Cone snails are incredibly rich sources of bioactive conopeptides with potential for use in neuroscience research and novel drug development. In order to investigate the synthesis of diversified conopeptides in venom glands, the proteome and peptidome profiles of conus venom were analyzed using HPLC and mass spectrometry. The peptidome profile of the venom components with a molecular weight under 10 kDa showed that the peptides with unique mass values from the venom glands of Conus caracteristicus, Conus lividus and Conus textile are 188, 413 and 265, respectively, and there are 39 overlapping peptides among the three species. Proteome profiling of the components with molecular weights above 10 kDa showed that the most abundant proteins (38.6%) are involved in metabolism and that approximately 6.8% of proteins are involved in protein synthesis, folding and post-translational modification. Among these proteins, PPIase is one protein identified from C. textile based on proteomic analysis. Conus PPIase was successfully expressed as a fusion protein with TRX in an Escherichia coli expression system for further function study. In-vitro enzyme activity assays showed that cone snail PPIase could induce the cis-trans isomerization of the substrate succinyl-Ala-Ala-Pro-Phe-p-nitroanilide. The HPLC mapping analyses of linear lt14a, a conotoxin with 3 prolines, showed that different lt14a isoforms appear after incubation with PPIase. Our results suggest that PPIase may modify conotoxins containing prolines and play an important role in the process of peptide folding and modification in venom glands and contribute to conotoxin diversity.