Fig. 6: wcSOP-MS analysis of 5 × single voxels at the size of 100 µm × 100 µm from amyloid plaque and adjacent non-plaque region of FFPE AD patient tissue.

a Thioflavidin staining to identify amyloid plaques for single voxel collection. In the image of thioflavin staining the amyloid plaque containing region framed with square shape was defined as “APR” and the adjacent non-plaque region was defined as “NPR”. b The number of identified protein groups for 5 × single voxels from APR and NPR (APR: amyloid plaque region; NPR: non-plaque region) with an average of 2805 and 3024 protein groups and median CVs of 11% and 2% for APR and NPR, respectively (n = 4 pooled biological replicates for APR and NPR; data are presented as mean values ± SD). c PCA analysis of the commonly expressed protein abundance for 5 × single voxels between APR and NPR. d Volcano plots between 5 × single voxels from APR and NPR (p < 0.01 and ≥2-fold change). DEPs are displayed with blue and red dots for upregulated proteins in NPR and APR, respectively (two-sided t-test, FDR < 0.05, s₀ = 0.1, n = 4 pooled biological replicates for NPR and APR). e The enriched signaling pathways between APR and NPR via KEGG pathway analysis (FDR < 0.05). f Network analysis of differentially expressed proteins. Except the middle AD associated proteins APP, APOE4, and MAPT, the network proteins at the left and the right sides were upregulated in NPR and APR, respectively. g Examples of 6 differentially expressed protein signatures between APR and NPR (n = 4 pooled biological replicates for APR and NPR). The p value is estimated by Welch’s t-test (two-sided). The box plots define the range of the data (whiskers), 25th and 75th percentiles (box), and medians (solid line). Outliers are plotted as individual dots outside the whiskers. Source data are provided as a Source Data file.