This project contains raw mass spectrometry data and Spectronaut analysis files from a comparative quantitative proteomic analysis of Vibrio parahaemolyticus WT-P2C and the vscW deletion mutant, ΔvscW-P2C. Three independent biological replicates were analyzed for each strain to investigate protein abundance changes associated with bacterial secretion systems, membrane transport, motility, chemotaxis, biofilm formation, and virulence-related functions.