Add info. This project investigates the proteomic basis of antifungal activity generated by fermenting agar waste liquid with Streptomyces rubiginosoheloolus. Agar waste liquid at different concentrations was fermented, and extracellular proteins from active cultures were enriched by ammonium sulfate precipitation and anion-exchange chromatography, followed by mass-spectrometry-based identification. The ProteomeXchange dataset contains the raw and processed MS data for these antifungal protein fractions, which enabled the discovery of key proteins (histone-like nucleoid-structuring protein H-NS, a hypothetical protein and a ribosomal protein) that disrupt Alternaria spp. via membrane damage, ROS accumulation and lipid peroxidation, providing a basis for agar waste valorization into antifungal bioproducts.