The synthesis of novel small molecules and oligonucleotides able to catch and label specific proteins in living cells is in the post genome area urgently needed to understand protein functions and protein networks. The state of the art in the field of proteomics is measuring global enzyme expression profiles by gel-electrophoresis based only on protein abundance (Görg). While this technology is useful for monitoring expression changes of all proteins present in a given proteome, it does not provide much information about the function of a specific enzyme class. The chemical probes prepared by Carell/Sieber put a handle on selected enzymes, which can then be enriched, identified, and studied in further detail. Unlike gel-based proteomics, the new method achieves superiour sensitivity and is also applicable to membrane proteomes, both crucial aspects for the investigation of cancer invasiveness. This allows to combine the proposed technical advances in small molecule development and enzyme detection with an in depth analysis of disease relevant biological pathways to contribute a better understanding of selected disease processes. Small molecules able to modify protein functions in living cells are now world wide developed as tools in cell biology to decipher biochemical pathways. This is an emerging field in which the Mayer group has already an excellent standing. The modulation of protein-protein interactions by small organic molecules represents one of the most challenging topics of current research at the interface of organic chemistry and biochemistry (Berg). The tremendous progress made in the RNAi field strongly demands new delivery strategies, e.g. chemically modified RNA. Small RNA-guided gene silencing (especially RNAi) is a rapidly developing research field. During the past few years remarkable progress in siRNA design has been made but still one siRNA out of three is inactive and the potential off-target effects are only poorly characterized. Therefore, it is highly relevant to improve the specificity and efficiency of siRNAs (Meister). With the development of the first method for the production of functional antibody fragments in E. coli, Skerra was one of the founders of the field of antibody engineering and has made many important contributions since then. With the development of the Anticalin technology he is one of the pioneers in the area of engineering protein scaffolds to yield novel ligand-binding proteins. Owing to the tremendous prospects of these novel proteins for practical applications, in particular in medical therapy, he was able to found the Pieris Proteolab AG, a biotech startup with ca. 30 employees situated at the Weihenstephan campus. Furthermore, the so-called Strep-tag was one of the first short affinity peptides that have been specifically designed to permit both the detection and the purification of recombinant proteins. Together with the His6 tag, the Strep-tag nowadays is among the most widely applied research tools for this purpose and it has turned out to be a particularly useful and simple tool for the elucidation of protein interaction networks in proteomics as well as for the preparative production of proteins for structural analysis. The Skerra laboratory currently applies – and continuously optimizes – this gentle and efficient technique, which is based on the molecular interaction between an artificial nine amino acid sequence and streptavidin, to crystallize biologically proteins that are difficult to handle, e.g. because of poor heterologous expression yields or limited stabilisation (especially in the case of non-covalent functional complexes). The Strep-tag methodology will be provided to other members within CIPS^M. The Langosch group was the first to identify transmembrane domain interactions in SNARE proteins and to develop an in vitro fusion assay where natural full-length fusogenic proteins are substituted by natural or de novo designed fusogenic synthetic transmembrane sequences. By a combination with biochemical methods and mass spectrometry (hydrogen/deuterium exchange), this assay allows for the clear-cut investigation of transmembrane domain structure/function relationships. They developed the ToxR/POSSYCCAT system as an in vivo tool for combinatorial library screening and were the first to identify tryptophan as promoter of transmembrane domain interactions. Furthermore, this research has potential for the development of improved molecular drug delivery systems based on fusogenic peptides (Patent filed), which will be further exploited in collaboration with Roche BioSciences, Penzberg to investigate the use of fusogenic peptides in liposomal delivery systems. The Braun group has outstanding experience in the biogenesis of photosynthetic membranes and the design of membrane-associated proteins that bind cofactors such as (bacterio)chlorophylls. The Budisa laboratory is internationally recognized for its innovative achievements in the biosynthesis of proteins with an expanded amino acid code, a current research topic previously dominated by scientists in the USA which is expected to boost the entire field of protein engineering. The research group of Prof. Görg (Proteomics) is internationally renowned for its pioneering work in the field of proteomics. The amount of proteins expressed in a cell, a tissue or an organism, as well as their specific activity, post-translational modifications, or interactions with other proteins or biomolecules are crucial for the description of biological systems. Linking the synthesis of small molecules able to label a subset of proteins in cells with the capabilities of the Görg group will define CIPS^M as a leading center for chemical tool based proteomics research.