Extended Data Figure 6. AD Protein Network Module Changes in Other Neurodegenerative Diseases by PRM Analysis.

(A-C) Protein levels for 323 proteins across 108 brains from the UPenn cohort were measured by parallel reaction monitoring targeted mass spectrometry (PRM-MS) (A). Targeted peptides and individual protein measurements by disease group are provided in Supplementary Table 4 and Supplementary Figure 11, respectively. (B) Protein levels across all cases were highly correlated between LFQ and PRM measurements (n=307 paired protein measurements). Correlation was performed by Pearson’s rho and Student’s significance (p). (C) A synthetic eigenprotein was created from proteins that mapped to an AD network module and measured across the different disease groups (control case samples n=46, AD n=49, ALS n=59, FTLD-TDP n=29, PSP n=27, CBD n=17, PD/PDD n=80, and MSA n=23 after network connectivity outlier removal). Analyses for all modules are provided in Supplementary Figure 12. Differences in module synthetic eigenproteins were assessed by Kruskal-Wallis one-way ANOVA. Differences between AD and other case groups were assessed by two-sided Dunnett’s test, the results of which are provided in Supplementary Table 4. Boxplots represent the median, 25^th, and 75^th percentiles, and whiskers represent measurements to the 5^th and 95^th percentiles.