Project Z04


The proteomics platform provides access to proteomic methodologies and high-end mass-spectrometry using state-of-the-art orbitrap technologies. This covers the whole range from sample preparation to mass spectrometry and data analysis, but also includes a set of biochemical tools dedicated to quantitative proteomics, phospho-proteomics and secretome analysis. Over the past years we have developed a range of proteomic techniques for global quantitative proteome profiling of cells and tissues. This includes an ultra-sensitive application using a novel approach for sample preparation based on magnetic bead technology requiring only very little sample input. We have introduced methods for the analysis of specific sub-proteomes that play crucial roles in cell regulation, especially secreted and chromatin-bound proteins. These are all quantitative methodologies through the use of stable isotope labeling, including SILAC and dimethyl labeling, combined with advanced mass spectrometry-based platforms. A particularly powerful approach combines SILAC labeling and click-chemistry that has allowed us to examine protein synthesis and secretion upon stimulation of cells. In this project, we will use these methodologies to gain a better mechanistic understanding of various aspects of Wnt signaling. We will use global and phospho-proteomics to analyze Wnt and Wnt/STOP signaling. Secretion of Wnt proteins will be investigated by identifying interaction partners of proteins that mediate Wnt translocation through the secretory system. We will use a recently developed methodology combining chromatin-immunoprecipitation (ChIP) with MS to study protein interactions in chromatin to understand the network around transcription factors downstream of signaling cascades. These combined technologies will be used for the in-depth and quantitative proteomic characterization of cells and tissues to gain mechanistic insight in secretion, trafficking and downstream signaling of Wnt.