The quantitative proteomics analysis was performed according to a routine protocol 52 (link). For TMT-labeling proteomic analysis, small extracellular vesicles from SW620 and NCM460 cells were extracted three times independently for trypsin digestion. Then, TMT 6-plex reagent (90061; Thermo Scientific) was used to label SW620EXO and NCM460EXO. Control NCM460-EXO samples C1, C2, C3 were tagged with TMTs 126.1, 127.1 and 128.1 and SW620-EXO samples A1, A2, A3 with TMTs 129.1, 130.1 and 131.1, respectively, for the next LC-MS/MS analysis. Protein identifications, quantifications, and database searches were performed by Proteome Discoverer (RRID:SCR_014477). The raw files from the fractions were searched against a Homo sapiens Swiss-Prot UniProt protein database (www.uniprot.org/). The protein ratio was computed as 129+130+131 over 126+127+128. Differentially expressed proteins were selected with protein ratio > 1.5 or < 0.67 above the 95% confidence level in the comparison. Channel 126 was used for labeling the internal reference sample. The raw data and the analysis result are presented in Supplementary Table 2.
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