DKTK Core Facilities: Proteomics

Proteomics Facility München

The Core Facility Proteomics at the DKTK Partner site comprises five high-end mass spectrometers, several liquid chromatography systems and terabyte scale computing infrastructure.

The range of supported applications span quantitative protein expression profiling of human and animal tissues, tumors, cell lines and body fluids, dynamic analysis of post-translational modifications, protein-protein interactions, drug target identification, drug mechanism of action analysis and many more. We can offer discovery type proteomic experiments using multidimensional chromatography coupled to the latest Orbitrap technology as well as targeted assays using parallel reaction monitoring. All major quantification workflows are established in the laboratory including SILAC, TMT and a range of label-free analysis. We typically work on the basis of scientific collaboration in which we engage our expertise along the entire path from experiment design through to data acquisition and bioinformatic analysis.

Proteomics Core Facility Frankfurt

The Proteomics Core Facility at the Frankfurt location is an initiative of the DKTK and is equipped with three Q Exactive mass spectrometers from Thermo Fisher (one Q Exactive, one Q Exactive Plus and one Q Exactive HF instrument). The available technology can be used to e.g. identify and quantify protein expression patterns, post-translational protein modifications such as phosphorylation, acetylation and ubiquitination, and protein complexes.

This makes it possible to conduct a comprehensive characterisation of oncogenic mechanisms at the protein level, which includes mapping of oncogenic signal transduction processes. The technical advances made in recent years mean that it is now possible to identify and quantify in relative terms several thousand proteins from just a few micrograms of protein. The main activities of the Proteomics Core Facility relate to translational research topics in the field of acute leukaemia, lymphoma, lung cancer, rectal cancer and brain tumours. The research uses cell culture models and freshly isolated tumour cells, as well as fresh frozen and formalin-fixed tissue samples. All the procedures necessary for sample preparation are established at the Proteomics Core Facility and are available to users. For the relative quantification of protein samples, the methods available include stable isotope labelling (SILAC), iTRAQ and label-free methods. Absolute protein quantification is also possible. Besides biochemical analysis, the Proteomics Core Facility is also used to conduct bioinformatic analyses of mass spectrometry data, making it possible to provide DKTK scientists with complex datasets once the data has been suitably processed.

Cancer Metabolomics Platform Berlin

The metabolome reflects the current functional status of the cell. Metabolomic changes play a central role in the pathogenesis and therapy of malignant diseases. The at the DKTK partner site Berlin established gas chromatography, coupled with high resolution mass spectrometry (GC-MS), is a sensitive and robust platform for the analysis of metabolites of the primary metabolism (amino acids, sugars, nucleic acids) (Fig. 2). This technique offers a broad applicability in tumor biology and interdisciplinary problems. The MS technology (APCI Q-TOF) allows quantitative statements and is particularly suitable for the elucidation of the structure of unknown analytes and for the analysis of very small samples volumes. Metabolic flux analysis is currently under establishment. As increasingly important extension of other, in Berlin reproached omics platforms, the cancer metabolomics platform enables functional, systems biology insights into the tumor metabolism and contributes to the identification of novel therapeutic principles.

Scientific Core Facilities and Services Heidelberg

Scientists at the DFKZ and its partner sites can rely on broad portfolio of research infrastructures for their research projects. These include experimental core facilities, data management and IT services. Core facilities are centralized laboratories that operate as user laboratories or as full service units, or both, depending on the technology in question. They offer access to high-end instrumentation, provide scientific and technical advice to users, and are engaged in method development and technology-oriented research. Data management and IT services cover the IT infrastructure demands of the DKFZ and provide also software tools for organizing and handling research data properly.

Below, the DKFZ Core Facilities are listed according to their area of specialty.

Genome, Transcriptome & Epigenome
Next Generation Sequencing (S. Wolf)
Microarray (M. Bewerunge-Hudler)
Single Cell OpenLab (J.-P. Mallm)

Proteome
Proteomics (D. Helm)
Single Cell OpenLab (J.-P. Mallm)
Microarray (M. Bewerunge-Hudler)
Antibodies (I. Hofmann)

Metabolome
Metabolomics (G. Poschet, with Heidelberg University)

Cellular and Preclinical Imaging
Light Microscopy (F. Bestvater)
Electron Microscopy (K. Richter)
Small Animal Imaging (M. Jugold)
Radiopharmaceuticals and Preclinical Trials (I. Kurth)

Cytometry and Screening
Flow Cytometry (S. Schmitt)
Chemical Biology (U.Uhrig, with EMBL)

Whole Tissue Analyses 
Light Microscopy (F. Bestvater)
Single Cell OpenLab (J.-P. Mallm)

Reagents ans Resources for Cancer Resarch
Antibodies (I. Hofmann)
Cellular Tools and Clone Repository (R. Will)
Radiopharmaceuticals and Preclinical Trials (I. Kurth)
Dieter Morszeck Biorepository (S. Röhling)

Animal Services
Center for Preclinical Research (K. Reifenberg)
Tumor Models (N.N.)
Microbiological Diagnostics (K. Schmidt)
Transgenic Service (F. van der Hoeven / B. Armstrong)

Research Data Management 
Omics-IT and Data Management (I. Buchhalter)
OMERO@DKFZ (internal link)

Library & IT Services
Information Technology (C. Galuschka)
Central Library (D. Sitek)