Supplemental data files that include the results of complexome profiling experiments from the manuscript entitled "Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling" by Potter et al. Supplemental Data 1: comparison of mitochondrial complexomes obtained with either Blue Native (BNE) or high resolution Clear Native (hrCNE) gel electrophoresis. Supplemental Data 2: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented or not with DNase I. Supplemental Data 3: comparison of mitochondrial complexomes obtained with hrCNE from samples supplemented with only DNase I or a combination of DNase I and RNase A. Supplemental Data 4: comparison of mitochondrial complexomes obtained with hrCNE from control cells, cells treated with ethidium bromide and cells recovering after ethidium bromide treatment. Supplemental Data 5: results of LFQ-based analysis of profiles obtained from samples supplemented or not with DNase I. Supplemental Data 6: individual profiles (replicates), alignment and mass calibration results for the presented data.