Updated project metadata. This dataset contains mass spectrometry raw files and identification results from intact N-glycoproteomic analysis of extracellular vesicles (EVs) isolated from human seminal plasma. Intact N-glycopeptides were enriched and analyzed using an Orbitrap Fusion Lumos mass spectrometer coupled to an Easy-nLC 1200 system. The uploaded dataset includes: (1) Data-dependent acquisition (DDA) LC-MS/MS files acquired via stepped collision energy higher-energy collision dissociation (StepHCD) across discovery cohort samples; and (2) StepHCD-based parallel reaction monitoring (PRM) targeted LC-MS/MS files across validation cohort samples. Raw data files were searched against the human UniProt reviewed database using Glyco-Decipher software with a 1% false discovery rate (FDR).