Figure 1. Experimental design and workflow for predicting aggregating proteins in vivo in mice . Following a treatment period, mice are metabolically labeled with 2H3-Leu over a specified timeframe (e.g. 17 days) to allow the calculation of protein turnover. Tissues are collected from mice in all experimental groups over multiple timepoints and processed into three fractions: ubiquitinated proteins, insoluble proteins, and soluble proteins. The ubiquitinated protein fraction is prepared via antibody enrichment. A multi-omic analysis that combines information about protein ubiquitination state, abundance in either the soluble or insoluble fractions, and turnover rate predicts proteins which are likely components of insoluble protein aggregates.