This dataset contains raw LC-MS/MS data from a quantitative proteomics study investigating the role of B4GALNT4 in prostate cancer progression. Data were generated from control (shNC) and B4GALNT4-knockdown (shB4GALNT4) C4-2 cell lines (biological triplicates) using label-free acquisition on an Orbitrap Fusion Tribrid mass spectrometer. Proteins were digested with trypsin, separated via nano-LC, and analyzed in DDA mode. These data enable exploration of B4GALNT4-regulated protein networks and pathways in cancer biology.