“…Specifically, mitochondria were purified by differential centrifugation, with 2-3 additional washing steps implemented for experiments in Figure 5, Figure 6D, Supplemental Figure 4A, Supplemental Figure 4, C-F, and Supplemental Figure 5; by density gradient centrifugation for experiments in Figure 2F, Figure 3B, Figure 4, Figure 6, A-C, Figure 7, A-C, Figure 8, and Supplemental Figure 3; by a combination of density gradient centrifugation and ZE-FFE purification for experiments in Figure 2, A-E, Figure 3A, Figure 3C, Figure 7D, and Supplemental Figure 2, B-E. Fresh mitochondria were used for respiratory measurements or copper and calcium challenge experiments and were sub-sequently analyzed for swelling, transmembrane potential (Δψm), and ATP synthesis or subjected to ZE-FFE analysis, electron microscopy, and redox proteomics. Mitochondrial samples isolated by density gradient purification were stored at -192°C in preservation buffer (50) and used for the assessments of enzymatic activities, lipid peroxidation, and quantification of structural alterations. For the latter analysis, samples were subsequently purified by ZE-FFE on the same day and subjected to electron microscopy analysis in parallel.…”