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

Abstract

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.

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“…In Peptide Ranker analysis, peptides with scores higher than 0.9 were considered to have more biological potential activity ( 38 ). Peptide 3–phosphokinase–1–carboxyvinyltransferase’s in amino acid metabolism ranker scores reached 0.971099 and 0.998508.…”

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“…In gel-free approaches, also known as shotgun proteomics, the proteins are directly digested in the extract with a selected enzyme, and the obtained mixture of peptides is subsequently analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) [15,16]. It is possible to perform multidimensional LC separations, combining, for example, strong anion/cation exchange chromatography and reverse-phase chromatography [17].…”

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“…In gel-free approaches, also known as shotgun proteomics, the proteins are directly digested in the extract with a selected enzyme, and the obtained mixture of peptides is subsequently analyzed by liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) [15,16]. It is possible to perform multidimensional LC separations, combining, for example, strong anion/cation exchange chromatography (SA/CX) and reverse phase (RP) chromatography [17].…”