The analysis and the identification of proteins within larger assemblies such as enzyme complexes, chromosomal arrays or sub-nuclear domains lies at the heart of the collaborative research centre. It is therefore of crucial importance to have easy access to state-of-the-art equipment that is properly maintained and operated by well-trained personnel. One of the key technologies in today’s protein analytics is high performance mass spectrometry that can be either used off-line or coupled to highly resolving, miniaturized protein and peptide separation techniques such as HPLC and capillary electrophoresis. In order to make sure that such equipment is available for the scientists of the collaborative research centre, a proteomics core facility was established at the Adolf-Butenandt Institute that maintains a high level of analytical services and provides the opportunity to perform large scale quantitative proteomic studies such as a the comprehensive mapping of post-translational modifications or the characterisation of protein-protein interaction surfaces using crosslinking techniques. The core facility will not only provide valuable services to maintain the high quality of research within the CRC, but will also be crucial for the detailed analysis of protein structure and function as well as the investigation of regulatory processes.