Chapter 14
Shotgun Proteomics and Protein-Based Bioinformatics
for the Characterization of Food-Derived Bioactive Peptides
Mo ´ nica Carrera, Manuel Pazos, Santiago P. Aubourg,
and Jose ´ M. Gallardo
Abstract
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.
Key words Shotgun proteomics, Mass spectrometry (MS), Protein-based bioinformatics, Bioactive
peptides, Food, Seafood, Marine by-product
1 Introduction
Food-derived bioactive peptides can exert health beneficial properties and are considered as lead compounds for the development of
functional foods or nutraceuticals [1, 2]. Such compounds are
short chain peptides (3–20 amino acid residues) from diverse
sources such as animal, plant, microbe, and even synthetic [3–
5]. Bioactive peptides are commonly inactive or latent in the context of their parent proteins but can be released into an active form
after proteolytic gastrointestinal digestion or by fermentation during food processing [6]. These food-derived bioactive peptides may
be absorbed through the intestine and subsequently enter into the
circulatory system where they exert their biological effects. Bioactive peptides are more bioavailable and potentially less allergenic
when compared to total protein [7]. Bioactive peptides have shown
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4_14, © Springer Science+Business Media, LLC, part of Springer Nature 2021
215
Shotgun Proteomics and Protein-Based Bioinformatics
for the Characterization of Food-Derived Bioactive Peptides
Mo ´ nica Carrera, Manuel Pazos, Santiago P. Aubourg,
and Jose ´ M. Gallardo
Abstract
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.
Key words Shotgun proteomics, Mass spectrometry (MS), Protein-based bioinformatics, Bioactive
peptides, Food, Seafood, Marine by-product
1 Introduction
Food-derived bioactive peptides can exert health beneficial properties and are considered as lead compounds for the development of
functional foods or nutraceuticals [1, 2]. Such compounds are
short chain peptides (3–20 amino acid residues) from diverse
sources such as animal, plant, microbe, and even synthetic [3–
5]. Bioactive peptides are commonly inactive or latent in the context of their parent proteins but can be released into an active form
after proteolytic gastrointestinal digestion or by fermentation during food processing [6]. These food-derived bioactive peptides may
be absorbed through the intestine and subsequently enter into the
circulatory system where they exert their biological effects. Bioactive peptides are more bioavailable and potentially less allergenic
when compared to total protein [7]. Bioactive peptides have shown
Mo ´ nica Carrera and Jesu ´ s Mateos (eds.), Shotgun Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2259,
https://doi.org/10.1007/978-1-0716-1178-4_14, © Springer Science+Business Media, LLC, part of Springer Nature 2021
215