Pathway Processor is a tool for integrating whole-genome expression results into metabolic networks.

Real time and immunohistochemistry analysis was performed in a study to evaluate whether iNOS can serve as a prognostic factor in stage III melanoma survival. The analysis showed that both iNOS and COX-2 alone significantly predicted OS. The BRAF/NRAS mutation status did not significantly differ between patient groups, although iNOS significantly correlated with BRAF mutation frequency. Furthermore, iNOS and COX-2 were significantly linked to a number of metastatic lymph nodes. However, iNOS maintained its statistical significance together with a number of lymph node...

Using MAGE-A3 as a model antigen we established a functional read-out system by transfection of CD4 T cells with RNA encoding T cell receptors recognizing MHC DP4 restricted MAGE-A3 epitopes.

Our lab has know-how in the functional annotation of upregulated and downregulated genes by gene ontology classification and pathway analysis by several bioinformatics approaches, among them Ontologizer. Preliminary results obtained from querying DAVID (http://david.abcc.ncifcrf.gov/) and Ontologizer (http://www.charite.de/ch/medgen/ontologizer/) show statistically significant enrichment for immunological-relevant signaling pathways and immunology-related GO terms of the upregulated proteins in mature DCs.

In our work, we have experience in applying peptide-tetramer assays. Primary and secondary CTL response against the C8 T cell epitope SIINFEKL was monitored in a study for maturing myeloid DCs and plasmacytoid DCs.

RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented. A co...

This platform with its state-of-the-art mass spectrometry facilities is led by Mann (P33). To enhance the platform, two additional groups were recruited as Third Parties: P114 Edwin Lasonder in Nijmegen (NL), and P113 Juri Rappsilber in Edinburgh (GB). The mass spectrometer has been used, for instance, to identify and quantify chemokine dependent tyrosine phosphorylation events. Furthermore, the success of SILAC labelling was analysed using the mass spectrometer.

Our lab has expertise in lipofection of tumor-antigen-encoding RNA into DC. The method was compared to RNA electroporation into DC.

We have access to and experience with using a linear ion trap / Fourier Transform (LTQ-FT) hybrid mass spectrometer. For example, we use it to analyse purified tryptic peptides.

A comprehensive protein inventory of clinical grade immature and cytokine cocktail matured (Il-6, IL-1 beta, TNF alpha, PGE2; 48 hours) monocyte derived human dendritic cells (DC) from a healthy donor has been established by using high accuracy, high sensitivity protein identification technology. We have identified 2794 proteins in DCs by liquid chromatography tandem mass spectrometry.

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing hi...

Our laboratory has a mass spectrometer at its disposal.

We have developed a MAGE-ML export feature in collaboration with the European Bioinformatics Institute (EBI).

In our lab, we have know-how about performing MPLC assays, such as using it in the establishment of immunomonitoring vaccination trials with RNA transfected DC by using overlapping peptides.

Iterative calibration algorithms were used to achieve a final, absolute mass accuracy of better than 10 parts per million (p.p.m.) for all peptide ions. These high-accuracy spectra were searched against a human protein database, using MASCOT probability-based scoring in which the fragment ions are matched against the calculated fragments of all tryptic peptides from the human sequences. Additional constraints were set by searches against a reversed human database to minimize false positive protein identifications.

We have experience in multicolour flow cytometry. Besides ELISPOT, tetramer based 8-colour flow cytometry has become our routine monitoring assay, allowing extended phenotypic and functional characterization of T cell subpopulations. Of special interest has become the identification of polyfunctional T cells (capable to simultaneously exert several functions, i.e. production of various cytokines and killing activity) since these have been shown to elicit more effective immune responses in HIV vaccination trials.

In the lab, there is a multi-photon microscope available. It is used, for instance, in the analysis of in vivo distribution and motility of NK cells.

There is a MACS separator (Miltenyi Biotech) at the disposal of our lab. It is used, for example, to purify CD8 T cells.

Our lab has an MRI scanner at its disposal. We use it, e.g., to track dendritic cells in melanoma patients for monitoring of cellular therapy.

The MaxQuant software is designed to make it possible to compare cell subsets quantitatively based on the extracted ion current (XIC) and without any need of stable isotope labels.