Fig. 6: Comparative mitochondrial proteomics for diabetic and healthy mice.

a Schematic view of CAT-S-enabled comparative mitochondrial proteomics for diabetic and nondiabetic mouse kidneys. Samples were treated with Ir1 and SF2 followed by blue LED irradiation. b Filtering of MS data to produce a protein list for comparative proteomics. First column from left, proteins detected with ≥2 unique peptides and quantified ratios by MS. Second column, retained proteins after cutoff based on diabetic/Ctrl or nondiabetic/Ctrl ratios (set to 1.2) to remove non-biotinylated proteins while maximizing the retention of labeled proteome (Filter 1). The diabetic and nondiabetic protein lists were intersected to produce lists for relative quantification (Filter 2). Lists from three independent experiments were intersected to generate the final proteome. c Labeling signals measured by immunoblotting analysis. d Venn diagram showing the overlap between the comparative proteomes of three experiments. e Mitochondrial specificity analysis with bars showing the fraction of proteome with prior mitochondrial annotation (red) in the database. f Volcano plot showing the regulation of proteins in diabetic and nondiabetic mouse kidney (n = 3 biologically replicates). Red dots, proteins with prior mitochondrial annotation. p Values were calculated by unpaired two-tailed t test. g Cluster map showing regulations of functionally associated molecular complexes according to STRING analysis⁶¹ and Markov clustering. Gray lines denote protein–protein interactions with high confidence (interaction score > 0.7). h Top six enriched biological processes for up- and down-regulated mitochondrial proteins in obese-diabetic mouse kidney by Gene Ontology analysis, with p values calculated by cumulative hypergeometric test. i–j Validation for three lipid-metabolism mitochondrial proteins by immunoblotting. i Blot images. j Intensity quantification. Data are represented as mean ± SEM (n = 3 biological replicates) with p values shown (unpaired one-tailed t test). Source data are provided as a Source Data file. Created with BioRender.com (agreement number HV26IJOCW8).