Fig. 1: Native-state proteomics of PV-INs by CIBOP.

A Experimental outline to achieve native-state proteomics of PV-INs by CIBOP. B–D Immunohistochemistry of fixed brain sections confirmed biotinylation (red) of PV-INs (Pvalb: green) in PV-CIBOP but not in control mice (B: 4x and C: 20x magnification; D: Higher magnification (60x) images show biotinylation in PV-INs). E Top: Western Blot (WB) of input and streptavidin affinity pulldown samples confirms strong protein biotinylation in PV-CIBOP as compared to limited biotinylation in control animals. Bottom: Silver-stained gels of inputs and pulldown samples corresponding to WB images above. F Volcano plot representation of differential abundance of biotinylated protein, from PV-CIBOP and control mice. Red dots represent proteins biotinylated in PV-INs as compared to control mice (unpaired two-tailed T-test p ≤ 0.05). G Top PV-enriched proteins are shown on the left (including TurboID, Cnk1, Kcnc2, Kcnc3, Erbb4, Slc32a1 and GABA-ergic proteins). In contrast, non-neuronal (Mbp, Gfap, Aldh1l1, Cotl1) and excitatory neuronal (Slc17a7) proteins were not enriched (Data are presented as mean + SD, n = 3/group; unpaired two-tailed T-test *p < 0.05, **p < 0.01, ***p < 0.005). H Gene Ontology (GO) analyses of PV-enriched proteins compared to whole brain show enrichment of synaptic vesicle, GTPase binding, cytoskeletal and cell-projection related proteins. I SynGO analysis of PV-enriched proteins reveals labeling of proteins in pre- and post-synaptic compartments. J STRING analysis of PV-enriched synaptic proteins (>4-fold enriched over control) involved in synaptic vesicle and exocytosis, including complexins, ankyrins, synucleins. K Venn Diagram representing degree of overlap between proteins enriched in PV neurons, with whole brain proteomes from matched animals. L Top proteins differentially enriched in PV-INs as compared to the whole brain bulk proteome and those enriched in the bulk as compared to PV-INs, are highlighted. M Analysis of protein vs mRNA concordance in PV-INs, using PV-enriched proteins identified by PV-CIBOP and existing single nuclear transcriptomic data from mouse PV-INs. Based on differentials in rank abundances (protein vs. mRNA), discordant and concordant protein/mRNA pairs are highlighted. Also see Supplementary Figs. S1, S2, S3 and Supplementary Data 1 for related analyses and datasets. Source data are provided as a Source Data file. Image was created using BioRender.com.