This dataset contains mass spectrometry-based proteomic data for matrix proteins extracted from the ventral scales of Acanthopleura loochooana. EDTA-soluble and EDTA-insoluble matrix fractions were analyzed to characterize the matrix-protein composition of ventral scales. The dataset includes raw and processed proteomic data used for protein identification, functional classification, and comparative analysis with shell plates and dorsal scales. These data support the investigation of the conserved and structure-specific molecular components involved in chiton body-surface biomineralization.