Using proteomic data to compare small urinary extracellular vesicles (suEVs) isolation methods and the in-solution digestion methods, to provide an integrated workflow for suEV proteomic studies. Three sets of proteomic data were obtained in this research. Datasets A and B were intended to compare different isolation methods, while Dataset C was designed to compare two in-solution protein digestion methods. The MS instrument raw output and the search engine results from Proteome Discoverer (PD) (version 2.4.1.15) for three datasets were provided.