Core Facilities Munich

Proteomics Facility

© Bernhard Küster/ Technische Universität München

The Core Facility Proteomics at the DKTK Partner site comprises seven 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.

Prof. Dr. Bernhard Küster

Chair of Proteomics and Bioanalytics

Technische Universität München

Emil Erlenmeyer Forum 5
85354 Freising


MTBIO - Tissue bank of the University Hospital rechts der Isar and Technical University of Munich

© kfbfotografie

The tissue bank of the University Hospital rechts der Isar and the Technical University of Munich (MTBIO) has been systematically preserving fresh unfixed tumor tissue and corresponding non-neoplastic tissue since 1989.

For this purpose, there has been a close link between the routine laboratory of the pathology department and the tissue bank since that time. Currently, the tissue collection of MTBIO comprises about 28,000 samples from approx. 18,000 patients, of which approx. 15,000 samples are malignant tumor tissue and 13,000 samples are non-neoplastic tissue, benign tumors and tumor precursors.

Service and support

  • Project consultation: Preliminary discussion with project leader, advice and assistance in selection of patient collectives, advice on control cohorts, advice on methods, information on preanalytics
  • Histopathology: Preparation of tissue sections from FFPE blocks, histological H&E diangotics, immunohistochemistry, design and preparation of tissue microarrays (TMAs), preparation of tissue sections from frozen tissues, PAXgene: Tissue System, formalin free tissue fixation, preparation of tissue sections, H&E diagnostics
  • Molecular Pathology: FFPE Tissue, Frozen Tissue, and PAXgene Tissue (each DNA isolation, RNA isolation, protein/phosphorprotein isolation)

Tissue bank MTBIO

Prof. Dr. Wilko Weichert

Klinikum rechts der Isar

Institut für Allgemeine Pathologie und Pathologische Anatomie

Trogerstr. 18
81675 München


Xenograft mouse model of acute leukemias

The Core Facility “Xenograft mouse model of acute leukemias” studies primary patients´ tumor cells growing in mice, performs preclinical treatment trials and molecular studies on basic disease biology.

In vivo bioluminescence imaging (BLI) allows reliable and sensitive follow-up of preclinical treatment trials © AG Jeremias

The core facility offers:

  • engrafting and amplifying primary tumor cells from patients with ALL or AML as patient-derived xenografts (PDX) in mice
  • biobank of re-transplantable PDX samples for in vitro studies, >50 for ALL and >10 for AML
  • genetic engineering in PDX (GEPDX) cells for overexpression of transgenes
  • preclinical in vivo treatment trials monitored by bioluminescence in vivo imaging
    • quantifying treatment responses as early as 4 days after treatment
    • covering all disease stages including minimal residual disease
    • focusing on challenging sub-populations such as dormant stem cells

More information on the Xenograft Facility München

Characteristics of AML PDX samples that were established within the first DKTK funding period © AG Jeremias


Prof. Dr. Irmela Jeremias

Dr. von Haunersches Kinderspital

Klinikum der Universität München Helmholtz Zentrum München

Marchioninistraße 25
81377 München

Leukemia Genomics Facility

© angellodeco /

Genetic characterisation plays a central role for diagnostics, treatment selection and prognostication in patients with leukemia. In close cooperation with local and DKTK partners, we support DKTK scientists exploring the biology and pathogenesis of leukemia.

Our aim is to develop innovative techniques for leukemia diagnostics. Our location at the Ludwig-Maximilians-Universität München (LMU) in the Department of Hematology and Oncology provides a close collaboration with the clinic and translational research groups. We have access to a large number of well-annotated patient specimens that have been collected at our routine diagnostics laboratory (Laboratory for Leukemia Diagnostics).


MiSeq personal sequencer © AG Spiekermann

Our facility can provide the following services to DKTK-affiliated groups:

Genetic characterization of human tissue specimens (primarily peripheral blood and bone marrow) using a variety of approaches including

  • Metaphase and molecular cytogenetics
  • Conventional molecular genetics (Sanger sequencing, fragment analysis and qPCR; various assays established for recurrent mutations in hematopoietic neoplasms)
  • Targeted next-generation sequencing (established panels of recurrently mutated genes in myeloid and lymphoid neoplasms)
  • Whole-exome and whole-genome sequencing
  • Single-cell genotyping


Analyse rekurrenter Genmutationen in 664 AML-Patienten mittels ‘targeted sequencing’ © AG Metzeler

Our main areas of research focus on the following topics

  • Genetic characterisation of myeloid neoplasias
  • Evaluation of novel prognostic and predictive markers in leukemia
  • New therapeutic targets in leukemias
  • Identification of markers for minimal residual disease (MRD)
  • Research on clonal evolution of leukemia

Core facility members: Prof. Dr. Karsten Spiekermann, PD Dr. Klaus Metzeler, PD Dr. Tobias Herold, PD Dr. Philipp Greif, Dr. Sebastian Vosberg, Sebastian Tschuri

Prof. Dr. Karsten Spiekermann

Klinikum der Universität München

Medizinische Klinik und Poliklinik III

Marchioninistr. 15
81377 München

Immune Analytics

Labor Krackhardt.jpg
© A. Krackhardt / Klinikum rechts der Isar München

The Core Facility Immune Analytics at the DKTK partner site Munich has a broad expertise in identification and characterization of tumor-specific immune responses and offer support in a variety of in-depth analyses in tumor immunology.

Activities supported by the faciltiy include logistics and sampling of fresh tumor material and blood, preparation of tumor and blood material, phenotyping of PBMC and cells of the tumor microenvirnoment by flos cytometry using established panelds, cultivation and expansion fo tumor-infiltrating lymphocytes, establishment of tumor cell lines and EBV-transformed B cells, identification of tumor antigens, immunoprecipitation of MHC class I and II peptide complexes, isolation and genetic transfer of T cell receptors, sorting of single cells of the tumor microenvironment by flow cytometry, preparation of cell suspensions and signle cell solutions for sequencing, establishment of xenogeneic mouse models, immunoimaging, clinical correlation, support and counseling in preparation of clinical trials of immunotherapeutic approaches in cancer. The cooperation typically bases on scientific collaboration.

Prof. Dr. Angela Krackhardt

Klinikum rechts der Isar

III. Medizinischen Klinik

Ismaninger Str. 22
81675 München

Genomics Technology and Informatics Platform

Genome research deploying next generation sequencing and other genomic technologies is a major driver of discoveries in life science. Profiling genomes, epigenomes or transcriptomes in organisms, tissues or single cells has become a standard.

At the same time, a rapidly growing number of sequencing applications is transforming the way we perform basic research across life sciences, with high-throughput sequencing-based methods complementing - and in many cases entirely replacing - classic "gene by gene" based experimental approaches.

The Genomic Technology Unit aims to address the increasing need for sequencing applications and analytical capabilities in biomedical research. We develop genomic tools and protocols, implement emerging sequencing applications as well as bioinformatics methods and pipelines in various research ares, including genomics, epigenetics, (epi)transcriptomics and functional genomics. We cover a broad spectrum of applications, ranging from sequencing based profiling of genomes, chromatin or transcriptomes over genome-scale genetic screening methodologies to numerous individualized sequencing and bioinformatics requests.

Prof. Dr. Roland Rad

Klinikum rechts der Isar

II. Medizinischen Klinik

Real-Time Cell Metabolic Analysis // Seahorse // Agilent

The Seahorse XF HS Mini Analyzer (Agilent Biotechnologies) measures mitochondrial respiration (oxygen consumption rate OCR) and glycolysis (extracellular acidification ECAR) of living cells (cultured cells and ex vivo samples) in an 8 well plate in real time. OCR and ECAR are key indicators of oxidative phophorylation and glycolysis. The instrument also allows the addition of substances and can therefore also make statements about their utilization.


PD Dr. med. Matthias Ilmer
LMU Klinikum
+49 89 4400 71218

Prof. Dr. Alexandr Bazhin
LMU Klinikum
+49 89 4400 73440

Location of device

LMU Klinikum, Campus Großhadern
Labor für Experimentelle Forschung Chirurgie


on request

Radiochemistry Synthesizer // All-In-One // Trasis

The synthesizer merges in a single integrated instrument a synthesizer and a HPLC with reformulation capability, which allows implementing both very simple and the most complex radiochemistry. If there is a need to evolve towards more complex tracers, the synthesizer can be upgraded to a different configuration model. The synthesizer includes 30 valves, HPLC, multiple radioactivity, and UV detection for GMP compliant routine production of 18F tracers and /or for R&D.

Das All-In-One Synthesemodul (Fa. TRASIS) in einer Blei-abgeschirmten Synthesezelle (einer sog. „Heisszelle“, Ansicht bei geöffneter Zellentür) in einem Reinraum der Radiopharmazie © AG Bartenstein


Dr. Franz J. Gildehaus
089 4400 69944

Prof. Dr. Peter Bartenstein
089 4400 74611

Location of device

LMU Klinkum, Campus Großhadern, Radiopharmacy Center, Building BT028, Marchioninistrasse 15, 81377 München


In the synthesis module, a sample is equivalent to a synthesis run. The cost of doing so varies greatly depending on the complexity of the chemical synthesis to be performed, how expensive the starting components are, and how the GMP requirements are defined. Normally the costs / synthesis are between 800 € and 2.600 €.


Production of 18F-labeled compounds for in vivo PET imaging. These include:
- Radiofluorinations of small molecules, peptides and biomolecules
- development of labeling strategies
- automation of radiosynthesis
- GMP-compliant implementation


Cell Imaging Multi-Mode Reader // Cytation 1 // Biotek

Cytation 1 © AG Theurich

Cytation™ 1 Cell Imaging Multi-Mode Reader combines fluorescence and high contrast brightfield imaging with conventional multi-mode detection. This design provides both quantitative phenotypic cellular information with well-based quantitative data. Cytation 1's multi-mode detection module includes high sensitivity filter-based fluorescence and a monochromator system for UV-Vis absorbance. For long-term measurements the device is able to control temperature, CO2 and O2. The reader is also equipped with an injector that allows imaging of immediate cell responses upon compound exposure.



Prof. Dr. Sebastian Theurich
Medizinische Klinik III, LMU Klinikum 
Marchioninistr. 25, 81377 München

Prof. Dr. Michael von Bergwelt
Medizinische Klinik III, LMU Klinikum
Marchioninistr. 25, 81377 München

Location of device

Genzentrum LMU
AG Theurich / AG Bergwelt
Feodor-Lynen-Str. 25, 81377 München


on request


Monochromator: 6- to 384-well plates /// Filters: 6- to 1536-well plates /// Imaging: 6- to 1536-well plates /// Microscope slides, Petri and cell culture dishes, cell culture flasks (T25), counting chambers (hemocytometer) /// Take3 Micro-Volume Plates


Digital Single Molecule Quantification // nCounter Sprint // NanoString Technologies

The nCounter technology allows direct quantification of up to 800 targets in a single assay without the necessity of amplifying target molecules. Possibility to measure mRNA, miRNA, lncRNA, dsDNA, und ssDNA (pre-designed or customized code sets available; multiple samples can be multiplexed) in a variety of specimens (tissue biopsies, blood, bone marrow, etc.). No library preparation or sophisticated pre-analytical processing required.

nCounter © NanoString Technologies


Michael Heide
Medizinische Klinik III, ELLF, LMU Klinikum

Prof. Dr. Oliver Weigert
Medizinische Klinik III, ELLF, LMU Klinikum

Location of device

Experimentelle Leukämie- und Lymphom-Forschung (ELLF)
Max-Lebsche-Platz 30, 81377 München

Service & Costs

Technical support via Weigert lab
User bears the cost of consumables, currently no user fee applied


Automated Quantitative Pathology Imaging System // Vectra® Polaris™ // Perkin Elmer

Vectra® Polaris™ © AG Jung

State of the art multispectral imaging to detect and measure multiple biomarkers within a single tissue.


Prof. Dr. Martina Rudelius

Dr. Peter Jung

Location of device

Institut für Pathologie der LMU München, Campus Innenstadt
Thalkirchner Str. 36, 80337 München

Service & Costs

Basic material: FFPE tissue sections stained with up to 6 established antigens and using OPAL dyes

Costs: on request


Bioluminescence tomography // MuriGlo // Xstrahl

MuriGlo is an in vivo optical imaging system for bioluminescence tomography. It can be used as stand-alone-imaging device or in combination with the existing conebeam-CT-platform for bioluminescence imaging in small animal models (preferentially in mice).

MuriGlo © Xstrahl


Prof. Dr. Kirsten Lauber
Moleculare Oncology, Department of Radiation Oncolgoy

Location of device

LMU Klinikum, Campus Großhadern
Animal facility of the Department of Radiation Oncology

Service & Costs

Basic material: small animal models with bioluminescence features

Service: bioluminescence tomography imaging (+/- conebeam CT scanning), consulting for animal experimentation proposals

Costs: on request; one sample represents one bioluminescence tomography scan of one animal


Pre-clinical CT-Scanner // X-Cube // Molecubes

X-Cube © AG Mayerle, Bartenstein

The X-Cube is a high-throughput x-ray CT-scanner for pre-clinical mouse and rat models. The CT imaging procedure is very fast and gives images of the complete animal body at extremely low dosages and with an excellent soft tissue contrast. Advanced workflows such as gated and dynamic contrast enhanced imaging can be achieved in a functional and integrated set up.


Dr. Ivonne Regel

Prof. Dr. Sybille Ziegler

Location of device

LMU Klinikum, Campus Großhadern
Preclinical Imaging Lab

Service & Costs

Basic material: small animal models (mouse or rat) with an approve health report

Costs: on request