An advanced systems biology approach will be applied to understanding the molecular mechanisms of neurodegenerative cytotoxicity, triggered by aberrantly folded proteins. Three established cellular models of cytotoxicty of the misfolding-prone proteins synuclein, TPD-43 and the Abeta peptide will be analyzed. In a discovery-phase, advanced proteome and phosphoproteome-wide screens,coupled to biochemica ltools for monitoring cellular toxicity and protein aggregation, will highlight biological processes sequentially affected by expression and aggregation of the misfolded proteins. The analysis will contribute to identifying triggering events and consequent phenomena, cellular responses that are specific to each protein and those associated to generic stress responses. Quantitative phosphoproteomics measurements will unravel signaling states associated to the cytotoxic mechanisms. Transcriptomics analysis will highlight protein changes that are not anticipated by gene expression data and suggest post-transcriptional regulation, possibly including protein aggregation phenomena. Emerging hypotheses will be validated by targeted proteomics based on selected reaction monitoring and biochemical and genetic experiments on the disregulated pathways. A set of protein and phosphoprotein markers will be selected that characterize the onset of cytotoxicity at different biological modules and stages and an assay will be designed that measures them in a fast and reproducible manner. This fingerprinting will be used to screen a set of chemical and genetic modulators, to characterize their mechanisms and strength. Overall, such multi-level approach will provide a global picture of the mechanisms that accompany the onset of proteinopathies and lead to neurodegenerative cell death, provide insight on the mechanism of action of specific modulators, ultimately setting us towards identifying the most suitable therapeutic strategies.