Fig. 2: MTS-APEX2 transgenic (MAX-Tg) mice resolve distinct matrix proteomes of different muscle tissues.

a, Heatmap of correlations between mass signal intensities of each replicate sample from WT mice, MAX-Tg mice and HEK293T cells (heart, TA, soleus, HEK293T cells stably expressing MTS-APEX2). Pearson correlation coefficients were calculated from each comparison. Hierarchical clustering was performed based on Pearson correlation coefficients. b, Volcano plot of the DBP-labeled proteome labeled by MTS-APEX2 in HEK293T cells (left) versus the TA muscle (right) from MAX-Tg mice. Statistical significance against the fold change revealed significantly different proteins between the HEK293T and TA muscle proteomes. The top 20 DBP-labeled proteins based on the normalized mass intensities in each sample are marked with filled circles with their gene names (see Supplementary Data 2 for detailed information). c, Top ten abundant DBP-labeled proteins labeled by MTS-APEX2 in TA tissue or HEK293T cells based on the normalized mass intensity. d, Venn diagram of identified mitochondrial matrix proteins from the heart, TA and soleus tissues. Representative proteins are shown with the current subcellular information in UniProt (see Supplementary Data 3 for detailed information). e, Venn diagram showing the overlap in MTS-APEX2-labeled mitochondrial protein identification between genetically different Tg mouse models (MAX-Tg mice and Myf5-Cre;LSL-MAX-Tg mice). See Supplementary Data 5 for detailed information.