Extended Data Fig. 3: iPEX analysis of mouse cerebellum tissues and tandem MS validations of selected peptide ions.
From: iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion
a, H&E staining of mouse cerebellum. b, Coomassie blue staining and bright-field image of mouse cerebellum sections. c, The MS1 spectra of expanded mouse cerebellum iPEX sample. Scatter plots showing the average ion intensity of iPEX detected peptides in mouse cerebellum. d, Peptide delocalization assessment using Cy5-NHS ester-mediated protein labeling. e, Ion intensity heatmap of representative ions with enhanced expression in the Purkinje neuron soma alignment in two iPEX sections of mouse cerebellum. The white arrow points to Purkinje neuron soma. f, Ion information for 8 selected proteolysis-dependent precursor ions of which the MS2 spectra are matching with the MS1 annotated peptide sequences. GL: granule layer; FT: fibre tract; CBN: cerebellar nuclei; ML: molecular layer. Scale bars indicated in images. The schematic in d was created using BioRender (https://www.biorender.com).
