Core Facilities Frankfurt/Mainz

Proteomics Core Facility

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 Genomics Core Facility Frankfurt

The DKTK Cancer Genomics Core Facility was set up at the DKTK location in Frankfurt/Mainz in 2015 in response to rapid developments in the field of tumour genetics and next-generation sequencing (NGS). The unit is equipped with an Illumina MiSeq sequencing system and is located within the unit at the Department of Medicine II (Haematology/Oncology) at University Hospital Frankfurt.

The following methods/techniques are currently available:

• Quality control of NGS libraries (e.g. before sequencing on HiSeq sequencing systems)
• Targeted sequencing of tumour samples (targeted/amplicon sequencing)
• Analysis of genetic screens

Large sequencing projects, including exome sequencing, full genome sequencing and RNA sequencing, can be carried out in collaboration with the Genomics & Proteomics Core Facility at the DKFZ.

Cancer Structural Biology (NMR and X-ray) Core Facility Frankfurt

For the efficient development of novel drugs and therapies the understanding of biological processes and mechanisms at molecular level is of utmost importance. Therefore, the 3D structure determination of proteins, DNA, RNA and their complexes is essential for Drug Development to gain molecular insight into the function and dynamic of drugs with their interaction partners in cancer patients.

The DKTK partner site in Frankfurt/Mainz highlights a Cancer Structural Biology Platform with the Biomolecular Magnetic Resonance Centre (BMRZ), one of the leading centers of NMR-based structural biology in the world.

In the near future the BMRZ will be equipped with a 1.2 Gigahertz spectrometer, which will enable BMRZ (equipped with 14 high-field liquid-state NMR spectrometers (up to 950 MHz), two high-field widebore solid-state NMR spectrometers (850 and 600 MHz), a liquid-state and a solid-state NMR DNP setup) to maintain and expand its leading position as research facility for structure and dynamics of biomedically relevant macromolecules.
In addition Frankfurt hosts a leading key expertise in the development of drugs for protein kinases as well as on the research fields autophagy and epigenetic via structure-based drug design (NMR und X-ray).