Fig. 1: Brain MS analysis reveals proteomic changes that are shared in AD mouse models.

a Schematic plan of this study. Mouse cortical tissues from AD models of amyloidosis (5xFAD, NLF, NLGF, and matched WT, total n = 66 for 16 conditions, averaged n = ~4 per condition) were analyzed by TMT-LC/LC-MS/MS and compared with human metadata. b Proteins quantified at different ages (3-18 months). c Aβ levels quantified by MS using the peptide HDSGYEVHHQK (Average value ± SD, n = 2, 5, 6, 2, 2, 2, 3, 2, 3, for each group, left to right). The values were averaged for each age and model, then normalized to 12-month-old 5xFAD (100%). d DEPs between AD mice and WT controls at increasing ages, defined by moderated t-test with statistical cutoffs (FDR < 0.05, |log2FC | > 2 SD). e Representative volcano plot for NLGF-WT comparison (moderated t-test). Individual proteins correspond to data points and are color coded red or blue if up- or down-regulated as defined by statistical cutoffs, respectively (FDR < 0.05, |log2FC | > 2 SD, dashed lines). f Heatmap of DEPs identified in AD mice at any age or genotype, including the proteins enriched in 5xFAD or NLGF and those shared by both mice. g Pathway analysis of shared DEPs in 5xFAD and NLGF. FDR was derived from p values (Fisher’s exact test) by the Benjamini-Hochberg procedure. h, Enriched PPI modules from biological processes using the shared DEPs. Brain images created in BioRender. Yarbro, J. (2025) https://BioRender.com/a05v379.