Additional file 1 of Optimization of polyethylene glycol-based isolation of exosomes from mesenchymal stem cells for regenerative medicine applications

These spectra support the proteomic findings shown in Fig. 6 and validate the successful enrichment of exosomal marker proteins in the isolated vesicle fraction. Figure S2. Protein–protein interaction (PPI) network of the 357 proteins identified in MSC-derived exosomes.

The network was constructed in Cytoscape using the STRING database to visualize experimentally supported and predicted protein–protein interactions. Node color represents node degree on a continuous scale, with purple indicating the highest connectivity and yellow indicating the lowest connectivity. Network parameters for each protein—including degree, betweenness centrality, clustering coefficient, and average shortest path length—are provided in Supplementary Table S1.

These parameters were used to identify the top 20 high-degree and top 20 high-betweenness proteins. The 13 proteins shared between these two groups were selected as key hub proteins. Functional enrichment of these 13 hub proteins was performed using the CluGO plugin in Cytoscape, and the resulting functional clusters and interaction maps are shown in Fig. 7.

Figure S3. Full-length western blots for Calreticulin, Calnexin, CD63, CD9, and LGALS3BP, corresponding to the images in Fig. 5(B). Table S1.

Network analysis metrics of MSC-derived exosomal proteins identified by LC–MS/MS. Table S2. List of metabolites identified in MSC-derived exosomes by LC–MS/MS.

Table S3. Pathway enrichment analysis of metabolites identified in MSC-derived exosomes.