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General workflow for α-Lys11-IgG based UbiChEM-MS analysis. Batches of cells are grown under different conditions and lysed. The clarified lysates are then incubated with α-Lys11-IgG:Protein A resin to enrich for ubiquitin chains. The isolated chains are subjected to minimal trypsinolysis yielding the three Ub1–74 species. These samples are then characterized by high-resolution mass spectrometry coupled with reverse phase chromatography.
