entities, so-called proteins. They are responsible for operating and controlling a vast array of molecular mechanisms in any biological system and ubiquitous in (patho)physiology as a result. Besides, proteins are the primary target of drugs and...
Preprint
Full-text available
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including fresh frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated p...
Article
Posterior fossa A (PFA) ependymomas comprise one out of nine molecular groups of ependymoma. PFA tumors are mainly diagnosed in infants and young children, show a poor prognosis and are characterized by a lack of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark. Recently, we reported overexpression of CXorf67 as hallmark of PFA ep...
Article
Background: Posterior fossa A (PFA) ependymomas comprise one out of nine molecular groups of ependymoma. PFA tumors are mainly diagnosed in infants and young children, show a poor prognosis and are characterized by a lack of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark. Recently, we reported CXorf67 overexpression as hallmark...
Article
Full-text available
Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 int...
Article
Full-text available
Aberrant protease activity has been implicated in the etiology of various prevalent diseases including neurodegeneration and cancer, in particular metastasis. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has recently been established as a key technology for bioanalysis of multiple biomolecular classes such as...
Preprint
Full-text available
The independent reproduction of research results is a cornerstone of experimental research, yet it is beset by numerous challenges, including the quality and veracity of reagents and materials. Much of life science research depends on life materials, including human tissue culture cells. In this study we aimed at determining the degree of variabili...
Article
Full-text available
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 protein turnover in fibroblasts from a monozygotic twin pair discordant for T21, and to profile protein expression in 11 unrelated DS individuals and matched controls. The integration...
Article
Full-text available
Reduction and alkylation of cysteine residues is part of virtually any proteomics workflow. Despite its frequent use, up to date no systematic investigation of the impact of different conditions on the outcome of proteomics studies has been performed. In this study, we compared common reduction reagents (dithiothreitol, tris-(2-carboxyethyl)-phosph...

Questions

Question (1)
Question
I acquired a large dataset on an LTQ-Orbitrap mass spectrometer. I processed the raw files with Proteome Discoverer Daemon. Now I have been trying to perform an error tolerance search with Mascot. Both the manual and the automatic why lead to a browser crash. The computer hardware should not be a problem. Are there any alternatives available to find PTMs? Is it possible to somehow reduce the file size?

Projects

Project (1)
Project
Goal of this project is the integrative characterization of the morphological and molecular intratumoral heterogeneity of lung adenocarcinoma in order to delineate resulting implications for molecular diagnostics, therapy decision making and patient outcome.