Proteomics for the Food Industry: Opportunities and Challenges

Marker Peptides for Indicating the Spoilage of Milk-Sample Preparation and Chemometric Approaches for Yielding Potential Peptides in a Raw Milk Model

The diminishing of food waste is gaining increasing importance, especially in context with a growing population and a need for the sustainable use of food resources. A more precise determination of the best-before date can contribute to this general aim. As proteoforms can be regarded as indicators for ecophysiological influences, their suitability for determining the spoilage and, consequently, the shelf-life of food is suggested. Proteoforms reflect the spoilage of food more accurately. The aim of the present study was to develop an efficient proteomics workflow to determine the shelf-life of milk as a prominent target. In this case, raw milk was chosen as model, as it degrades much faster. The integration of different multivariate analysis techniques was used to analyze the spoilage of raw milk with regard to aspects of its proteome. As the feasibility of such an approach has already been demonstrated in previous studies, it is further necessary to enable a robust and reproducible workflow, primarily gaining appropriate numbers and amounts of peptides when the research question differs and other dairy products are evaluated. In the present study, two approaches for gaining peptides were considered: In addition to a direct hydrolysis of a protein-rich sample solution, in-gel hydrolysis is another common approach in proteomics. By separating the proteins in a traditional gel electrophoresis before hydrolysis, the change in the individual proteins and, consequently, potential peptides can be monitored more specifically during storage. However, the traditional approach offers not only possibilities but also limitations that must be considered. The study showed that it is beneficial to apply a combination of different application strategies, as they complement each other and can thus increase the information content of a sample or confirm a theory. Mass spectrometric features, which represent a chemical-structural change of all kinds of compounds during storage, were selected, and three of them were identified as peptides, originating from α-s1-casein.

Evaluation of the Immune Response of Patulin by Proteomics

Patulin, an emerging mycotoxin with high toxicity, poses great risks to public health. Considering the poor antibody production in patulin immunization, this study focuses on the four-dimensional data-independent acquisition (4D-DIA) quantitative proteomics to reveal the immune response of patulin in rabbits. The rabbit immunization was performed with the complete developed antigens of patulin, followed by the identification of the immune serum. A total of 554 differential proteins, including 292 up-regulated proteins and 262 down-regulated proteins, were screened; the differential proteins were annotated; and functional enrichment analysis was performed. The differential proteins were associated with the pathways of metabolism, gene information processing, environmental information processing, cellular processes, and organismal systems. The functional enrichment analysis indicated that the immunization procedures mostly resulted in the regulation of biochemical metabolic and signal transduction pathways, including the biosynthesis of amino acid (glycine, serine, and threonine), ascorbate, and aldarate metabolism; fatty acid degradation; and antigen processing and presentation. The 14 key proteins with high connectivity included G1U9T1, B6V9S9, G1SCN8, G1TMS5, G1U9U0, A0A0G2JH20, G1SR03, A0A5F9DAT4, G1SSA2, G1SZ14, G1T670, P30947, P29694, and A0A5F9C804, which were obtained by the analysis of protein-protein interaction networks. This study could provide potential directions for protein interaction and antibody production for food hazards in animal immunization.

The Impact of the Fresh Pork Display Lamps on the Sensory Response of Consumers to Fresh Pork

Two studies were conducted to investigate the impact of fresh pork display lamps on consumers' sensory responses to pork products. In the first experiment, 63 participants were asked to evaluate pork products with different degrees of freshness under four fresh pork display lights and two LED lights. In the other experiment, 30 subjects participated in the Farnsworth-Munsell 100 hue test under the same lamps, with the aim of showing whether the fresh pork display lamps impaired color discrimination. The results showed that the light source had a significant effect on the color appearance evaluation of the pork products. The ratings for perceived freshness under the fresh pork display lamps were significantly higher than those of ordinary LED lamps, while the color discrimination performance of the subjects under those lamps was poor. It was demonstrated that improper component proportions of the light spectrum could influence observers' assessment of meat quality and weaken the observers' ability to distinguish the freshness level. Through this study, the authors would like to remind lamp users and manufacturers to not only be concerned about the improvement in the color appearance of pork, but also the need for consumers to be aware of the authentic freshness of the pork products.

Cold stress resilience of Iranian olive genetic resources: evidence from autochthonous genotypes diversity

Olive (Olea europaea L.) is one of the most cultivated tree species in Iran. This plant is characterized by its tolerance to drought, salt, and heat stresses while being vulnerable to frost. During the last decade, periods of frost have occurred several times in Golestan Province, in the northeast of Iran, which caused severe damage to olive groves. This study aimed to evaluate and individuate autochthonous Iranian olive varieties with regard to frost tolerance and good agronomic performance. For this purpose, 218 frost-tolerant olive trees were selected from 150,000 adult olive trees (15-25 years old), following the last harsh autumn of 2016. The selected trees were reassessed at different intervals, i.e., 1, 4, and 7 months after the cold stress in field conditions. Using 19 morpho-agronomic traits, 45 individual trees with relatively stable frost-tolerance were reevaluated and selected for this research. Ten highly discriminating microsatellite markers were used for the genetic profiling of the 45 selected olive trees, and, ultimately, five genotypes with the highest tolerance among 45 selected ones were placed in a cold room at freezing temperatures for image analyses of cold damage. The results of morpho-agronomic analyses evidenced no bark splitting or symptoms of leaf drop in the 45 cold-tolerant olives (CTOs). The oil content of the cold-tolerant trees comprised almost 40% of the fruit dry weight, highlighting the potential of these varieties for oil production. Moreover, through molecular characterization, 36 unique molecular profiles were individuated among the 45 analyzed CTOs that were genetically more similar to the Mediterranean olive cultivars than the Iranian ones. The present study demonstrated the high potential of local olive varieties, which would be promising and more suitable than commercial olive varieties, with regard to the establishment of olive groves under cold climate conditions. This could be a valuable genetic resource for future breeding activities to face climate changes.

Lateral flow immunoassay-based absolute point-of-care technique for authentication of meat and commercial meat products

Point-of-care (POC) assay is an emerging technique for rapid initial screening of meat fraud incidents in a resource-limited environment. To achieve this goal, a simple extraction protocol is proposed for efficient recovery of meat proteins from raw, heat-processed, and commercial samples as well as meat offals without utilizing sophisticated laboratory settings. A sandwich-format lateral flow immunoassay (LFIA) was developed based on gold nanoparticles as labels and immunoglobulins (IgG and IgY) as biomarkers for meat species identification in raw and cooked meat mixes. The test system showed a sensitivity of 10 ng/mL allowing the detection of as low as 0.063% pork and chicken meat and 0.125% sheep meat (lamb) in meat mixes within 15 min including sample preparation. Reproducibility of the assay was confirmed by the fully consistent intra- and inter-laboratory tests and RT-PCR method. The current study developed a field-deployable extraction technique and highly-specific, sensitive, reproducible, cost-effective, and user-friendly LFIA-based assay for rapid species authentication in raw, cooked, and commercial meat samples and meat offals.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05663-2.

Comparison of Total Soluble Protein Content and SDS-PAGE Pattern Between Four Different Types of Honey

Generally, there are two types of beekeeping: the Apini tribe and the Meliponini tribe. Both tribes produce honey and have a good demand due to their health benefit properties. Considering the influence of diverse factors on honey composition and the lack of studies, establishing quality standards for stingless bee honey (Meliponini tribe) is still challenging and need to do to protect the consumer. In this sense, this study aimed to determine the total soluble protein content and compare the SDS-PAGE profile between two species of Apini tribe and two species of Meliponini tribe. Protein concentrations in honey samples were varied and resulted in a micro component in honey. SDS-PAGE profile for Meliponini tribe showed more number of protein bands compared to protein from Apini tribe. The unique protein bands that appeared in the Meliponini tribe may have potential as a biomarker to justify the authenticity and quality of that honey, which is known as Unique Kelulut Factor (UKF).

Proteomic and metabolomic studies on chilling injury in peach and nectarine

Peaches and nectarines are temperate climate stone fruits, which should be stored at 0°C to prevent the ripening of these climacteric fruits. However, if stored for too long or if stored at a higher temperature (4 or 5°C), they develop chilling injury. Chilling injury damage includes (1) dry, mealy, wooly (lack of juice) fruits, (2) hard-textured fruits with no juice (leatheriness), (3) flesh browning, and (4) flesh bleeding or internal reddening. There are genetic components to these disorders in that early season fruits are generally more resistant than late season fruits, and white-fleshed fruits are more susceptible to internal browning than yellow-fleshed fruits. A recent review covered the recent research in genomic and transcriptomic studies, and this review examines findings from proteomic and metabolomics studies. Proteomic studies found that the ethylene synthesis proteins are decreased in cold compromised fruits, and this affects the processes initiated by ethylene including cell wall and volatile changes. Enzymes in metabolic pathways were both higher and lower in abundance in CI fruits, an indication of an imbalance in energy production. Stress proteins increased in both fruits with or without CI, but were higher in damaged fruits. Metabolomics showed the role of levels of sugars, sucrose, raffinose, galactinol, and glucose-6-phosphate in protection against chilling injury, along with other membrane stabilizers such as polyamines. Amino acid changes were inconsistent among the studies. Lipid species changes during storage could be correlated with sensitivity or resistance to CI, but more studies are needed.

Optimization of the Bacteriophage Cocktail for the Prevention of Brown Blotch Disease Caused by Pseudomonas tolaasii

Brown blotch disease, caused by Pseudomonas tolaasii, is one of the most serious diseases in mushroom cultivation, and its control remains an important issue. This study isolated and evaluated pathogen-specific bacteriophages for the biological control of the disease. In previous studies, 23 varieties of P. tolaasii were isolated from infected mushrooms with disease symptoms and classified into three subtypes, Ptα, Ptβ, and Ptγ, based on their 16S rRNA gene sequences analysis and pathogenic characters. In this study, 42 virulent bacteriophages were isolated against these pathogens and tested for their host range. Some phages could lyse more than two pathogens only within the corresponding subtype, and no phage exhibited a wide host range across different pathogen subtypes. To eliminate all pathogens of the Ptα, Ptβ, and Ptγ subtype, corresponding phages of one, six, and one strains were required, respectively. These phages were able to suppress the disease completely, as confirmed by the field-scale on-farm cultivation experiments. These results suggested that a cocktail of these eight phages is sufficient to control the disease induced by all 23 P. tolaasii pathogens. Additionally, the antibacterial effect of this phage cocktail persisted in the second cycle of mushroom growth on the cultivation bed.

Integrated multi-omics approaches to understand microbiome assembly in Jiuqu, a mixed-culture starter

The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, we review the varieties of Jiuqu and their production processes, with particular attention to factors shaping the microbiota of Jiuqu. Then, the potentials of integrated omics approaches used in Jiuqu research are examined in order to understand the assembly of the microbiome and improve the quality of the products. A variety of different approaches, including molecular and mass spectrometry-based techniques, have led to scientific advances in the analysis of the complex ecosystem of Jiuqu. To date, the extensive research on Jiuqu has mainly focused on the microbial community diversity, flavor profiles, and biochemical characteristics. An integrative approach to large-scale omics datasets and cultivated microbiota has great potential for understanding the interrelation of the Jiuqu microbiome. Further research on the Jiuqu microbiome may explain the inherent property of compositional stability and stable performance of a complex microbiota coping with environmental perturbations and provide important insights to reconstruct synthetic microbiota and develop modern intelligent manufacturing procedures for Jiuqu.

Proteomics as a promising biomarker in food authentication, quality and safety: A review

Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.

The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community

Labeo rohita (Rohu) is one of the most important fish species produced in world aquaculture. Integrative omics research provides a strong platform to understand the basic biology and translate this knowledge into sustainable solutions in tackling disease outbreak, increasing productivity and ensuring food security. Mass spectrometry-based proteomics has provided insights to understand the biology in a new direction. Very little proteomics work has been done on 'Rohu' limiting such resources for the aquaculture community. Here, we utilised an extensive mass spectrometry based proteomic profiling data of 17 histologically normal tissues, plasma and embryo of Rohu to develop an open source PeptideAtlas. The current build of "Rohu PeptideAtlas" has mass-spectrometric evidence for 6015 high confidence canonical proteins at 1% false discovery rate, 2.9 million PSMs and ~150 thousand peptides. This is the first open-source proteomics repository for an aquaculture species. The 'Rohu PeptideAtlas' would promote basic and applied aquaculture research to address the most critical challenge of ensuring nutritional security for a growing population.

Effect of creatine and EDTA supplemented diets on European seabass (Dicentrarchus labrax) allergenicity, fish muscle quality and omics fingerprint

The relatively easy access to fish worldwide, alongside the increase of aquaculture production contributes to increased fish consumption which result in higher prevalence of respective allergies. Allergies to fish constitute a significant concern worldwide. β-parvalbumin is the main elicitor for IgE-mediated reactions. Creatine, involved in the muscle energy metabolism, and ethylenediamine tetraacetic acid (EDTA), a calcium chelator, are potential molecules to modulate parvalbumin. The purpose of this study was to test creatine (2, 5 and 8%) and EDTA (1.5, 3 and 4.5%) supplementation in fish diets to modulate β-parvalbumin expression and structure and its allergenicity in farmed European seabass (Dicentrarchus labrax) while assessing its effects on the end-product quality. Fish welfare and muscle quality parameters were evaluated by plasma metabolites, rigor mortis, muscle pH and sensory and texture analysis. Proteomics was used to assess alterations in muscle proteome profile and metabolic fingerprinting by Fourier transform infrared spectroscopy was used to assess the liver metabolic profile. In addition, IgE-reactivity to parvalbumin was analysed using fish allergic patient sera. Metabolic fingerprinting of liver tissue revealed no major alterations in infrared spectra with creatine supplementation, while with EDTA, only absorption bands characteristic of lipids were altered. Comparative proteomics showed up regulation of (tropo) myosin and phosphoglycerate mutase 2 with Creatine supplementation. In the case of EDTA proteomics showed up regulation of proteins involved in cellular and ion homeostasis. Allergenicity seems not to be modulated with creatine or EDTA supplementation as no decreased expression levels were found and IgE-binding reactivity showed no quantitative differences.

Big Data Analytics in Chemical Engineering

Big data analytics is the journey to turn data into insights for more informed business and operational decisions. As the chemical engineering community is collecting more data (volume) from different sources (variety), this journey becomes more challenging in terms of using the right data and the right tools (analytics) to make the right decisions in real time (velocity). This article highlights recent big data advancements in five industries, including chemicals, energy, semiconductors, pharmaceuticals, and food, and then discusses technical, platform, and culture challenges. To reach the next milestone in multiplying successes to the enterprise level, government, academia, and industry need to collaboratively focus on workforce development and innovation.

Enzyme-Linked Immunosorbent Assay (ELISA)

Food allergy is a public health concern especially after recognizing its constantly increased prevalence and severity. Despite careful reading of food ingredient statements, food allergic individuals may experience reactions caused by "hidden", "masked", or "contaminated" proteins that are known major allergens. Many techniques have been developed to detect even small traces of food allergens, for clinical or laboratory purposes. Enzyme-linked immunosorbent assay (ELISA) is one of the best validated and most routinely used immunoassay in allergy research, in allergy diagnosis in allergy-related quality control in various industries. Although as a technique it has been implemented for the last 45 years, the evolution in biochemistry allowed the development of ultrasensitive ELISA variations that are capable of measuring quantities in the scale of picograms, rendering ELISA attractive, robust, and very famous.

Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: a case study on apple fruit

Complex peptide extracts from non-model crops are troublesome for proper identification and quantification. To increase the identification rate of label free DIA experiments of Braeburn apple a new workflow was developed where a DDA database was constructed and linked to the DIA data. At a first level, parent masses found in DIA were searched in the DDA database based on their mass to charge ratio and retention time; at a second level, masses of fragmentation ions were compared for each of the linked spectrum. Following this workflow, a tenfold increase of peptides was identified from a single DIA run. As proof of principle, the designed workflow was applied to determine the changes during a storage experiment, achieving a two-fold identification increase in the number of significant peptides. The corresponding protein families were divided into nine clusters, representing different time profiles of changes in abundances during storage. Up-regulated protein families already show a glimpse of important pathways affecting aging during long-term storage, such as ethylene synthesis, and responses to abiotic stresses and their influence on the central metabolism.

BIOLOGICAL SIGNIFICANCE

Proteomics research on non-model crops causes additional difficulties in identifying the peptides present in, often complex, samples. This work proposes a new workflow to retrieve more identifications from a set of quantitative data, based on linking DIA and DDA data at two consecutive levels. As proof of principle, a storage experiment on Braeburn apple resulted in twice as much identified storage related peptides. Important proteins involved in central metabolism and stress are significantly up-regulated after long term storage. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Precipitation of champagne base wine proteins prior to 2D electrophoresis

Numerous methods have been employed to depict the protein content of wines. Among them, two-dimensional electrophoresis (2D-E) presents a powerful resolution, but has been poorly applied to wine. Furthermore, 2D-E was coupled with various extraction methods of proteins without any reference method for wine. Here, we describe a rapid method to extract proteins from a champagne base wine through ultrafiltration followed by precipitation with ethanol and trichloroacetic acid. More than 50 spots were visualized on 2D-gels (7 cm, pH 3-6) by colloidal Coomassie Brilliant Blue staining.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

Post-harvest proteomics and food security

To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.

Food Analysis: Present, Future, and Foodomics

This paper presents a revision on the instrumental analytical techniques and methods used in food analysis together with their main applications in food science research. The present paper includes a brief historical perspective on food analysis, together with a deep revision on the current state of the art of modern analytical instruments, methodologies, and applications in food analysis with a special emphasis on the works published on this topic in the last three years (2009–2011). The article also discusses the present and future challenges in food analysis, the application of “omics” in food analysis (including epigenomics, genomics, transcriptomics, proteomics, and metabolomics), and provides an overview on the new discipline of Foodomics.

Translational plant proteomics: a perspective

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.