Food Proteomics: Technological Advances, Current Applications and Future Perspectives

Food Proteomics: Technological Advances, Current Applications and Future Perspectives addresses many of the food proteomic issues in the industry today. Food proteomics continues to be an emerging field, becoming increasingly important in product innovation, food safety, food quality and health. The book is divided into sections describing the role of proteomics in the field of food science, conceptual background methodological aspects, and bioinformatic tools employed in the field. The book describes proteomic studies collected from the most relevant animal and vegetables species in food production and discusses important food challenges from a proteomic point-of-view.

This is an essential and practical reference that provides analytical tools to help introduce technical innovations in the food industry with the latest scientific information useful and accessible to new researchers in the field as well as advanced.

• Includes precise proteomic information on a specific category
• Provides proteomic studies of the most common vegetable and animal species
• Presents proteomic methodologies, including bioinformatics for effective analysis in food science
• Discusses food challenges such as allergens, authentication and food safety

• Language: English
• Publisher: Academic Press
• Release date: Jun 2, 2022
• ISBN: 9780323908900

Book preview

Preface

In recent years, food science is undergoing a great change encouraged by technological developments. Specifically, food biotechnology will be a great impact on new production methods and novel ingredients and additives. All these tools must be used to achieve better health, consumer safety, and the protection of the environment. It also clear that globalization creates new challenges in the field of preservation and control quality, as well as the sustainability of the food industry and animal welfare have become relevant challenges. To achieve all these goals, proteins as one of the most important components of food are decisive for improving the nutritional and functional properties of foodstuffs.

Proteins consist of 21 amino acids in different sequences and post-translational modifications resulting in a wide variety of conformations. This complex heterogeneity of proteins further complicates its study. Considering the living organism of food origin, the proteins through enzymes and hormones lead the vital functions of the animal or vegetal. Changes in feeding, environmental stress, and/or diseases of animals unleash a cascade of events altering the proteins. In the case of vegetables, changes of proteins associated with climate change such as drought and salinity are the most studied. On the other hand, proteins are very species-specific which can provide good clues of breeding animal and plant variety through the food chain. A further important point to consider is the nutritional aspect of food whereby the proteins also play a key role. The nutritional quality of proteins together with the digestibility and bioavailability of proteins should be considered by the food industry. The processing of food is often designed to increase food safety, but this fact could affect dramatically protein digestibility. For all these reasons, protein research is an important field within food science.

Current advances in food proteomics and its main applications may contribute to the development and innovation of the food industry. The qualitative and quantitative analysis of food proteomes derived from complex matrix provides accurate measurements of proteins, protein–protein interactions, and interactions with other food components. All these factors play a key role in the quality traits of raw and processed foods. However, the rapid developments of mass spectrometry instruments as well as new bioinformatics tools require us to update knowledge for researchers and professionals. Accordingly, this book aims to organize the necessary information about new protein biomarkers and proteomic approaches of classical issues as allergenicity, authentication, or food safety.

This book is divided into an introduction and three sections. In the introduction, the role of proteomics in the field of food science as well as the conceptual background is described. Following, the first section methodological tackle aspects and bioinformatic tools employed in the field of food proteomics practically. The second section includes proteomic studies collected from the most relevant animal and vegetable species in food production. Finally, important food challenges from a proteomic point of view will be discussed and analytical tools will be described to introduce technical innovations in the food industry.

Thanks to all the authors for their great effort and dedication to this book. The editors were truly impressed by the result, and we hope to collaborate again with all of them in the future.

María, Daniel, and Lorenzo

Chapter 1

Introduction Food proteomics: technological advances, current applications and future perpectives

María López-Pedrousoa, José M. Lorenzob,c, Daniel Francob

aDepartment of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain

bCentro Tecnológico de la Carne de Galicia, Ourense, Spain

cUniversidade de Vigo, Ourense, Spain

Abstract

Current advances in food proteomics and its main applications may contribute to the development and innovation of the food industry. The qualitative and quantitative analysis of food proteomes derived from complex matrix provides accurate measurements of proteins, protein–protein interactions, and interactions with other food components. All these factors play a key role in the quality traits of raw and processed foods. However, the rapid developments of mass spectrometry instruments, as well as new bioinformatics tools, require from researchers and professionals an adequate updating in the knowledge. Accordingly, the aim of this introduction is to organize the latest information about the main challenges in the food industry related to the protein field. These challenges are focused on food quality and safety as well as the search of new protein biomarkers and proteomic approaches of classical issues as allergenicity, or authentication among others.

Keywords

Food challenges; Food quality; Food safety; Food security; Protein biomarkers; Sustainability

1.1 Importance of the food industry and emerging trends in food science

The food industry plays a major role in the global economy. According to USDA, the food system is described as the whole food industry—from farming and food production, packaging, and distribution, to retail and catering (USDA, 2021). This includes farmers, food processors, wholesalers, retailers, and food service establishments among others. In 2021, the revenue in the food market amounted to US$8,049,240 m and it is expected a compound annual growth rate of 3.14% during 2021–2025.

Current times also bring the main challenge of ensuring food security and food safety. Both terms are closely linked and concern society. Food security relates to have physical and economic access to sufficient, safe, and nutritious food for the population, meeting their dietary needs, and food preferences for a healthy life. Nevertheless, food safety refers to handling, preparation, and storage of food with proper conditions or practices which reduce the risk of individuals becoming sick from foodborne illnesses (FAO, 2008). The economic growth of the food industry will be further reinforced by the world population increase. Indeed, it should be noted that the world population is expected to reach nine billion people by 2050 (United Nations, 2019). Hence, the security of the food supply will be a challenging task maintaining the current level of food consumption of about 338.9 kg/person in 2021 (Statista, 2021). To meet this demand, agriculture in 2050 will need to double its production to generate almost 50% more food, feed, and biofuel than it did in 2012 (FAO, 2017). Apart from the growth of the population, food security will be also seriously threatened by climate change. Particularly, the primary sector (agriculture, livestock, and aquaculture) is expected to rise production in a more sustainable way (Cole, Augustin, Robertson, and Manners, 2018). Overall, a huge technological development will be required to enhance processing, distribution, and retailing.

The globalization of the food industry faces important nutritional and economic challenges. Emerging food processing technologies are advancing in preservation and control quality boosted by growing consumer demands and price war at the global level. Food processing and new technologies play a key role to achieve the long shelf life of food commodities traveling long distances. Certainly, improvement in the food shelf-life is necessary, because in the world approximately one-third of all food produced is lost or wasted along the food chain (HLPE, 2012), indicating an inefficiency of current food systems. In this sense, to provide the best answer to the rising demands of society, the food industry has to face increasingly complex challenges that require the best available science and technology (e.g., smart and active packaging).

Furthermore, environmental issues should be considered from farms to processors. The environmental impact and sustainability should be assessed and enhanced at every stage. Animal-based foods have a higher environmental impact than vegetal products and this fact is influencing consumer behavior. In developed countries, a huge amount of food wastes has been produced and recycling of by-products should be effectively carried out. In this sense, the sustainability of the food industry is an essential goal (Cucurachi, Scherer, Guinée, and Tukker, 2019). Subsequently, the main ecological aspects like biodiversity loss, nitrogen cycle acceleration, and carbon cycle acceleration should be taken into consideration. These facts could be behind currently dietary changes, toward diets based on plant protein products (Aiking and de Boer, 2020).

There is a close relationship between what we eat (food) and our health. In other words, food quality and its relationship with human health in terms of its nutritional value (i.e., protein and fatty acid profile) play a key role. Therefore, food is currently considered not only a source of energy, macro-, and micro-nutrients, but also one of the best strategies to prevent future diseases. Indeed, the increasing evidence of food-related disorders and chronic diseases have prompted consumers to bring about vital changes in their diet and lifestyle, making them more health-conscious than ever. However, paradoxically, the triple burden (undernutrition, micronutrient deficiencies, and overweight) of malnutrition remains a global health emergency in developing states in contrast with nutrition problems present in developed countries. In the latter ones, processed foods are linked to an increased risk of death from heart disease, diabetes, or other illnesses.

In the field of the agri-food industry, there is a need to ensure food designing new crops within sustainable agriculture. Simultaneously, strategies for maximizing production with minimal effect on the environment improving yield, nutritional quality, the efficiency of resources, and tolerance of biotic and abiotic stress are priority objectives (Tian, Wang, Li, and Han, 2021). Moreover, food safety should give an upgraded level for producers and retailers of fruits and vegetables. A change in consumer behavior is evidenced and a new market for fresh and minimally processed fruits and vegetables is emerging. Packaging and preservation are being enhanced using novel chemicals and the latest developments without compromising the product quality (De Corato, 2020). The mechanical operations of cutting and peeling are the most sensitive steps, disinfection and washing procedures avoiding the growth of pathogenic and spoilage microorganisms should be implemented (Ali, Yeoh, Forney, and Siddiqui, 2018). The market of ready-to-eat leafy green salads and other fresh products is demanding higher microbiological quality in industrialized countries (Arienzo et al., 2020). But increasing demand for vegan or vegetarian products requires further research to tackling new solutions for new situations.

Despite the fact that animal products such as meat, milk, and eggs are essential components of our diets. There is a great concern about health problems associated with red and processed meat intake and a strategy to reduce saturated fat and cholesterol consumption is being carried out. On the contrary, poultry and pork production has been growing exponentially during the last few years, mainly in less developed countries. It is important, however, to bear in mind also the link between an extensive intake of sugars and the occurrence of chronic diseases. In any case, efforts to improve meat quality from a nutritional point of view are constantly in the meat industry via reducing/replacing fat, salt, and additives and incorporating new sources of protein and fiber in the meat products. Furthermore, healthier meat products are being developed via the incorporation of bioactive compounds into them to elaborate functional meat products (Pogorzelska-Nowicka, Atanasov, Horbańczuk, and Wierzbicka, 2018; Ruiz-Capillas and Herrero, 2021). On other hand, environmental concerns of meat consumption and other ethical issues related to animal welfare are changing the consumer attitude (López-Pedrouso et al., 2020a; Sanchez-Sabate and Sabaté, 2019). Additionally, the potential impact of animal diseases on human health is magnified further by increasing levels of resistance in bacteria, parasites, viruses, and fungi to antimicrobial drugs, such as antibiotics, antifungals, antivirals, antimalarials, and anthelmintics. Today, some 700,000 people die of drug-resistant infections every year (FAO, 2017). Hence, the livestock industry should seriously consider all these issues in the future.

Food from aquatic environments is important in the human diet, providing significant health benefits. In this sense, aquaculture production is a growing industry versus traditional fisheries. Its production is continuously increasing due to issues related to the lack of sustainability of capture fisheries and climate change. As in other farm production, the main goal is to achieve a maximum growth rate and at the same time a minimum production cost. To achieve this purpose, strategies of maximizing food conversion with formulated diets, ensuring fish welfare are developed, as a quality indicator of the product. Moreover, the utilization of fish wastes (heads, skin, trimmings, fins viscera, frames, and others) to generate bioactive protein hydrolysates is a current challenge, that can economically help the global process. Indeed, these fish protein hydrolysates could be used for food, nutraceuticals, and dietary supplement industries (Gao et al., 2021; López-Pedrouso et al., 2020a). Simultaneously to these production aspects, aquatic food production must be guaranteed high standards of food safety. In this sense, one of the main constraints in fish and seafood consumption is the allergenicity induced by parvalbumin, tropomyosin, and arginine kinase which must be reduced and, in any case, labeled (López-Pedrouso, Lorenzo, Gagaoua and Franco, 2020b). The second limitation relates to aquatic pollution, which poses a risk for seafood safety in the consumption of contaminated fish species (Okpala, Sardo, Vitale, Bono, and Arukwe, 2018).

To sum up, emerging concerns as globalization, food security, and sustainability pose the main challenges to the food industry and a knowledge gap between food technologies and new market demands should be fill in recent years. At the same time, new opportunities including healthy products, long-life products, and ready to eat should be exploited by food product developers.

1.2 An overview of technological applications based on food proteins

Fig. 1.1 presents the main challenges in the food industry directly related to the protein field. The following aspects will be briefly discussed in the next lines.

Fig. 1.1 Main currently food challenges in the food industry related to the protein field.

1.2.1 The impact of proteins on food quality and safety

Growing consumer demands in a globalized market lead the food industry to seek the highest standards of food quality. Adding nutritional value to food products without diminishing their quality or compromising on taste and flavor, maintaining the cost-effectiveness and the shelf-life adds to the long list of current challenges in the food industry. Proteins are one of the most important components in our diet playing a key role in human nutrition and the functional properties of foodstuffs. The nutritional quality of proteins, formed by 21 different amino acids, is very heterogeneous, and our dietary requirements of essential amino acids depend on body weight, physiological state, and physical activity level among others. Moreover, protein digestibility is an important factor for the evaluation of their nutritive value, as well as, their bioaccessibility and bioavailability, bearing in mind that their effects on human health will be determined by the food processing (López-Pedrouso, Lorenzo, Zapata, and Franco, 2019). It should be noted also that functional properties of proteins (e.g., gel formation, emulsifying effect, viscosity, solubility, foam formation), not only influence textural aspects because protein colloidal structures can alter the nutritional properties and biological activity of foodstuffs (Foegeding and Davis, 2011).

In the context of globalization, food safety has still unresolved challenges. Indeed, transboundary pests and plant and animal diseases are producing highly contagious epidemic outbreaks that spread rapidly across national borders, causing high rates of death and illness. The risk of serious outbreaks is increasing as more people, animals, plants, and agricultural products move across international borders, and as animal production systems become more intensive (FAO, 2017). This requires routine food safety analysis from the primary sector to the final consumer, rapid, in-field, and low-cost techniques are needed. The contaminants which cause great concern to the population are microbes, mycotoxins, pesticides, packaging components, seafood toxins, veterinary drugs and preservatives. These pollutants alter the biological process of the organic matrix, inducing changes in the proteome as a response to these environmental factors. The detection of protein biomarkers to control food safety could be performed by immunoassay (ELISA or western blotting) measuring the concentration of biomolecule through an antigen or antibody interaction. The search for protein biomarkers constitutes a previous step to implement other technologies. A great level of sensitivity and selectivity of antibodies could have a practical application of surface-enhanced Raman spectroscopy (SERS). Aptamers as an emergent biomaterial have also been described to detect alterations in the food matrix (Hermann, Duerkop, and Baeumner, 2019; Yaseen, Pu, and Sun, 2018). In recent years, it is important to highlight that the nanotechnology field, including magnetic nanoparticles, quantum dots, carbon nanotubes, and nanosensors is being developed to detect and biomonitoring foodborne diseases many using protein biomarkers (Krishna et al., 2018). These biomarkers are mainly based on protein-related molecules (e.g. nucleic acids, proteins, antigens, and metabolites) present in the food matrix.

1.2.2 Bioactive peptides from food proteins

Technological advances are focused on the extraction and identification of new bioactive compounds. These compounds present in small quantities from food have a beneficial effect on human health including the prevention of cardiovascular disease and cancer (Kris-Etherton et al., 2002). In the case of peptides, the fragmentation of proteins increases their bioactivity in numerous physiological functions. Indeed, amino acids and small peptides (4-6 amino acids) were demonstrated to have high digestibility and fast absorption with relevant biological activities (López-Pedrouso et al., 2020a). Therefore, protein hydrolysates obtained from chemical and enzymatic digestion are being investigated and, isolation and purification of the biopeptides is a priority of the food industry. It is certainly possible that protein hydrolysates with biological activity (e.g. antihypertensive, antioxidant, antithrombotic and antimicrobial) give it an added value to new foodstuffs formulations (Borrajo, López-Pedrouso, Franco, Pateiro, and Lorenzo, 2020).

The food industry is an important source of by-products and wastes, that need to be recycling and/or recovery. For instance, discards from the fish industry (fish frame, skin, and viscera) are used to extract polyunsaturated fatty acids, collagen, gelatin, and bioactive peptides. Specifically for bioactive peptides, antioxidant and angiotensin-converting enzyme (ACE) inhibitory effects have been described (Atef a Mahdi Ojagh, 2017). Regarding processed meats, it has been described that endogenous enzymes and microbial peptidases act during the ripening process of dry-cured hams and other dry-fermented meat products affecting the taste and flavor and generating bioactive peptides (Mora, Gallego, Reig, and Toldrá, 2017). Another relevant source of biopeptides is milk and dairy products from mammalian animals. Fragments from casein (αs1-, αs2-, b-, and ĸ-casein) and whey proteins (α-lactalbumin, β-lactoglobulin, and lactoferrin) have been demonstrated to be active, exhibiting antimicrobial, antihypertensive, and antioxidant functions among others. In this sense, fermentation is the elected process to generate the biopeptides (Egger and Ménard, 2017; Nielsen, Beverly, Qu, and Dallas, 2017). The future commercialization of these biopeptides will be introduced in nutraceuticals and functional foods although the low concentration of the peptide in the food matrix decreases the bioactivity. Other disadvantages of biopeptides are their hydrophobic nature and the sensory issues which hamper the formulating products (Li-Chan, 2015), hence further research will be needed to implement their production and functionality.

1.2.3 Allergenicity of food proteins

New formulations and industrial process, as well as, the novel sources of proteins, requires more technological advances in the field of food allergens. They represent a major concern and a global food challenge because food allergies are increasingly important in western countries, particularly in children. In the period from 2014 to 2016, 6.9% and 7.6% of children suffer from food allergies in Europe and United States, respectively (Jiang, Warren, and Gupta, 2020). The most abundant allergens are proteins that trigger a mediated or non-mediated IgE response. The severity of symptoms including alterations in skin and oral mucosa, respiratory, gastrointestinal, cardiovascular, and anaphylactic shock as well as its prevalence results in high economic losses for the health system. In this regard, the detection and quantification of the allergens for correct food labeling seem of utmost relevance. The food industry needs to considerably improve in this field. A large quantity of these allergens are proteins with different biological functions. In the case of plant-based food, peanuts, soy, tree nuts, and wheat trigger allergies in connection with gluten proteins, globulin, albumin, and other storage proteins. On the other hand, milk, eggs, and fish also have a significant number of protein allergens such as lactalbumin, lactoglobulin, and parvalbumin (López-Pedrouso et al., 2020a). The food industry must identify the proper and routine method to avoid the allergic component or label it and this issue must be considered an important priority. After a thorough knowledge of food allergens, numerous industrial applications of the proteins could be introduced like biosensors of allergens (Zhou et al., 2019).

1.2.4 Food authenticity and traceability based on proteomic profiles

In the global food chain, traceability and authenticity of origin and food processing must be monitored to meet the consumer requirements. The definition of food traceability is the ability to follow the movement of food and ingredients across all steps in the supply chain according to the FDA (https://www.fda.gov/food/new-era-smarter-food-safety/tracking-and-tracing-food). Thus, tracking the food information through the food supply is critical to improve consumer trust and purchase willingness. The knowledge of the product life cycle to ensure the safety, sustainability, and quality of the product must be strongly enhanced. One of the food categories with the highest risk of adulteration or substitution is meat and several cases have been reported (Li et al., 2020). Additionally, in the case of meat, ethical values (organic food, fair trade), cultural issues (vegan, halal, kosher) are highly important for numerous populations groups. Thus, technological advances including isotope analysis, chemometrics, and NIR and DNA coding are being developed to increase traceability (Badia-Melis, Mishra, and Ruiz-García, 2015). From a molecular point of view, for example, DNA-based methods and rapid evaporative ionization mass spectrometry could be used to identify several species of animals in minced meat matrices (Cavin, Cottenet, Cooper, and Zbinden, 2018). Equally important and with the problem of a higher number of commercial species the fishery products are also susceptible to food frauds, hence analytical methods including DNA-based, chromatographic and spectroscopic technologic are being developed (Fiorino et al., 2018). In this sense, proteins could be used as the major target for mass spectrometry, high-performance liquid chromatography, and immunoassays. For this purpose, proteomic fingerprint detecting differences in protein/DNA structure is a valuable tool for quantitative and qualitative analysis (Esteki, Regueiro, and Simal-Gándara, 2019).

1.3 Why proteomics?

Food proteomics is becoming more frequent to address issues in the field of food quality and food safety. The need to develop new analytical strategies for proteins makes food proteomics an essential tool. Food protein composition has a key influence on the nutritional quality and technological properties of foods. Therefore, high-throughput research in proteins for food traceability as well as food quality and safety detecting allergens or microbial contaminants is the way forward (Cunsolo, Muccilli, Saletti, and Foti, 2014). To fulfill this goal, the proteomics has been developed to find biomarkers for predicting sensory and technological quality traits of foodstuffs along with a better understanding of molecular mechanisms (Gagaoua et al., 2021; Huang et al., 2020). A biomarker is related to a functional, physiological or biochemical process at the cellular and molecular level influencing a specific feature (Strimbu and Tavel, 2010). A protein biomarker is an indispensable tool to monitor and predict these quality traits but a large amount of information and preparatory steps including, verification and validation, should be achieved (Fig. 1.2).

Fig. 1.2 Main stages to discover protein biomarkers.

Further, proteomic technologies also give information about protein isoforms, posttranslational modifications, molecular interactions which define the quality features. The understanding of molecular mechanisms and their relationship with food quality drive current proteomic research.

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Section I

Technological advances in food proteomics

2 Quantitative proteomics by mass spectrometry in food science 15

3 Technological developments of food peptidomics 49

Chapter 2

Quantitative proteomics by mass spectrometry in food science

M.D.P. Chantada-Vázqueza,b, C. Núñeza, S.B. Bravob

aResearch Unit, Hospital Universitario, Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain

bProteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela,