PPIP: Automated Software for Identification of Bioactive Endogenous Peptides

Shotgun Proteomics and Protein-Based Bioinformatics for the Characterization of Food-Derived Bioactive Peptides

A workflow for the characterization of food-derived bioactive peptides is described in this chapter. The workflow integrates two consecutive steps: a discovery phase and a protein-based bioinformatic phase. In the first step (discovery phase), a shotgun bottom-up proteomics approach is used to create a reference data set for a selected food proteome. Afterward, in a second step (bioinformatic phase), the reference proteome is subjected to several in silico protein-based bioinformatic analyses to predict and characterize potential bioactive peptides after an in silico human gastrointestinal digestion. Using this workflow, bioactive collagen peptides, antihypertensive, antimicrobial, and antitumor peptides were predicted as potential valuable bioactive peptides from seafood and marine by-products. It is concluded that the combination of the global shotgun proteomic analysis and the analysis by protein-based bioinformatics can provide a rapid strategy for the characterization of new potential food-derived bioactive peptides.

Characterization of the Jumbo Squid (Dosidicus gigas) Skin By-Product by Shotgun Proteomics and Protein-Based Bioinformatics

Jumbo squid (Dosidicus gigas) is one of the largest cephalopods, and represents an important economic fishery in several regions of the Pacific Ocean, from southern California in the United States to southern Chile. Large and considerable discards of this species, such as skin, have been reported to constitute an important source of potential by-products. In this paper, a shotgun proteomics approach was applied for the first time to the characterization of the jumbo squid (Dosidicus gigas) skin proteome. A total of 1004 different peptides belonging to 219 different proteins were identified. The final proteome compilation was investigated by integrated in-silico studies, including gene ontology (GO) term enrichment, pathways, and networks studies. Potential new valuable bioactive peptides such as antimicrobial, bioactive collagen peptides, antihypertensive and antitumoral peptides were predicted to be present in the jumbo squid skin proteome. The integration of the global proteomics results and the bioinformatics analysis of the jumbo squid skin proteome show a comprehensive knowledge of this fishery discard and provide potential bioactive peptides of this marine by-product.