Fig. 3
Proteomic results by SWATH-MS and DDA analysis of SEC-EVs and UC-EVs samples. (a) Principal Component Analysis (PCA) bi-plot depicting the separation of both groups (dark green: SEC-EVs; light green: UC-EVs). (b) Volcano plot representing the proteins identified by SWATH-MS. Proteins with a fold change < 0.5 and p < 0.05 were upregulated in UC-EVs (light green); and proteins with fold change > 2 and p < 0.05 were upregulated in SEC-EVs (dark green). (c) Heatmap illustrates the 16 proteins differentially expressed among EVs samples. Each row represents a protein, and each column represents an EV sample. Protein expression values were log2-normalized, and cluster analysis was performed using Z-score. Color intensity indicates the relative protein abundance across samples, with green colors indicating more abundant levels, while red colors indicate reduced levels. (d) Venn diagram representing the number of protein clusters identified by DDA in the SEC-EVs samples (dark green) compared to the UC-EVs samples (light green). (e) Venn diagram indicating the number of proteins clusters previously described in Vesiclepedia database. (f–k) Bioinformatic Gene Ontology analysis of biological process, molecular function, and cellular components of the proteins identified by DDA in the SEC-EVs samples (f, h, and j; dark green) and in the UC-EVs samples (g, i, and k; light green). Each row represents a process, function or cellular component and they are sorted by the corresponding p value.
