We Are What We Eat: Food Safety and Proteomics

Foodomics-Based Approaches Shed Light on the Potential Protective Effects of Polyphenols in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic and progressive inflammatory disorder affecting the gastrointestinal tract (GT) caused by a wide range of genetic, microbial, and environmental factors. IBD is characterized by chronic inflammation and decreased gut microbial diversity, dysbiosis, with a lower number of beneficial bacteria and a concomitant increase in pathogenic species. It is well known that dysbiosis is closely related to the induction of inflammation and oxidative stress, the latter caused by an imbalance between reactive oxygen species (ROS) production and cellular antioxidant capacity, leading to cellular ROS accumulation. ROS are responsible for intestinal epithelium oxidative damage and the increased intestinal permeability found in IBD patients, and their reduction could represent a potential therapeutic strategy to limit IBD progression and alleviate its symptoms. Recent evidence has highlighted that dietary polyphenols, the natural antioxidants, can maintain redox equilibrium in the GT, preventing gut dysbiosis, intestinal epithelium damage, and radical inflammatory responses. Here, we suggest that the relatively new foodomics approaches, together with new technologies for promoting the antioxidative properties of dietary polyphenols, including novel delivery systems, chemical modifications, and combination strategies, may provide critical insights to determine the clinical value of polyphenols for IBD therapy and a comprehensive perspective for implementing natural antioxidants as potential IBD candidate treatment.

Food for Thought: Proteomics for Meat Safety

Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.

Comparison of grain protein profiles of Brazilian cowpea (Vigna unguiculata) cultivars based on principal component analysis

This study aims to compare the grain protein profile of four Brazilian cowpea cultivars (BRS Aracê, BRS Itaim, BRS Pajeú, and BRS Xiquexique) by two-dimensional electrophoresis (2-DE) and principal component analysis (PCA). 2-DE efficiently separate cowpea protein profiles, showing high homogeneity among the four cultivars. In addition, the principal component analysis indicated that there is a difference in abundance of proteins among the cultivars. The cultivars BRS Aracê and BRS Xiquexique, both biofortified in iron and zinc, were separated from the cultivars BRS Itaim and BRS Pajeú. These results demonstrate that protein profiles can be used to discriminate cowpea varieties.

Graphical Abstract

Smartphone-Integrated Photoacoustic Analytical Device for Point-of-Care Testing of Food Contaminant Azodicarbonamide

Azodicarbonamide (ADA) is widely used as a flour additive due to its oxidizing and bleaching properties, but it reacts with wet flour during heat processing and is easily decomposed into semicarbazide with genotoxicity and carcinogenicity. In order to improve the efficiency of food safety supervision and expand the scope of food safety control, it is of great significance to develop a facile method for point-of-care testing (POCT) of ADA. Herein, a field-portable and universal smartphone-based photoacoustic (PA) integration device is constructed for quantitative POCT of ADA in flour. The recognition probe Prussian blue with favorable stability is loaded on a flexible substrate for fabricating a portable test strip. In the presence of target ADA, the PA signal changes driven by a modulated 808 nm laser beam can be conveniently collected through the recording application (Audio Lab) of the smartphone. By combining the economic test strip and portable PA device with smartphone readout, it not only greatly simplifies the operation steps but also dramatically reduces the size and cost of the instrument. There is a favorable linear relationship between the PA signal and ADA concentration in the range of 10-200 μmol L^-1 (R² = 0.9928), and a detection limit of 5 μmol L^-1 obtained is much lower than the maximum allowable ADA level in the extract of flour (388 μmol L^-1). The present miniature PA device with strong POCT ability holds enormous public health significance and economic value in the field of food safety, especially in resource-limited settings.

Proteomic Technologies and their Application for Ensuring Meat Quality, Safety and Authenticity

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Proteomic tools were extensively used to understand the relationship between muscle proteome and conversion of muscle to meat, post-mortem proteolysis, meat texture, and variation in meat color. Developments in proteomic tools have also resulted in their application for addressing the safety and authenticity issues including meat species identification, detection of animal byproducts, non-meat ingredients and tissues in meat products, traceability, identification of genetically modified ingredients, chemical residues and other harmful substances. Proteomic tools are also being used in some of the potential areas like understanding the effect of animal transportation, stunning, slaughter stress, halal authentication and issues related to animal welfare. Emerging advances in proteomic and peptidomic technologies and their application in traceability, meat microbiology, safety and authentication are taking a major stride as an interesting and complementary alternative to DNA-based methods currently in use. Future research in meat science need to be linked to emerging metabolomic, lipidomic and other omic technologies for ensuring integrated meat quality and safety management. In this paper, a comprehensive overview of the use of proteomics for the assessment of quality and safety in the meat value chain and their potential application is discussed.

Blockchain-Based Wine Supply Chain for the Industry Advancement

The wine sector is one of the most ‘amazing’ and significant agri-food sectors worldwide since ancient times, considering revenue or employment as well as health aspects. This article aims to describe the impact of the implementation of blockchain technology (BCT) in the wine supply chain. After the literature review, the study is based on Agent Based Models (ABMs) and carried out by the GAMA program. Then, the model and simulation of BCT wine supply chain is designed. Finally, the paper compares traditional and BCT-based supply chains, and the advantages of the last one are evident. Blockchain is a useful tool to ensure a traceability system and to protect the production from any type of fraud and contamination.

Proteomic Advances in Cereal and Vegetable Crops

The importance of vegetables in human nutrition, such as cereals, which in many cases represent the main source of daily energy for humans, added to the impact that the incessant increase in demographic pressure has on the demand for these plant foods, entails the search for new technologies that can alleviate this pressure on markets while reducing the carbon footprint of related activities. Plant proteomics arises as a response to these problems, and through research and the application of new technologies, it attempts to enhance areas of food science that are fundamental for the optimization of processes. This review aims to present the different approaches and tools of proteomics in the investigation of new methods for the development of vegetable crops. In the last two decades, different studies in the control of the quality of crops have reported very interesting results that can help us to verify parameters as important as food safety, the authenticity of the products, or the increase in the yield by early detection of diseases. A strategic plan that encourages the incorporation of these new methods into the industry will be essential to promote the use of proteomics and all the advantages it offers in the optimization of processes and the solution of problems.

Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.

Understanding the Gastrointestinal Protective Effects of Polyphenols using Foodomics-Based Approaches

Plant polyphenols are rich sources of natural anti-oxidants and prebiotics. After ingestion, most polyphenols are absorbed in the intestine and interact with the gut microbiota and modulated metabolites produced by bacterial fermentation, such as short-chain fatty acids (SCFAs). Dietary polyphenols immunomodulatory role by regulating intestinal microorganisms, inhibiting the etiology and pathogenesis of various diseases including colon cancer, colorectal cancer, inflammatory bowel disease (IBD) and colitis. Foodomics is a novel high-throughput analysis approach widely applied in food and nutrition studies, incorporating genomics, transcriptomics, proteomics, metabolomics, and integrating multi-omics technologies. In this review, we present an overview of foodomics technologies for identifying active polyphenol components from natural foods, as well as a summary of the gastrointestinal protective effects of polyphenols based on foodomics approaches. Furthermore, we critically assess the limitations in applying foodomics technologies to investigate the protective effect of polyphenols on the gastrointestinal (GI) system. Finally, we outline future directions of foodomics techniques to investigate GI protective effects of polyphenols. Foodomics based on the combination of several analytical platforms and data processing for genomics, transcriptomics, proteomics and metabolomics studies, provides abundant data and a more comprehensive understanding of the interactions between polyphenols and the GI tract at the molecular level. This contribution provides a basis for further exploring the protective mechanisms of polyphenols on the GI system.

A novel colorimetric immunoassay for sensitive monitoring of ochratoxin A based on an enzyme-controlled citrate-iron(iii) chelating system

Schematic illustration of an enzyme-controlled citrate-iron(iii) chelating system-based colorimetric immunoassay for sensitive determination of ochratoxin A.

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

Parallel Reaction Monitoring Mass Spectrometry Method for Detection of Both Casein and Whey Milk Allergens from a Baked Food Matrix

Milk allergy is among the most common food allergies present in early childhood, which in some cases may persist into adulthood as well. Proteins belonging to both casein and whey fractions of milk can trigger an allergic response in susceptible individuals. Milk is present as an ingredient in many foods, and it can also be present as casein- or whey-enriched milk-derived ingredients. As whey proteins are more susceptible to thermal processing than caseins, conventional methods often posed a challenge in accurate detection of whey allergens, particularly from a processed complex food matrix. In this study, a targeted mass spectrometry method has been developed to detect the presence of both casein and whey allergens from thermally processed foods. A pool of 19 candidate peptides representing four casein proteins and two whey proteins was identified using a discovery-driven target selection approach from various milk-derived ingredients. These target peptides were evaluated by parallel reaction monitoring of baked cookie samples containing known amounts of nonfat dry milk (NFDM). The presence of milk could be detected from baked cookies incurred with NFDM at levels as low as 1 ppm using seven peptides representing α-, β-, and κ-casein proteins and three peptides representing a whey protein, β-lactoglobulin, by this consensus PRM method.

Species-Specific Discrimination of Insect Meals for Aquafeeds by Direct Comparison of Tandem Mass Spectra

Insect protein has the potential to become a sustainable feed ingredient for the rapidly growing aquaculture industry. In the European Union, insect derived protein is placed under the same legislation as processed animal proteins (PAP). It is therefore of interest to develop methods for regulatory use, which unambiguously identify the species origin of insect-based ingredients. We performed (i) total protein quantification of insect samples using the traditional nitrogen-to-protein conversion factor of 6.25 and the sum of anhydrous amino acids, (ii) quantitative amino acid profiling and (iii) high-throughput tandem mass spectrometry to describe and differentiate 18 different commercial-grade insect meal samples derived from Hermetia illucens (8), Tenebrio molitor (5), Alphitobius diaperinus (3) and Acheta domesticus (2). In addition, we investigated and compared different protein extraction and digestion protocols for proteomic analysis. We found that irrespective of sample preparation, shotgun proteomics in combination with direct spectral comparison were able to differentiate insect meal according to their taxonomic classification. The insect specific spectral libraries created in the present work can in future be used to develop more sensitive targeted methods of insect PAP identification and quantification in commercial feed mixtures.

Effect of Cd on growth, physiological response, Cd subcellular distribution and chemical forms of Koelreuteria paniculata

Koelreuteria paniculata were cultivated in nutrient solution with different concentrations of Cd (0, 50, 150, 250 and 500 µM) and sampled after 90 days. The resistance, translocation, accumulation and stress responses in Koelreuteria paniculata were investigated by hydroponic experiments. The results showed that Koelreuteria paniculata is an efficient Cd excluder that can tolerate high concentrations of Cd (up to 150-250 µM of Cd). The concentration of Cd never exceeds 5 ppm in leaves and 10 ppm in roots. The high concentration of Cd (≥ 250 µM) had a toxic effect on K. paniculata and significantly restricted the plant growth. The accumulation ability of Cd by different plant tissues followed the sequence of roots > leaves > stems. The bioconcentration factors and translocation factors both were less than 1. Cd has the highest content in the cell wall and is migrated to soluble fractions and organelles at high concentrations. Undissolved Cd phosphate, pectates and protein-bound Cd were the predominant forms. The low concentration of Cd (≤150 µM) promoted the synthesis of soluble proteins, AsA and GSH, while high concentration of Cd clearly inhibited the physiological and biochemical process, caused membrane lipid peroxidation and severe membrane damages, and increased MDA and H₂O₂ contents. POD, CAT and SOD exhibited positive and effective responses to low concentration Cd stress, but could not remove the toxicity caused by high concentration Cd stress. The content of IAA, GA and ZT decreased and ABA content was significantly increased under high-concentration Cd stress.

An integrated multi-omics analysis of the NK603 Roundup-tolerant GM maize reveals metabolism disturbances caused by the transformation process

Glyphosate tolerant genetically modified (GM) maize NK603 was assessed as 'substantially equivalent' to its isogenic counterpart by a nutrient composition analysis in order to be granted market approval. We have applied contemporary in depth molecular profiling methods of NK603 maize kernels (sprayed or unsprayed with Roundup) and the isogenic corn to reassess its substantial equivalence status. Proteome profiles of the maize kernels revealed alterations in the levels of enzymes of glycolysis and TCA cycle pathways, which were reflective of an imbalance in energy metabolism. Changes in proteins and metabolites of glutathione metabolism were indicative of increased oxidative stress. The most pronounced metabolome differences between NK603 and its isogenic counterpart consisted of an increase in polyamines including N-acetyl-cadaverine (2.9-fold), N-acetylputrescine (1.8-fold), putrescine (2.7-fold) and cadaverine (28-fold), which depending on context can be either protective or a cause of toxicity. Our molecular profiling results show that NK603 and its isogenic control are not substantially equivalent.

Identification of specific bovine blood biomarkers with a non-targeted approach using HPLC ESI tandem mass spectrometry

Animal by-products are valuable protein sources in animal nutrition. Among them are blood products and blood meal, which are used as high-quality material for their beneficial effects on growth and health. Within the framework of the feed ban relaxation, the development of complementary methods in order to refine the identification of processed animal proteins remains challenging. The aim of this study was to identify specific biomarkers that would allow the detection of bovine blood products and processed animal proteins using tandem mass spectrometry. Seventeen biomarkers were identified: nine peptides for bovine plasma powder; seven peptides for bovine haemoglobin powder, including six peptides for bovine blood meal; and one peptide for porcine blood. They were not detected in several commercial compound feed or feed materials, such as blood by-products of other animal origins, milk-derived products and fish meal. These biomarkers could be used for developing a species-specific and blood-specific detection method.

Species and tissues specific differentiation of processed animal proteins in aquafeeds using proteomics tools

The rapidly growing aquaculture industry drives the search for sustainable protein sources in fish feed. In the European Union (EU) since 2013 non-ruminant processed animal proteins (PAP) are again permitted to be used in aquafeeds. To ensure that commercial fish feeds do not contain PAP from prohibited species, EU reference methods were established. However, due to the heterogeneous and complex nature of PAP complementary methods are required to guarantee the safe use of this fish feed ingredient. In addition, there is a need for tissue specific PAP detection to identify the sources (i.e. bovine carcass, blood, or meat) of illegal PAP use. In the present study, we investigated and compared different protein extraction, solubilisation and digestion protocols on different proteomics platforms for the detection and differentiation of prohibited PAP. In addition, we assessed if tissue specific PAP detection was feasible using proteomics tools. All work was performed independently in two different laboratories. We found that irrespective of sample preparation gel-based proteomics tools were inappropriate when working with PAP. Gel-free shotgun proteomics approaches in combination with direct spectral comparison were able to provide quality species and tissue specific data to complement and refine current methods of PAP detection and identification.

SIGNIFICANCE

To guarantee the safe use of processed animal protein (PAP) in aquafeeds efficient PAP detection and monitoring tools are required. The present study investigated and compared various proteomics workflows and shows that the application of shotgun proteomics in combination with direct comparison of spectral libraries provides for the desired species and tissue specific classification of this heat sterilized and pressure treated (≥133°C, at 3bar for 20min) protein feed ingredient.

Proteomics in quality control: Whey protein-based supplements

The growing consumption of nutritional supplements might represent a problem, given the concern about the quality of these supplements. One of the most used supplements is whey protein (WP); because of its popularity, it has been a target of adulteration with substitute products, such as cheaper proteins with lower biological value. To investigate this type of adulteration, this study used shotgun proteomics analyses by MS(E) (multiplexed, low- and high-collision energy, data-independent acquisition) of WP-based supplements. Seventeen WP-based supplement samples were evaluated. Chicken, maize, rice, potato, soybean, and wheat proteins were considered as probable sources of bovine whey adulteration. Collectively, 523 proteins were identified across all 16 samples and replicates, with 94% of peptides inside a normal distribution within 10ppm of maximum error. In 10 of the 16 samples analyzed, only proteins from bovine whey could be detected, while in the other samples several other protein sources were detected in high concentrations, especially soybean, wheat, and rice. These results point out a probable adulteration and/or sample contamination during manufacturing that could only be detected using this proteomic approach.

SIGNIFICANCE

The present work shows how shotgun proteomics can be used to provide reliable answers in quality control matters, especially focusing on Whey Protein nutritional supplements which are a very popular subject in food and nutrition. In order to achieve an appropriate methodology, careful evaluation was performed applying extremely rigorous quality criteria, established for the proteomic analysis. These criteria and the methodological approach used in this work might serve as a guide for other authors seeking to use proteomics in quality control.

Identification of Proteins and Peptide Biomarkers for Detecting Banned Processed Animal Proteins (PAPs) in Meat and Bone Meal by Mass Spectrometry

The outbreak of bovine spongiform encephalopathy (BSE) in the United Kingdom in 1986, with processed animal proteins (PAPs) as the main vector of the disease, has led to their prohibition in feed. The progressive release of the feed ban required the development of new analytical methods to determine the exact origin of PAPs from meat and bone meal. We set up a promising MS-based method to determine the species and the source (legal or not) present in PAPs: a TCA-acetone protein extraction followed by a cleanup step, an in-solution tryptic digestion of 5 h (with a 1:20 protein/trypsin ratio), and mass spectrometry analyses, first without any a priori, with a Q-TOF, followed by a targeted triple-quadrupole analysis. Using this procedure, we were able to overcome some of the major limitations of the official methods to analyze PAPs, detecting and identifying prohibited animal products in feedstuffs by the monitoring of peptides specific for cows, pigs, and sheep in PAPs.

Rapid detection of water buffalo ricotta adulteration or contamination by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

RATIONALE

The improvement and development of novel technologies and analytical tools are an important first line of defence for both detecting and deterring food frauds. In order to protect the authenticity of traditional foods and safeguard geographical indications and traditional specialities at European level, Protected Designation of Origin (PDO) legislation has been introduced as a guarantee of quality (Council Regulation ECC 2081/92). Dairy products, especially those certified as PDO products, are amongst the most common targets of fraudulent activities. Recently, the buffalo ricotta, a dairy product exclusively made with buffalo milk and produced in the same geographical area of most widely known buffalo mozzarella, has gained PDO recognition.

METHODS

In the present work, a fast and simple matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS)-based methodology has been developed for detecting the adulteration or contamination of buffalo ricotta with bovine milk.

RESULTS

We optimized a fast procedure for digesting milk proteins and identified a novel specific proteotypic marker, corresponding to region 149-162 of β-lactoglobulin, as highly diagnostic for the presence of cow milk within ricotta matrices.

CONCLUSIONS

By exploiting the advantages of MALDI-TOFMS, the proposed methodology represents a useful tool for the assessment of buffalo ricotta authenticity and to guarantee the PDO certification against frauds.

Proteomics in food: Quality, safety, microbes, and allergens

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.

Proteomic and metabolic profiles of Cakile maritima Scop. Sea Rocket grown in the presence of cadmium

Recent physiological reports have documented how Cakile maritima Scop. Sea Rocket could accumulate high doses of Cd without altering its physiological parameters. In the present study, we performed an integrated proteomics (2DE) and metabolomics (HPLC-MS) investigation to determine the molecular mechanisms underlying cadmium (Cd) tolerance of this halophyte. Peculiar features were observed: (i) up-regulation of thiol compound anabolism, including glutathione and phytochelatin homeostasis, which allows an intracellular chelation of Cd and its compartmentalization into vacuole by a significant up-regulation of vacuolar transporters; (ii) up-regulation of the PPP and Calvin cycle (both at the enzyme and metabolite level), which utterly promoted the maintenance of NADPH/NADP(+) homeostasis, other than the accumulation of triose-phosphates (serving as anabolic intermediates for triacylglycerol biosynthesis) and the glyoxylate precursor phosphoglycolate, to promote photorespiration and consequently CO2 release. An up-regulation of carbonic anhydrase was also observed. This halophyte is also correlated with a highly efficient antioxidant system, especially a high up-regulation of SOD1, resulting more efficient in coping with heavy metals stress than common plants. Interestingly, exposure to high Cd concentrations partly affected photosystem integrity and metabolic activity, through the up-regulation of enzymes from the Calvin cycle and glutathione-ascorbate homeostasis and PAP3 which stabilizes thylakoid membrane structures. In addition, up-regulation of Peptidyl-prolyl isomerase CYP38 increases stability and biogenesis of PSII. Finally, metabolomics results confirmed proteomics and previous physiological evidence, also suggesting that osmoprotectants, betaine and proline, together with plant hormones, methyl jasmonate and salicylic acid, might be involved in mediating responses to Cd-induced stress. Taken together, these peculiar features confirm that Cakile maritima Scop. Sea Rocket seemed to be naturally equipped to withstand even high doses of Cd pollution.

Omics integrating physical techniques: aged Piedmontese meat analysis

Piedmontese meat tenderness becomes higher by extending the ageing period after slaughter up to 44 days. Classical physical analysis only partially explain this evidence, so in order to discover the reason of the potential beneficial effects of prolonged ageing, we performed omic analysis in the Longissimus thoracis muscle by examining main biochemical changes through mass spectrometry-based metabolomics and proteomics. We observed a progressive decline in myofibrillar structural integrity (underpinning meat tenderness) and impaired energy metabolism. Markers of autophagic responses (e.g. serine and glutathione metabolism) and nitrogen metabolism (urea cycle intermediates) accumulated until the end of the assayed period. Key metabolites such as glutamate, a mediator of the appreciated umami taste of the meat, were found to constantly accumulate until day 44. Finally, statistical analyses revealed that glutamate, serine and arginine could serve as good predictors of ultimate meat quality parameters, even though further studies are mandatory.

Mass spectrometry in food proteomics: a tutorial

In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed.

Application to proteomics to understand and modify meat quality

The use of proteomics in the field of meat science has gained in robustness and accuracy. This is consistent with the genomic and bioinformatic tools. Its application to sensorial and technological meat quality traits is discussed as well as the emergence of sanitary and nutritional issue which will grow in a next future.

It's time to pop a cork on champagne's proteome!

Champagne is a world-renowned French sparkling wine, which undergoes many steps (fermentation, aging …) for its elaboration. Various compounds might evolve during this winemaking process and thus modify its final quality. Here, we report the first proteome analysis of two standard commercial Champagne wines, using the powerful Combinatorial Peptide Ligand Library (CPLL) technique. Indeed, wine proteins are present in small amounts but they are key compounds, likely to impact on both foam quality and aroma behavior. Forty-three unique gene products were retrieved in a single-varietal champagne and a blended champagne. Several proteins from Vitis vinifera together with seven yeast proteins were undoubtedly identified in these Champagne wines.

BIOLOGICAL SIGNIFICANCE

The main advantage of CPLLs was the detection of low abundance proteins despite the absence of purification or pre-concentration step. It is an important fact to take into account, since Champagne wines generally contain a low amount of proteins (5-10mg/L) that implies to usually concentrate wine proteins before 1D or 2D electrophoresis. Most Champagne proteins are grape and yeast glycoproteins which are considered as good foam "promoters". Some of these proteins might also interact with wine aromas, and thus contribute to the overall quality of Champagne wines. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Detection of high molecular weight proteins by MALDI imaging mass spectrometry

MALDI imaging mass spectrometry (IMS) is a unique technology to explore the spatial distribution of biomolecules directly on tissues. It allows the in situ investigation of a large number of small proteins and peptides. Detection of high molecular weight proteins through MALDI IMS still represents an important challenge, as it would allow the direct investigation of the distribution of more proteins involved in biological processes, such as cytokines, enzymes, neuropeptide precursors and receptors. In this work we compare the traditional method performed with sinapinic acid with a comparable protocol using ferulic acid as the matrix. Data show a remarkable increase of signal acquisition in the mass range of 20k to 150k Th. Moreover, we report molecular images of biomolecules above 70k Th, demonstrating the possibility of expanding the application of this technology both in clinical investigations and basic science.

Cadmium stress responses in Brassica juncea: hints from proteomics and metabolomics

Among heavy metal stressors, cadmium (Cd) pollution is one leading threat to the environment. In this view, research efforts have been increasingly put forward to promote the individuation of phytoextractor plants that are capable of accumulating and withstanding the toxic metals, including Cd, in the aerial parts. We hereby adopted the hyperaccumulator B. juncea (Indian mustard) as a model to investigate plant responses to Cd stress at low (25 μM) and high (100 μM) doses. Analytical strategies included mass-spectrometry-based determination of Cd and the assessment of its effect on the leaf proteome and metabolome. Results were thus integrated with routine physiological data. Taken together, physiology results highlighted the deregulation of photosynthesis efficiency, ATP synthesis, reduced transpiration, and the impairment of light-independent carbon fixation reactions. These results were supported at the proteomics level by the observed Cd-dependent alteration of photosystem components and the alteration of metabolic enzymes, including ATP synthase subunits, carbonic anhydrase, and enzymes involved in antioxidant responses (especially glutathione and phytochelatin homeostasis) and the Calvin cycle. Metabolomics results confirmed the alterations of energy-generating metabolic pathways, sulfur-compound metabolism (GSH and PCs), and Calvin cycle. Besides, metabolomics results highlighted the up-regulation of phosphoglycolate, a byproduct of the photorespiration metabolism. This was suggestive of the likely increased photorespiration rate as a means to cope with Cd-induced unbalance in stomatal conductance and deregulation of CO2 homeostasis, which would, in turn, promote CO2 depletion and O2 (and thus oxidative stress) accumulation under prolonged photosynthesis in the leaves from plants exposed to high doses of CdCl2. Overall, it emerges that Cd-stressed B. juncea might rely on photorespiration, an adaptation that would prevent the over-reduction of the photosynthetic electron transport chain and photoinhibition.

Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.

Red blood cell metabolism under prolonged anaerobic storage

Oxygen dependent modulation of red blood cell metabolism is a long investigated issue. However, the recent introduction of novel mass spectrometry-based approaches lends itself to implement our understanding of the effects of red blood cell prolonged exposure to anaerobiosis. Indeed, most of the studies conducted so far have addressed the short term issue, while the limited body of literature covering a 42 days storage period only takes into account a handful of metabolic parameters (ATP, DPG, glucose, glyceraldehyde 3-phosphate, and lactate). We hereby performed a mass spectrometry-based untargeted metabolomics analysis in order to highlight metabolic species in erythrocyte concentrates stored anaerobically in SAGM additive solutions for up to 42 days, by testing cells on a weekly basis. We could confirm previous evidence about long term anaerobiosis promoting glycolytic metabolism in RBCs and prolonging the conservation of high energy phosphate reservoirs and purine homeostasis. In parallel, we evidenced that, in contrast to aerobic storage, anaerobiosis impairs erythrocyte capacity to cope with oxidative stress by blocking metabolic diversion towards the pentose phosphate pathway, which negatively affects glutathione homeostasis. Therefore, although oxidative stress was less sustained than in aerobically stored counterparts, oxidative stress markers still accumulate over anaerobic storage progression.

Foodomics: a new comprehensive approach to food and nutrition

In the past 20 years, the scientific community has faced a great development in different fields due to the development of high-throughput, omics technologies. Starting from the four major types of omics measurements (genomics, transcriptomics, proteomics, and metabolomics), a variety of omics subdisciplines (epigenomics, lipidomics, interactomics, metallomics, diseasomics, etc.) has emerged. Thanks to the omics approach, researchers are now facing the possibility of connecting food components, foods, the diet, the individual, the health, and the diseases, but this broad vision needs not only the application of advanced technologies, but mainly the ability of looking at the problem with a different approach, a "foodomics approach". Foodomics is the comprehensive, high-throughput approach for the exploitation of food science in the light of an improvement of human nutrition. Foodomics is a new approach to food and nutrition that studies the food domain as a whole with the nutrition domain to reach the main objective, the optimization of human health and well-being.

Proteomic evaluation of genetically modified crops: current status and challenges

Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. "Omics" techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques.