Fig. 3

Synaptic proteomes are altered by AD and APOE genotype a) Heat map with hierarchical clustering demonstrates the differential abundance of the 5678 individual proteins across “spared” and “vulnerable” brain regions and with APOE genotype. The ratios compare AD to control in each condition. b Stacked bar chart demonstrates there is a direct correlation between the number of proteins that are differentially expressed, by 20% or more (up or down regulation), with the “vulnerability status’ of the synapses as determined by both genotype and brain region. c Graphical representation of protein abundance ratios in the comparison AD vs. ctrl (APOE3/4, BA41/42) before (left) and after applying the filters of at least 2 unique peptide IDs and > 20% change between AD and control (right). The dotted lines indicate a change of 20% up or down (note 4 proteins out of 5678 which have abundance ratios higher than 5 are excluded from the graph in panel c). Western blot validation from non-demented control (NDC) and AD cases show examples of a synaptic protein that was decreased in the proteomics dataset (SNAP25 d, e, t-test p = 0.08), and a glial protein that was increased in AD (GFAP, f, g, Mann-Whitney p = 0.045). Data in panels b and e are shown as mean and error bars represent the standard error of the mean. Each dot represents the value from a single case. Normality of data were assessed with Shapiro-Wilks tests. When comparing the ratio of levels of 9 proteins in AD divided by non-demented controls of 9 proteins and comparing these ratios calculated from western blot vs proteomics data (h), we observe a significant correlation between ratios measured with the 2 methods (Pearson correlation R = 0.72, p = 0.03), validating the accuracy of our pooled proteomics method. Full blots of PSD95, alpha synuclein, tubulin, annexin V, SOD2, and TMEM97 are shown in Additional file 9: Figure S3