Progress in mass-spectrometry based proteomics has taken the technology to a level where clinical application is a logical next step. This consortium brings together an outstanding team of Munich-based experts in proteomics, medicine and informatics to perform cutting-edge research on diseases of the nervous system. The goal is to drive technological innovations, meet urgent medical needs and address important societal challenges. By highlighting four thematic focus areas, neuroinflammation, neurodegeneration, neuro-vascular diseases and neurooncology as examples, our overarching research goals are to demonstrate that mass spectrometry in systems medicine i) is technically and logistically feasible, ii) generates novel insights into disease biology, iii) uncovers biomarkers for diagnosis, prognosis and treatment response and iv) provides short-, medium- and long-term clinical translation opportunities aiding clinical decision making for individual patients.