Mass spectrometry for nutritional peptidomics: How to analyze food bioactives and their health effects

Bioactive peptides from food waste: New innovative bio-nanocomplexes to enhance cellular uptake and biological effects

Mastitis is the most important bovine disease, causing dramatic economic losses to the dairy industry, worldwide. This study explores the valorization of whey from cows affected by mastitis, through a novel separation approach. Surface Active Maghemite Nanoparticles (SAMNs) were used as magnetic baits to selectively bind bioactive peptides with potential health benefits. Advanced techniques such as HPLC and LC-MS/MS highlighted SAMN capability of isolating a restricted group of peptides, drastically diverging from the control profile (Solid Phase Extraction, SPE) and characterized by a peculiar acidic residue distribution. Most importantly, both magnetically purified and nano-immobilized peptides (SAMN@peptides) showed protective activity against oxidative stress and inflammation, when tested on Caco-2 cells; with SAMN@peptides being associated with the strongest biological effect. SAMNs exhibited excellent characteristics, they are environmentally sustainable, and their synthesis is cost-effective prompting at a scalable and selective tool for capturing bioactive peptides, with potential applications in functional foods and nutraceuticals.

Dairy, Plant, and Novel Proteins: Scientific and Technological Aspects

Alternative proteins have gained popularity as consumers look for foods that are healthy, nutritious, and sustainable. Plant proteins, precision fermentation-derived proteins, cell-cultured proteins, algal proteins, and mycoproteins are the major types of alternative proteins that have emerged in recent years. This review addresses the major alternative-protein categories and reviews their definitions, current market statuses, production methods, and regulations in different countries, safety assessments, nutrition statuses, functionalities and applications, and, finally, sensory properties and consumer perception. Knowledge relative to traditional dairy proteins is also addressed. Opportunities and challenges associated with these proteins are also discussed. Future research directions are proposed to better understand these technologies and to develop consumer-acceptable final products.

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Mass spectrometry as a lens into molecular human nutrition and health

Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.

A multi-centre peptidomics investigation of food digesta: current state of the art in mass spectrometry analysis and data visualisation

Mass spectrometry has become the technique of choice for the assessment of a high variety of molecules in complex food matrices. It is best suited for monitoring the evolution of digestive processes in vivo and in vitro. However, considering the variety of equipment available in different laboratories and the diversity of sample preparation methods, instrumental settings for data acquisition, statistical evaluations, and interpretations of results, it is difficult to predict a priori the ideal parameters for optimal results. The present work addressed this uncertainty by executing an inter-laboratory study with samples collected during in vitro digestion and presenting an overview of the state-of-the-art mass spectrometry applications and analytical capabilities available for studying food digestion. Three representative high-protein foods - skim milk powder (SMP), cooked chicken breast and tofu - were digested according to the static INFOGEST protocol with sample collection at five different time points during gastric and intestinal digestion. Ten laboratories analysed all digesta with their in-house equipment and applying theirconventional workflow. The compiled results demonstrate in general, that soy proteins had a slower gastric digestion and the presence of longer peptide sequences in the intestinal phase compared to SMP or chicken proteins, suggesting a higher resistance to the digestion of soy proteins. Differences in results among the various laboratories were attributed more to the peptide selection criteria than to the individual analytical platforms. Overall, the combination of mass spectrometry techniques with suitable methodological and statistical approaches is adequate for contributing to the characterisation of the recently defined digestome.

Smart systems in producing algae-based protein to improve functional food ingredients industries

Production and extraction systems of algal protein and handling process of functional food ingredients need to control several parameters such as temperature, pH, intensity, and turbidity. Many researchers have investigated the Internet of Things (IoT) approach for enhancing the yield of microalgae biomass and machine learning for identifying and classifying microalgae. However, there have been few specific studies on using IoT and artificial intelligence (AI) for production and extraction of algal protein as well as functional food ingredients processing. In order to improve the production of algal protein and functional food ingredients, the implementation of smart system is a must to have real-time monitoring, remote control system, quick response to sudden events, prediction and characterisation. Techniques of IoT and AI are expected to help functional food industries to have a big breakthrough in the future. Manufacturing and implementation of beneficial smart systems are important to provide convenience and to increase the efficiency of work by using the interconnectivity of IoT devices to have good capturing, processing, archiving, analyzing, and automation. This review investigates the possibilities of implementation of IoT and AI in production and extraction of algal protein and processing of functional food ingredients.

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.

Peptidomics as a useful tool in the follow-up of food bioactive peptides

There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.

Food-derived bioactive peptides-methods for purification and analysis

Bioactive peptides attract the attention of researchers thanks to their high potential to beneficially influence human health. Various activities are reported, and some of these peptides are commercialized as therapeutic agents. Food-related proteins represent an excellent source in this regard. However, the identification, purification, and characterization of bioactive peptides require а complex approach. The full range of analytical techniques is used in combination with the chemical and biological properties of the peptides. The emerging "omics" techniques and "in silico" methods have given a new direction to peptide analysis in recent years. Developing new methods, rapid and low-cost, for the identification, characterization and purification, is a challenging task because of the complexity of food samples. However, bioinformatics is a promising technique for their exploration. These new strategies can predict different types of peptides, their properties and represent a new horizon for releasing their potential. That is why, in this review, we summarize information about methods used for purification and analysis of food-derived bioactive peptides so far, as well as present our point of view about the role of bioinformatics in this process.

Peptides Isolated from Yak Milk Residue Exert Antioxidant Effects through Nrf2 Signal Pathway

Food-derived bioactive peptides are considered as the important sources of natural bioactive ingredients. Approximately 3094 peptides were identified by nESI-LC–MS/MS in the hydrolyzed yak milk residue. Peptide KALNEINQF (T10) is the strongest antioxidant peptide. The damage model of H₂O₂-induced human umbilical vein endothelial cells (HUVECs) was used to evaluate the antioxidant effect. After treatment with 25, 50, or 100 μg/mL T10 peptide, T10 obviously decreased H₂O₂-induced damage and increased the cell survival. Comparing with the H₂O₂-induced damage group, superoxide dismutase (SOD) activities were significantly increased 1.03, 1.1, and 1.33 times, and glutathione reductase (GR) activities were significantly increased 1.11, 1.30, and 1.43 times, respectively. Malondialdehyde (MDA) also reduced 1.41, 1.54, and 1.72 times, respectively. T10 inhibited H₂O₂-induced apoptosis in HUVECs, and protein expressions of the apoptosis-related genes bcl-2 and bax were increased and decreased by 1.95 and 1.44 times, respectively, suggesting T10 decreases apoptosis of the mitochondria-dependent pathway. Comparing with the H₂O₂-induced damage group, the RNA expressions of Nrf2, HO-1, and NQO1 were significantly increased by 2.00, 2.11, and 1.94 times; the protein expressions of p-Nrf2, HO-1, and NQO1 were significantly increased by 2.67, 1.73, and 1.04 times; and Keap1 was downregulated by 3.9 and 1.32 times, respectively. T10 also regulated the Nrf2 pathway and expressions of related genes (Keap1, HO-1, and NQO1), and blocking the Nrf2 pathway in the model decreased the protective effect of T10. Taken together, T10 peptide isolated from yak milk residue has a protective effect against H₂O₂-induced damage in HUVECs and the molecular mechanisms are involved in the regulation of Nrf2 signaling pathway and cell apoptosis.

Identification of dipeptides by MALDI-ToF mass spectrometry in long-processing Spanish dry-cured ham

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A simpler strategy was carried out to identify dipeptides in dry-cured ham.

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Ultrafiltration following MALDI-ToF MS allows a rapid peptide identification.

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AH, AL, DD, EV and VF were identified in samples with different processing times.

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Bioactive or tasting food-derived dipeptides can be identified by this methodology.

The processing of dry-cured ham results in the generation of small peptides by the action of endogenous enzymes on muscle proteins. Common proteomic workflows involve previous separation techniques based on liquid chromatography which are expensive and time-consuming. In this study, a convenient proteomic approach based on MALDI-ToF is proposed for the first time for the detection of dipeptides in Spanish dry-cured ham. Dipeptides AH, AL, DD, EV, and VF were identified in hams of 18 and 24 months of dry-curing. This work provides insights on the efficiency of a new peptidomic workflow for the short peptide identification from a complex food matrix and permits to evaluate the sample in terms of the presence of taste-related and bioactive dipeptides.

Artificial Intelligence in Functional Food Ingredient Discovery and Characterisation: A Focus on Bioactive Plant and Food Peptides

Scientific research consistently demonstrates that diseases may be delayed, treated, or even prevented and, thereby, health may be maintained with health-promoting functional food ingredients (FFIs). Consumers are increasingly demanding sound information about food, nutrition, nutrients, and their associated health benefits. Consequently, a nutrition industry is being formed around natural foods and FFIs, the economic growth of which is increasingly driven by consumer decisions. Information technology, in particular artificial intelligence (AI), is primed to vastly expand the pool of characterised and annotated FFIs available to consumers, by systematically discovering and characterising natural, efficacious, and safe bioactive ingredients (bioactives) that address specific health needs. However, FFI-producing companies are lagging in adopting AI technology for their ingredient development pipelines for several reasons, resulting in a lack of efficient means for large-scale and high-throughput molecular and functional ingredient characterisation. The arrival of the AI-led technological revolution allows for the comprehensive characterisation and understanding of the universe of FFI molecules, enabling the mining of the food and natural product space in an unprecedented manner. In turn, this expansion of bioactives dramatically increases the repertoire of FFIs available to the consumer, ultimately resulting in bioactives being specifically developed to target unmet health needs.

Measuring the oral bioavailability of protein hydrolysates derived from food sources: A critical review of current bioassays

BACKGROUND

Food proteins are a source of hydrolysates with potentially useful biological attributes. Bioactive peptides from food-derived proteins are released from hydrolysates using exogenous industrial processes or endogenous intestinal enzymes. Current in vitro permeability assays have limitations in predicting the oral bioavailability (BA) of bioactive peptides in humans. There are also difficulties in relating the low blood levels of food-derived bioactive peptides detected in preclinical in vivo models to pharmacodynamic read-outs relevant for humans.

SCOPE AND APPROACH

In this review, we describe in vitro assays of digestion, permeation, and metabolism as indirect predictors of the potential oral BA of hydrolysates and their constituent bioactive peptides. We discuss the relationship between industrial hydrolysis processes and the oral BA of hydrolysates and their peptide by-products.

KEY FINDINGS

Hydrolysates are challenging for analytical detection methods due to capacity for enzymatic generation of peptides with novel sequences and also new modifications of these peptides during digestion. Mass spectrometry and peptidomics can improve the capacity to detect individual peptides released from complex hydrolysates in biological milieu.

Characterization of Umami Dry-Cured Ham-Derived Dipeptide Interaction with Metabotropic Glutamate Receptor (mGluR) by Molecular Docking Simulation

Dry-cured ham-derived dipeptides, generated along a dry-curing process, are of high importance since they play a role in flavor development of dry-cured ham. The objective of this study was to analyze the residues of the less-studied metabotropic glutamate receptor 1 (mGluR1) implicated in the recognition of umami dry-cured ham dipeptides by molecular docking simulation using the AutoDock Suite tool. AH, DA, DG, EE, ES, EV, and VG (and glutamate) were found to attach the enzyme with inhibition constants ranging from 12.32 µM (AH) to 875.75 µM (ES) in the case if Rattus norvegicus mGluR1 and 17.44 µM (VG) to 294.68 µM (DG) in the case of Homo sapiens, in the open–open conformations. Main interactions were done with key receptor residues Tyr74, Ser186, Glu292, and Lys409; and Ser165, Ser186, and Asp318, respectively, for the two receptors in the open–open conformations. However, more residues may be involved in the complex stabilization. Specifically, AH, EE and ES relatively established a higher number of H-bonds, but AH, EV, and VG presented relatively lower Ki values in all cases. The results obtained here could provide information about structure and taste relationships and constitute a theoretical reference for the interactions of novel umami food-derived peptides.

Tri- and dipeptides identification in whey protein and porcine liver protein hydrolysates by fast LC-MS/MS neutral loss screening and de novo sequencing

We describe a fast (5 min) liquid chromatography tandem mass spectrometry method (LC-MS/MS) based on a 46 Da neutral loss of formic acid (H₂ O and CO) to identify tri- and dipeptides (DIPEP) in whey protein and porcine liver protein hydrolysates and confirmed by further de novo sequencing. Sample solutions were acidified to favor [dipep + H]⁺ ions, and a m/z range of 50-300 was used to improve sensitivity. All dipeptide candidates were selected based on all possibilities of the 20 amino acid combinations, and their collision-induced dissociation fragments were screened via de novo sequencing. To determine their biological activities, sequenced dipeptides were compared with the Biopep database and other data from literature. Altogether, 18 dipeptides and 7 tripeptides were identified from the whey protein hydrolysate; they seemed to be broadly active, and peptides were identified as active dipeptidyl peptidase IV inhibitors and active angiotensin-converting enzyme (ACE), according to available information. Porcine liver hydrolysate showed 14 dipeptides which exhibit similar biological activities to whey protein hydrolysate.

A Global Review on Short Peptides: Frontiers and Perspectives

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.

Whey Proteins and Its Derivatives: Bioactivity, Functionality, and Current Applications

With the increased consumer demand for nutritional foods, it is important to develop value-added products, which will not only catch the attention of a wider consumer group but also provide greater benefits in terms of enhanced nutrition and functionality. Milk whey proteins are one of the most valued constituents due to their nutritional and techno-functional attributes. Whey proteins are rich in bioactive peptides, possessing bioactive properties such as being antioxidant and antihypertensive as well as having antimicrobial activities, which, when ingested, confers several health benefits. These peptides have the potential to be used as an active food ingredient in the production of functional foods. In addition to their bioactivities, whey proteins are known to possess enhanced functional attributes that allow them to be utilized in broad applications, such as an encapsulating agent or carrier materials to entrap bioactive compounds, emulsification, and in edible and active packaging. Hence, over the recent years, several whey protein-based ingredients have been developed and utilized in making formulations for a wide range of foods to harness their beneficial properties. This review highlights the bioactive properties, functional characteristics, associated processing limitations, and applications of different whey protein fractions and derivatives in the field of food formulations, encapsulation, and packaging.

Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods

Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers 'nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.

Antioxidant activity and peptidomic analysis of porcine liver hydrolysates using alcalase, bromelain, flavourzyme and papain enzymes

Antioxidant peptides are increasingly being recognized as food additives due to their effects on body human, regulating in vivo oxidative stress against oxidation of lipids and proteins. Meat by-products are rich sources of protein that can be employed for this purpose. Specifically, porcine liver can be used to prepare hydrolysates with antioxidant activity employing proteolytic enzymes such as alcalase, bromelain, papain and flavourzyme. In this study, the antioxidant activity of these four porcine liver hydrolysates was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), ((2,2-azinobis-(3-ethyl-benzothiazoline-6-sulphonate) (ABTS), Ferric reducing antioxidant power assay (FRAP) and Oxygen radical absorbance capacity assay (ORAC) assays and the identification of bioactive peptides was carried out by SWATH-MS technology. According to the SDS-PAGE pattern, the proteolysis index and the free amino acids amount, the protein degradation was clearly different among the studied enzymes. Indeed, alcalase enzyme produced the release of small peptides, meanwhile flavourzyme produced higher level of free amino acids. The heatmap analysis showed a peptidomic pattern more differentiated for alcalase than for the other enzymes. The peptides most abundant and correlated with antioxidant capacity were APAAIGPYSQAVLVDR from uncharacterized protein, GLNQALVDLHALGSAR, ALFQDVQKPSQDEWGK and LSGPQAGLGEYLFER from ferritin and LGEHNIDVLEGNEQFINAAK from trypsinogen. The production and characterization of biopeptides is a new merging challenge of meat industry.

Recent Advances in Microalgae Peptides: Cardiovascular Health Benefits and Analysis

There is now great interest in food protein hydrolysates and food-derived peptides, because they may provide numerous health benefits. Among other foodstuffs, microalgae appear to be sustainable sources of proteins and bioactive peptides that can be exploited in foods and functional formulations. This review considers protein hydrolysates and individual peptides that may be relevant in cardiovascular disease prevention because they mimic the functions of mediators involved in pathologic processes that represent relevant risk factors for cardiovascular disease development, such as hypercholesterolemia, hypertension, diabetes, inflammation, and oxidative status. Some of these peptides are also multifunctional (i.e., they offer more than one benefit). Moreover, the most efficient techniques for protein extraction and hydrolyzation are commented on, as well as the best methodologies for high-throughput detection and quantification. Finally, current challenges and critical issues are discussed.

Preparation, Bioavailability, and Mechanism of Emerging Activities of Ile-Pro-Pro and Val-Pro-Pro

Ile-Pro-Pro and Val-Pro-Pro are two most well-known food-derived bioactive peptides, initially identified as inhibitors of angiotensin I-converting enzyme (ACE) from a sample of sour milk. These two peptides were identified in fermented and enzymatic hydrolyzed cow and non-cow (that is, goat, sheep, buffalo, yak, camel, mare, and donkey) milk, as well as sourdough prepared from wheat, rye, and malt. Similar to other bioactive peptides, bioavailability of these peptides is low (about 0.1%), reaching picomolar concentration in human plasma; they showed blood pressure lowering activity in animals and in human, via improved endothelial function, activation of ACE2, and anti-inflammatory property. Emerging bioactivities of these two peptides toward against metabolic syndrome and bone-protection received limited attention, but may open up new applications of these peptides as functional food ingredients. Further studies are warranted to determine the best source as well as to identify novel enzymes (particularly from traditional fermented milk products) to improve the efficiency of production, to characterize possible peptide receptors using a combination of omics technology with molecular methods to understand if these two peptides act as signal-like molecules, to improve their bioavailability, and to explore new applications based on emerging bioactivities.

Meta-Analysis for Correlating Structure of Bioactive Peptides in Foods of Animal Origin with Regard to Effect and Stability

Amino acid (AA) sequences of 807 bioactive peptides from foods of animal origin were examined in order to correlate peptide structure with activity (antihypertensive, antioxidative, immunomodulatory, antimicrobial, hypolipidemic, antithrombotic, and opioid) and stability in vivo. Food sources, such as milk, meat, eggs, and marine products, show different frequencies of bioactive peptides exhibiting specific effects. There is a correlation of peptide structure and effect, depending on type and position of AA. Opioid peptides contain a high percentage of aromatic AA residues, while antimicrobial peptides show an excess of positively charged AAs. AA residue position is significant, with those in the first and penultimate positions having the biggest effects on peptide activity. Peptides that have activity in vivo contain a high percentage (67%) of proline residues, but the positions of proline in the sequence depend on the length of the peptide. We also discuss the influence of processing on activity of these peptides, as well as methods for predicting release from the source protein and activity of peptides.

Discovery and quantification of bioactive peptides in fermented cucumber by direct analysis IR-MALDESI mass spectrometry and LC-QQQ-MS

Bioactive peptides have been identified in lactic acid bacteria fermented foods including cultured milk, sourdough, and cured meats; however, their presence has not been investigated in fermented vegetables. In this study, infrared, matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry (MS) was employed to identify bioactive peptides in fermented cucumber. Natural and starter culture fermented cucumbers were prepared in triplicate in sodium chloride brines and compared to acidified cucumbers. Putative matches of known food-derived bioactive peptides were identified by direct analysis using IR-MALDESI-MS. Peptides were confirmed by IR-MALDESI MS/MS and quantified by LC-MS/MS. Three angiotensin converting enzyme (ACE) inhibitory peptides, IPP (0.42-0.49 mg/kg), LPP (0.30-0.33 mg/kg), and VPP (0.32-0.35 mg/kg) were formed in fermented cucumbers. A fourth ACE inhibitory peptide, KP (0.93-1.5 mg/kg), was enhanced 3-5 fold in fermented cucumbers compared with acidified cucumbers. This work demonstrates that lactic acid bacteria fermentation can enhance bioactive peptide content in vegetables.

Production of antioxidant peptide fractions from a by-product of tomato processing: mass spectrometry identification of peptides and stability to gastrointestinal digestion

In this study, proteins were extracted from tomato seeds, the main by-product of tomato processing. The incubation for 138.62 min coupled with 3% alcalase was observed to be optimum to produce a tomato seed protein hydrolysate (TSPH) with the highest antioxidant properties. Under these conditions, predicted TSPH activities were 62.99% scavenging of DPPH radicals and 54.81% reduction of phosphomolybdate. Separation of TSPH by ultrafiltration provided three fractions (UF1-UF3) of which, UF3 (< 3 kDa) showed the strongest activity (73.15% DPPH scavenging and 60.1% phosphomolybdate reduction). UF3 was further separated by RP-HPLC into sub-fractions F1-F6. Biological testing found that F2 and F4 were the most active in scavenging DPPH radicals (60.36 and 21.23%) and reducing phosphomolybdate (57.3 and 48.0%). LC-ESI-MS/MS analysis showed that the higher activity of F2 might be explained by the presence of more peptides that contained tyrosine and histidine, known to enhance antioxidant activity through hydrogen or electron transfer. In the simulated gastrointestinal digestion test, peptides in F2 were more resistant compared to those in F4. These findings indicate that peptide fraction F2 might be more useful in the formulation of functional foods because of its greater antioxidant activity and resistance to digestion.

Bioactive hydrolysates from casein: generation, identification, and in silico toxicity and allergenicity prediction of peptides

BACKGROUND

Bioactive casein peptides have attracted considerable attention for their applications in industry. However, there is little clarity regarding mass spectrometric profiles for peptides in enzymatic hydrolysates of casein produced under varying conditions. In this study, the compositions of the peptides from casein hydrolysates were compared for different enzyme/substrate ratio (E/S) and hydrolysis times. The toxicity, allergenicity and bioactivity of the identified peptides were assessed in silico.

RESULTS

A total of 70 unique peptides were identified, and there were 28, 21, 13 and 8 peptides from α_s1 -casein, α_s2 -casein, β-casein and κ-casein respectively. The peptide number decreased with the increase in E/S and hydrolysis time. Moreover, peptides with relative molecular mass M_r ranging from 1000 to 1500 Da occupied the highest proportion of 31.43%, and almost all of the peptides showed M_r less than 5000 Da. In silico analysis showed that all of the peptides were non-toxic and non-allergenic, and several of them were assessed by PeptideRanker as having a relatively high likelihood of being bioactive peptides.

CONCLUSIONS

Composition of the peptides in the casein hydrolysates varied with the enzymolysis conditions. This study's results may facilitate the production of target bioactive peptides by controlling E/S and hydrolysis time, which is beneficial for the application of casein peptides in the functional food industry. © 2017 Society of Chemical Industry.

A peptidomic approach of meat protein degradation in a low-sodium fermented sausage model using autochthonous starter cultures

Fermented sausage technology is currently compromised in decreasing the addition of NaCl. Use of starter cultures with peptidogenic potential could be a valuable strategy that can mask or hide off flavors produced by the use of NaCl substituents. In the present work, the peptidogenic potential of four lactic acid bacteria species was evaluated in a low-sodium beaker sausage (BS) model. Using a peptidomic approach, a total of 86 low molecular weight (LMW) peptides were accurately identified, mostly derived from myofibrillar proteins, especially actin, which generated 53 peptides. The BS inoculated with L. curvatus CRL705 generated 56 LMW peptides, followed by Enterococcus (E.) mundtii CRL35 with 43 peptides. In addition, BS inoculated with Lactobacillus (L.) plantarum and with L. sakei produced higher amino acid amounts over time as compared to the rest of BS models, highlighting the importance of both, time and sample effect on the overall free amino acid generation. The presence of each LAB strain in BS models generated a unique profile of small peptides and amino acids that could serve as a distinctive biochemical trait to differentiate specific fermented products. According to these results, E. mundtii and L. sakei, which are compatible between them, are proposed as the most efficiently adapted to low-sodium conditions. The use of selected strains during the processing of low-sodium fermented sausages could have a positive effect on the production of small peptides and free amino acids.

Bioinformatics and peptidomics approaches to the discovery and analysis of food-derived bioactive peptides

There are emerging advancements in the strategies used for the discovery and development of food-derived bioactive peptides because of their multiple food and health applications. Bioinformatics and peptidomics are two computational and analytical techniques that have the potential to speed up the development of bioactive peptides from bench to market. Structure-activity relationships observed in peptides form the basis for bioinformatics and in silico prediction of bioactive sequences encrypted in food proteins. Peptidomics, on the other hand, relies on "hyphenated" (liquid chromatography-mass spectrometry-based) techniques for the detection, profiling, and quantitation of peptides. Together, bioinformatics and peptidomics approaches provide a low-cost and effective means of predicting, profiling, and screening bioactive protein hydrolysates and peptides from food. This article discuses the basis, strengths, and limitations of bioinformatics and peptidomics approaches currently used for the discovery and analysis of food-derived bioactive peptides.

Omics-prediction of bioactive peptides from the edible cyanobacterium Arthrospira platensis proteome

BACKGROUND

Bioinformatics approaches are widely used to evaluate the prospects of novel protein sources in bioactive peptide research. Edible cyanobacteria are considered as potential protein precursors. However, the abundance of unicellular cyanobacterial proteins is largely unknown and highly dynamic according to the cultivation conditions, which need to be considered in this research field. The objective of this work was to evaluate the protein abundance of Arthrospira platensis, as well as to map the bioactive peptide sequences from the high-abundance proteins of the A. platensis proteome.

RESULTS

The high-abundance proteins of the A. platensis proteome were identified with a high-performance liquid chromatography-tandem mass spectrometry-based method. A total of 593 proteins were detected and quantified. The occurrence frequency of the bioactive peptides in A. platensis proteome was calculated according to the amino acid sequences via the bioinformatics approaches. Further in silico digested by trypsin, pepsin and chymotrypsin, these proteins liberated 78, 99, and 96 bioactive peptides, respectively. In each case, angiotensin-converting enzyme inhibitors and dipeptidyl peptidase IV inhibitors were enriched.

CONCLUSION

This work will help rationally design the protocols for cyanobacterial cultivation, protein pre-treatment and peptide separation, and further produce more peptides with specific functions. © 2017 Society of Chemical Industry.

A peptide derived from enzymatic digestion of globulins from amaranth shows strong affinity binding to the replication origin of Tomato yellow leaf curl virus reducing viral replication in Nicotiana benthamiana

Tomato yellow leaf curl virus (TYLCV; genus Begomovirus; family Geminiviridae) infects mainly plants of the family Solanaceae, and the infection induces curling and chlorosis of leaves, dwarfing of the whole plant, and reduced fruit production. Alternatives for direct control of TYLCV and other geminiviruses have been reported, for example, the use of esterified whey proteins, peptide aptamer libraries or artificial zinc finger proteins. The two latter alternatives affect directly the replication of TYLCV as well as of other geminiviruses because the replication structures and sequences are highly conserved within this virus family. Because peptides and proteins offer a potential solution for virus replication control, in this study we show the isolation, biochemical characterization and antiviral activity of a peptide derived from globulins of amaranth seeds (Amaranthus hypochondriacus) that binds to the replication origin sequence (OriRep) of TYLCV and affects viral replication with a consequent reduction of disease symptoms in Nicotiana benthamiana. Aromatic peptides obtained from papain digests of extracted globulins and albumins of amaranth were tested by intrinsic fluorescent titration and localized surface resonance plasmon to analyze their binding affinity to OriRep of TYLCV. The peptide AmPep1 (molecular weight 2.076 KDa) showed the highest affinity value (Kd = 1.8 nM) for OriRep. This peptide shares a high amino acid similarity with a part of an amaranth 11S globulin, and the strong affinity of AmPep1 could be explained by the presence of tryptophan and lysine facilitating interaction with the secondary structure of OriRep. In order to evaluate the effect of the peptide on in vitro DNA synthesis, rolling circle amplification (RCA) was performed using as template DNA from plants infected with TYLCV or another begomovirus, pepper huasteco yellow vein virus (PHYVV), and adding AmPep1 peptide at different concentrations. The results showed a decrease in DNA synthesis of both viruses at increasing concentrations of AmPep1. To further confirm the antiviral activity of the peptide in vivo, AmPep1 was infiltrated into leaves of N. benthamiana plants previously infected with TYLCV. Plants treated with AmPep1 showed a significant decrease in virus titer compared with untreated N. benthamiana plants as well as reduced symptom progression due to the effect of AmPep1 curtailing TYLCV replication in the plant. The peptide also showed antiviral activity in plants infected with PHYVV. This is the first report, in which a peptide is directly used for DNA virus control in plants, supplied as exogenous application and without generation of transgenic lines.

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Enhancing bioactive peptide release and identification using targeted enzymatic hydrolysis of milk proteins

Milk proteins have been extensively studied for their ability to yield a range of bioactive peptides following enzymatic hydrolysis/digestion. However, many hurdles still exist regarding the widespread utilization of milk protein-derived bioactive peptides as health enhancing agents for humans. These mostly arise from the fact that most milk protein-derived bioactive peptides are not highly potent. In addition, they may be degraded during gastrointestinal digestion and/or have a low intestinal permeability. The targeted release of bioactive peptides during the enzymatic hydrolysis of milk proteins may allow the generation of particularly potent bioactive hydrolysates and peptides. Therefore, the development of milk protein hydrolysates capable of improving human health requires, in the first instance, optimized targeted release of specific bioactive peptides. The targeted hydrolysis of milk proteins has been aided by a range of in silico tools. These include peptide cutters and predictive modeling linking bioactivity to peptide structure [i.e., molecular docking, quantitative structure activity relationship (QSAR)], or hydrolysis parameters [design of experiments (DOE)]. Different targeted enzymatic release strategies employed during the generation of milk protein hydrolysates are reviewed herein and their limitations are outlined. In addition, specific examples are provided to demonstrate how in silico tools may help in the identification and discovery of potent milk protein-derived peptides. It is anticipated that the development of novel strategies employing a range of in silico tools may help in the generation of milk protein hydrolysates containing potent and bioavailable peptides, which in turn may be used to validate their health promoting effects in humans. Graphical abstract The targeted enzymatic hydrolysis of milk proteins may allow the generation of highly potent and bioavailable bioactive peptides.

Exploration of Potentially Bioactive Peptides Generated from the Enzymatic Hydrolysis of Hempseed Proteins

The seed of industrial hemp is an underexploited protein source. In view of a possible use in functional foods, a hempseed protein concentrate was hydrolyzed with pepsin, trypsin, pancreatin, or a mixture of these enzymes. A detailed peptidomic analysis using data-dependent acquisition showed that the numbers of peptides identified ranged from 90 belonging to 33 parent proteins in the peptic hydrolysate to 9 belonging to 6 proteins in the pancreatin digest. The peptic and tryptic hydrolysates resulted to be the most efficient inhibitors of 3-hydroxymethyl-coenzyme A reductase activity when tested on the catalytic domain of the enzyme. Using the open access tools PeptideRanker and BIOPEP, a list of potentially bioactive peptides was generated: the alleged activities included the antioxidant property, the glucose uptake stimulating activity, the inhibition of dipeptidyl peptidase-IV and angiotensin-converting enzyme I.

Features of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from dietary proteins

Dipeptidyl peptidase IV (DPP-IV) is involved in incretin hormone processing and therefore plays a key role in glycemic regulation. This review summarizes the latest developments in food protein-derived DPP-IV inhibitory peptides. The in silico approaches currently used to develop targeted strategies for the enzymatic release of DPP-IV inhibitory peptides from food proteins are outlined. The features within the primary sequences of potent DPP-IV inhibitory di-, tri-, and larger peptides, having half maximal inhibitory activity (IC₅₀ ) < 100 µM, were evaluated and the outcomes are presented herein. It is proposed that detailed analysis of those food derived peptides identified in humans following ingestion may constitute a practical strategy for the targeted identification of novel bioavailable DPP-IV inhibitory peptides. Human intervention studies are required as the specific role of food protein-derived DPP-IV inhibitory peptides in the regulation of glycaemia in humans remains to be fully elucidated. PRACTICAL APPLICATIONS: This review provides recent information on dipeptidyl peptidase IV (DPP-IV) inhibitory peptides arising from food protein hydrolysates. Small animal studies have demonstrated that food protein hydrolysates with in vitro DPP-IV inhibitory properties also display antidiabetic activity. DPP-IV inhibitory peptides may be used as food ingredients to improve glycemic regulation in Type 2 diabetics. Therefore, the development of potent DPP-IV inhibitory hydrolysates containing bioavailable peptides in humans is of significant interest. This may help in the formulation of foods containing physiologically relevant doses of bioactive hydrolysates/peptides. Acquisition of detailed knowledge of DPP-IV inhibitory peptide features via the utilization of in silico tools may help to optimize the release of potent DPP-IV inhibitory peptides during enzymatic hydrolysis of food proteins. This review provides information on features within the primary sequences of potent DPP-IV inhibitory peptides and current in silico strategies which may be used to inform on the targeted enzymatic hydrolysis of food proteins.

Identification of novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides in camel milk protein hydrolysates

Nine novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides (FLQY, FQLGASPY, ILDKEGIDY, ILELA, LLQLEAIR, LPVP, LQALHQGQIV, MPVQA and SPVVPF) were identified in camel milk proteins hydrolysed with trypsin. This was achieved using a sequential approach combining liquid chromatography tandem mass spectrometry (LC-MS/MS), qualitative/quantitative structure activity relationship (QSAR) and confirmatory studies with synthetic peptides. The most potent camel milk protein-derived DPP-IV inhibitory peptides, LPVP and MPVQA, had DPP-IV half maximal inhibitory concentrations (IC₅₀) of 87.0 ± 3.2 and 93.3 ± 8.0 µM, respectively. DPP-IV inhibitory peptide sequences identified within camel and bovine milk protein hydrolysates generated under the same hydrolysis conditions differ. This was linked to differences in enzyme selectivity for peptide bond cleavage of camel and bovine milk proteins as well as dissimilarities in their amino acid sequences. Camel milk proteins contain novel DPP-IV inhibitory peptides which may play a role in the regulation of glycaemia in humans.