Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish

Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the mass measurement accuracy of the instrument and the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software algorithms are able to identify a large number of post-translational modifications (PTMs). However, peptide and PTM identifications are challenging in the agrofood field due to non-specific cleavage sites of physiological- or food-grade enzymes and the number and location of PTMs. In this study, we show the importance of customized software programming to obtain a better peptide and PTM identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork, and fish), each digested by simulated gastrointestinal digestion, MS-grade trypsin, or both, were used to perform the comparisons. Two main points are illustrated: (i) the impact of the set-up of specific enzyme versus no specific enzyme use and (ii) the impact of a maximum of six PTMs allowed per peptide versus the standard of three. Prior knowledge of the composition of the raw proteins is an important asset for better identification of peptide sequences.

Proteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties

Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification.

A comprehensive review of bioactive peptides obtained from animal byproducts and their applications

Livestock generates high quantities of residues, which has become a major socioeconomic issue for the meat industry. This review focuses on the identification of bioactive peptides (BPs) in animal byproducts and meat wastes. Firstly, the main bioactivities that peptides can have will be described and the methods for their evaluation will be discussed. Secondly, the various origins of these BPs will be studied. Then, the techniques and tools for the generation of BPs will be detailed in order to discuss, in the final part, how peptides could be used and assimilated. BPs possess diverse biological activities and can be strategic candidates for substituting synthetic molecules. In silico potentiality studies are a helpful tool to understand and predict BPs released from proteins and their potential activities. However, in vitro validation is often required. Although BP use is compelled by strict regulations in relation to the field of application, they are also limited by their low bioavailability and bioaccessibility. Therefore, it is important to test peptide stability during gastrointestinal digestion. Protective strategies have been discussed since their use could improve the stability and effectiveness of BPs.

Safety of shrimp peptide concentrate as a novel food pursuant to Regulation (EU) 2015/2283

Following a request from the European Commission, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on shrimp peptide concentrate as a novel food (NF) pursuant to Regulation (EU) 2015/2283. The NF is a peptide mixture obtained by an enzymatic proteolysis from northern shrimp (Pandalus borealis) shells and heads. The information provided on the composition, specifications, batch‐to‐batch variability, stability and production process of the NF is sufficient and does not raise safety concerns. The intention of the applicant is to use this NF as an ingredient in food supplements and to market it to adult consumers at a maximum proposed level of intake of 1,200 mg/day (corresponding to 17 mg/kg body weight (bw) per day for a 70 kg person). There are no concerns with regard to genotoxicity. The available human data do not raise safety concerns. Considering the no observed adverse effect level (NOAEL) of 2,000 mg/kg bw per day from a 90‐day repeated‐dose oral toxicity study, the maximum proposed level of intake and the nature of the NF, the Panel concludes that the margin of exposure (of 117) is sufficient. The Panel concludes that the NF, shrimp peptide concentrate, is safe to be used as a food supplement at the proposed maximum dose of 1,200 mg/day. The target population is adults. The Panel considered that the conclusion on the safety of the NF could not have been reached without the data from the unpublished study report on repeated‐dose 90‐day oral toxicity and from the unpublished study reports on two human studies.

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. Graphical Abstract ᅟ.

Recent advances in the application of capillary electromigration methods for food analysis and Foodomics

This review work presents and discusses the main applications of capillary electromigration methods in food analysis and Foodomics. Papers that were published during the period February 2015-February 2017 are included following the previous review by Acunha et al. (Electrophoresis 2016, 37, 111-141). The paper shows the large variety of food related molecules that have been analyzed by CE including amino acids, biogenic amines, carbohydrates, chiral compounds, contaminants, DNAs, food additives, heterocyclic amines, lipids, peptides, pesticides, phenols, pigments, polyphenols, proteins, residues, toxins, vitamins, small organic and inorganic compounds, as well as other minor compounds. This work describes the last results on food quality and safety, nutritional value, storage, bioactivity, as well as uses of CE for monitoring food interactions and food processing including recent microchips developments and new applications of CE in Foodomics.

Simulated GI digestion of dietary protein: Release of new bioactive peptides involved in gut hormone secretion

Dietary proteins have been reported to induce a strong feeling of satiety that has been partially explained by gut hormone level increase. Up to date, various protein hydrolysates have demonstrated in vitro and in vivo their potential to stimulate gut hormone secretion related to food intake decrease and their mechanisms of action have just started to be resolved. In this context, this study aimed at identifying new peptide sequences involved in gut hormone secretion released by protein in vitro gastrointestinal digestion. Targeted gut hormones were Cholecystokinin (CCK) and Glucagon-Like Peptide 1 (GLP-1). The activity of DPP-IV was also considered as it strongly modulates GLP-1 action. In a previous study, simulated digestion of dietary protein has generated hydrolysates with enhancing effect on CCK and GLP-1 secretion in STC-1 cells as well as DPP-IV inhibitory properties. Successive purification steps were performed to isolate peptide fractions involved in these bioactivities whose sequence was determined by LC-MS-MS. Three peptide sequences ANVST, TKAVEH and KAAVT were pointed out for their stimulating effects on GLP-1 secretion. The sequence VAAA was isolated for its DPP-IV inhibitory properties. Two peptide groups were strongly involved in CCK release sharing a certain occurrence of aromatic amino acid residues.