Proteomics-Based Methodologies for the Detection and Quantification of Seafood Allergens

Multi-omics Analysis of Volatile Flavor Components in Pacific Chub and Spanish Mackerel during Freezing using GC-MS-O

This study employed gas chromatography-mass spectrometry with olfactory (GC-MS-O) and multi-omics methods to investigate the changes in volatile flavor compounds during the freezing process of Pacific chub mackerel (Scomber japonicus) from Japan and China, and Spanish mackerel (Scomberomorus niphonius). A total of 18 volatile flavor compounds were identified, and significant differences in volatile flavor components were observed among samples frozen for 1 week, 1 year, and 2 years. The results of the Partial least squares regression (PLSR) indicated that the fishy odor was correlated with independent variables such as fatty acids (FA 22:4, FA 28:6, FA 24:4), differentially expressed genes (Gene.2425 (NDUFA5), Gene.38 (GPX1), and Gene.2844 (DAD1)). Classification and regression tree (CART) analysis revealed that the peak area values of fatty acids (FA 22:5, FA 20:4) and fatty acid esters of hydroxy fatty acids (FAHFA 18:0/22:3) were the main differentiating factors for fishy odor perception.

Food allergen analysis: A review of current gaps and the potential to fill them by matrix-assisted laser desorption/ionization

Food allergy remains a public health, business, and regulatory challenge. Risk analysis (RA) and risk management (RM) of food allergens are of great importance and analysis for food allergens is necessary for both. The current workhorse techniques for allergen analysis (enzyme linked immunosorbent assay [ELISA] and real-time polymerase chain reaction) exhibit recognized challenges including variable and antibody specific responses and detection of species DNA rather than allergen protein, respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) enables protein identification, with potential for multiplex analysis and traceability to the System of International units (SI), aiding global measurement standardization. In this review, recent literature has been systematically reviewed to assess progress in LC-MS/MS and define the potential and benefits of matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-ToF-MS) technology for allergen analysis. MALDI-ToF-MS of initially intact protein is already applied to verify in silico-derived peptide sequences for LC-MS/MS analysis. We describe the origins of MALDI and its future perspectives, including affinity bead-assisted assays coupled to MALDI. Based on the proliferation of reliable and reproducible MALDI-based clinical applications, the technique should emulate the detection capability (sensitivity) of established allergen detection techniques, whilst reducing technical support and having equivalent multiplexing potential to competing techniques, for example, LC-MS/MS and ELISA. Although unlikely to offer inherent SI traceability, MALDI-based allergen analysis will complement existing MS approaches for allergens. Affinity bead-MALDI appears capable of higher throughput at lower cost per sample than almost any existing technique, enabling repeated sub-sampling as a way to reduce representative sampling issues.

Cross-reactivity analysis of milk proteins from different goat breeds with cow's milk allergens using a proteomic approach

INTRODUCTION

Goat's milk thought to be a good substitute for cow's milk protein allergic (CMPA) individuals. However, there is growing evidence that their proteins have cross-reactivities with cow's milk allergens. This study aimed to profile and compare milk proteins from different goat breeds that have cross-reactivity to cow's milk allergens.

METHODOLOGY

Proteomics was used to compare protein extracts of skim milk from Saanen, Jamnapari, and Toggenburg. Cow's milk was used as a control. IgE-immunoblotting and mass spectrometry were used to compare and identify proteins that cross-reacted with serum IgE from CMPA patients (n = 10).

RESULTS

The analysis of IgE-reactive proteins revealed that the protein spots identified with high confidence were proteins homologous to common cow's milk allergens such as α-S1-casein (αS1-CN), β-casein (β-CN), κ-casein (κ-CN), and beta-lactoglobulin (β-LG). Jamnapari's milk proteins were found to cross-react with four major milk allergens: α-S1-CN, β-CN, κ-CN, and β-LG. Saanen goat's milk proteins, on the other hand, cross-reacted with two major milk allergens, α-S1-CN and β-LG, whereas Toggenburg goat's milk proteins only react with one of the major milk allergens, κ-CN.

CONCLUSION

These findings may help in the development of hypoallergenic goat milk through cross-breeding strategies of goat breeds with lower allergenic milk protein contents.

Seafood allergy: Allergen, epitope mapping and immunotherapy strategy

Seafoods are fashionable delicacies with high nutritional values and culinary properties, while seafood belongs to worldwide common food allergens. In recent years, many seafood allergens have been identified, while the diversity of various seafood species give a great challenge in identifying and characterizing seafood allergens, mapping IgE-binding epitopes and allergen immunotherapy development, which are critical for allergy diagnostics and immunotherapy treatments. This paper reviewed the recent progress on seafood (fish, crustacean, and mollusk) allergens, IgE-binding epitopes and allergen immunotherapy for seafood allergy. In recent years, many newly identified seafood allergens were reported, this work concluded the current situation of seafood allergen identification and designation by the World Health Organization (WHO)/International Union of Immunological Societies (IUIS) Allergen Nomenclature Sub-Committee. Moreover, this review represented the recent advances in identifying the IgE-binding epitopes of seafood allergens, which were helpful to the diagnosis, prevention and treatment for seafood allergy. Furthermore, the allergen immunotherapy could alleviate seafood allergy and provide promising approaches for seafood allergy treatment. This review represents the recent advances and future outlook on seafood allergen identification, IgE-binding epitope mapping and allergen immunotherapy strategies for seafood allergy prevention and treatment.

Application of proteomics in shrimp and shrimp aquaculture

Since proteins play an important role in the life of an organism, many researchers are now looking at how genes and proteins interact to form different proteins. It is anticipated that the creation of adequate tools for rapid analysis of proteins will accelerate the determination of functional aspects of these biomolecules and develop new biomarkers and therapeutic targets for the diagnosis and treatment of various diseases. Though shrimp contains high-quality marine proteins, there are reports about the heavy losses to the shrimp industry due to the poor quality of shrimp production and many times due to mass mortality also. Frequent outbreaks of diseases, water pollution, and quality of feed are some of the most recognized reasons for such losses. In the seafood export market, shrimp occupies the top position in currency earnings and strengthens the economy of many developing nations. Therefore, it is vital for shrimp-producing companies they produce healthy shrimp with high-quality protein. Though aquaculture is a very competitive market, global awareness regarding the use of scientific knowledge and emerging technologies to obtain better-farmed organisms through sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful tool, has therefore been increasingly used to address several issues in shrimp aquaculture. In the present paper, efforts have been made to address some of them, particularly the role of proteomics in reproduction, breeding and spawning, immunological responses and disease resistance capacity, nutrition and health, microbiome and probiotics, quality and safety of shrimp production, bioinformatics applications in proteomics, the discovery of protein biomarkers, and mitigating biotic and abiotic stresses. Future challenges and research directions on proteomics in shrimp aquaculture have also been discussed.

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Major shrimp allergen peptidomics signatures and potential biomarkers of heat processing

It is important to develop tools that can be used to understand the effects of processing on allergenic foods in order to achieve personalized food labeling. To evaluate the effect of heating on the allergy-relevant structural properties of tropomyosin (TM), arginine kinase (AK), myosin light chain (MLC) and sarcoplasmic calcium-binding protein (SCP) shrimp allergens, trypsin digests of raw, fried and baked shrimp extracts were analyzed by peptidomics and epitope correlations. Processing altered the number of peptides released from the distinct allergens, and each treatment generated a specific epitope-matched peptide allergen fingerprint. Among the four allergens, TM led to a number of released peptides and epitope changes being detected, and AK provided the epitope-matched ³³¹MGLTEFQAVK³⁴⁰ sequence as a common differentiating peptide for heat processing. These results provide new views on the structural effects of processing on major shrimp allergens and peptide candidates as processing biomarkers.

Proteomics of Fish White Muscle and Western Blotting to Detect Putative Allergens

A detailed workflow is provided for preparation from teleost fish white muscle of extracts for proteomics analysis. The protocol generates samples that can be analyzed by SWATH (Sequential Window data independent Acquisition of the Total High-resolution-Mass Spectra), a modern MS-based quantitative label free technology. The main steps for the extraction of three independent protein fractions, (1) soluble sarcoplasmic, (2) soluble myofibrillar, and (3) insoluble material, from fish white muscle are detailed. Coupled to the protein extraction protocol a Western blotting approach is outlined for detection of common fish allergens, in this case β-parvalbumin, in the white muscle sarcoplasmic protein fraction.

The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics

Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.

An overview of tropomyosin as an important seafood allergen: Structure, cross-reactivity, epitopes, allergenicity, and processing modifications

Tropomyosin (TM) is a major allergen in crustaceans, which often causes allergy and is fatal to some consumers. Currently, the most effective treatment is to avoid ingesting TM, although most adverse events occur in accidental ingestion. In this review, the molecular characterization, epitopes, cross-reactivity, and pathogenesis of TM are introduced and elucidated. Modification of TM by traditional processing methods such as heat treatment and enzymatic hydrolysis, and innovative processing technologies including high-pressure treatment, cold plasma (CP), ultrasound, pulsed electric field (PEF), pulsed ultraviolet, microwave and irradiation are discussed in detail. Particularly, enzymolysis, PEF, and CP technologies show great potential for modifying TM and more studies are needed to verify their effectiveness for the seafood industry. Possible mechanisms and the advantages/disadvantages of these technologies for the mitigation of TM allergenicity are also highlighted. Further work should be conducted to investigate the allergenicity caused by protein segments such as epitopes, examine the interaction sites between the allergen and the processing techniques and reveal the reduction mechanism of allergenicity.

Aptamer-Based Fluorescent Biosensor for the Rapid and Sensitive Detection of Allergens in Food Matrices

Food allergies have seriously affected the life quality of some people and even endangered their lives. At present, there is still no effective cure for food allergies. Avoiding the intake of allergenic food is still the most effective way to prevent allergic diseases. Therefore, it is necessary to develop rapid, accurate, sensitive, and reliable analysis methods to detect food allergens from different sources. Aptamers are oligonucleotide sequences that can bind to a variety of targets with high specificity and selectivity, and they are often combined with different transduction technologies, thereby constructing various types of aptamer sensors. In recent years, with the development of technology and the application of new materials, the sensitivity, portability, and cost of fluorescence sensing technology have been greatly improved. Therefore, aptamer-based fluorescence sensing technology has been widely developed and applied in the specific recognition of food allergens. In this paper, the classification of major allergens and their characteristics in animal and plant foods were comprehensively reviewed, and the preparation principles and practical applications of aptamer-based fluorescence biosensors are summarized. In addition, we hope that this article can provide some strategies for the rapid and sensitive detection of allergens in food matrices.

DNA, protein and aptamer-based methods for seafood allergens detection: Principles, comparisons and updated applications

The increasing number of people with seafood allergy has caused a series of problems for practitioners and consumers in the seafood industry year by year. Thereby, development of efficient, convenient and low-cost allergen detection methods is urgently needed. This review introduces three important existing seafood allergen detection methods associated with DNA-based, protein-based and aptamer-based. Their principles and biological characteristics are firstly presented. The core of these three methods are DNA amplification techniques, specific binding of antigens and antibodies, and specific binding of aptamers and ligands, respectively. Among them, DNA-based detection method is an indirect analysis, which takes the gene of allergen as the detection object and is characterized by good stability and high sensitivity. Protein-based and aptamer-based, methods employ indirect analysis for allergen detection. The difference is that the latter uses an easily synthesized and highly efficient aptamer as the detection probe, showing great promising potentials. The advantages and disadvantages of the three mentioned detection methods are also discussed. In the future, as more efficient and reliable detection methods for seafood allergens come into practice, the possibility of seafood allergy patients eating seafood products by mistake will be greatly reduced, which will ensure the food safety and the health of allergy patients.

Untargeted Proteomics-Based Approach to Investigate Unintended Changes in Genetically Modified Maize for Environmental Risk Assessment Purpose

Profiling technologies, such as proteomics, allow the simultaneous measurement and comparison of thousands of plant components without prior knowledge of their identity. The combination of these non-targeted methods facilitates a more comprehensive approach than targeted methods and thus provides additional opportunities to identify genotypic changes resulting from genetic modification, including new allergens or toxins. The purpose of this study was to investigate unintended changes in GM Bt maize grown in South Africa. In the present study, we used bi-dimensional gel electrophoresis based on fluorescence staining, coupled with mass spectrometry in order to compare the proteome of the field-grown transgenic hybrid (MON810) and its near-isogenic counterpart. Proteomic data showed that energy metabolism and redox homeostasis were unequally modulated in GM Bt and non-GM maize variety samples. In addition, a potential allergenic protein-pathogenesis related protein -1 has been identified in our sample set. Our data shows that the GM variety is not substantially equivalent to its non-transgenic near-isogenic variety and further studies should be conducted in order to address the biological relevance and the potential risks of such changes. These finding highlight the suitability of unbiased profiling approaches to complement current GMO risk assessment practices worldwide.