Figure 4.

DIA results comparing PSD-enriched and pre-fractionation samples. (A) Box plot displaying quartile, median-normalized log₁₀ intensities for each sample group. (B) Quantitative CVs chart. The bold lines show the relationship between the mean log₁₀ protein intensity and the CV values for PSD-enriched (green) and pre-fractionation (purple) samples. The shaded areas around the plotted lines represent the 50% confidence interval for the CV values. The faint lines indicate the intensity distribution for all proteins within PSD-enriched (green) and pre-fractionation (purple) samples, which were calculated using a Gaussian kernel density estimate. (C) PCA. PCA plot displays the distribution of PSD-enriched (green) and pre-fractionation (purple) samples between PC1 and PC2. The percentages (%) in each axis represent the explained variance for each Principal Component. (D) Volcano plot displaying the log₁₀ p-values for each protein as a function of log₂ fold change (PSD-enriched/Pre-fractionation) values after performing a t-test. Proteins that are significantly (p < 0.05, uncorrected values) changing in expression between the two groups are highlighted in green, while proteins whose expression does not significantly differ are shown in black. (E) Heatmap of significantly differentially expressed proteins (p < 0.05) after t-test statistical analysis. In total, 1721 proteins were differentially expressed between PSD-enriched and pre-fractionation replicate samples. A hierarchical clustering tree is displayed on the left of the heatmap. The heatmap scale units are in log₁₀ intensity.