Characterization of Mustard 2S Albumin Allergens by Bottom-up, Middle-down, and Top-down Proteomics: A Consensus Set of Isoforms of Sin a 1

Food allergen detection by mass spectrometry: From common to novel protein ingredients

Food allergens are molecules, mainly proteins, that trigger immune responses in susceptible individuals upon consumption even when they would otherwise be harmless. Symptoms of a food allergy can range from mild to acute; this last effect is a severe and potentially life-threatening reaction. The European Union (EU) has identified 14 common food allergens, but new allergens are likely to emerge with constantly changing food habits. Mass spectrometry (MS) is a promising alternative to traditional antibody-based assays for quantifying multiple allergenic proteins in complex matrices with high sensitivity and selectivity. Here, the main allergenic proteins and the advantages and drawbacks of some MS acquisition protocols, such as multiple reaction monitoring (MRM) and data-dependent analysis (DDA) for identifying and quantifying common allergenic proteins in processed foodstuffs are summarized. Sections dedicated to novel foods like microalgae and insects as new sources of allergenic proteins are included, emphasizing the significance of establishing stable marker peptides and validated methods using database searches. The discussion involves the in-silico digestion of allergenic proteins, providing insights into their potential impact on immunogenicity. Finally, case studies focussing on microalgae highlight the value of MS as an effective analytical tool for ensuring regulatory compliance throughout the food control chain.

A systematic review on the recent advances of wheat allergen detection by mass spectrometry: future prospects

Wheat is one of the three major staple foods in the world. Although wheat is highly nutritional, it has a variety of allergenic components that are potentially fatal to humans and pose a significant hazard to the growth and consumption of wheat. Wheat allergy is a serious health problem, which is becoming more and more prevalent all over the world. To address and prevent related health risks, it is crucial to establish precise and sensitive detection and analytical methods as well as an understanding of the structure and sensitization mechanism of wheat allergens. Among various analytical tools, mass spectrometry (MS) is known to have high specificity and sensitivity. It is a promising non immune method to evaluate and quantify wheat allergens. In this article, the current research on the detection of wheat allergens based on mass spectrometry is reviewed. This review provides guidance for the further research on wheat allergen detection using mass spectrometry, and speeds up the development of wheat allergen research in China.

Isolation of the mustard Napin protein Allergen Sin a 1 and characterisation of its antifungal activity

Proteins and peptides belonging to the plant immune system can possess natural antibacterial, antifungal and antiviral properties. Due to their broad range of activity and stability, they represent promising novel alternatives to commonly used antifungal agents to fight the emergence of resistant strains. An isolation protocol was optimised to target proteins found in plants’ defence system, and it was applied to white mustard (Brassica hirta) seeds. Firstly, a ∼14 kDa protein with activity against S. cerevisiae was extracted and purified; secondly, the protein was identified as the mustard Napin protein named Allergen Sin a 1. Napin is the name given to seed storage (2S) albumin proteins belonging to the Brassicaceae family. While several Napins have been described for their antimicrobial potential, Sin a 1 has been mainly studied for its allergenic properties. The antimicrobial activity of Sin a 1 is described and characterised for the first time in this study; it possesses antifungal and antiyeast in vitro activity, but no antibacterial activity was recorded. The yeasts Zygosaccharomyces bailii Sa 1403 and Saccharomyces cerevisiae DSM 70449 along with the filamentous fungi Fusarium culmorum FST 4.05 were amongst the most senstitive strains to Sin a 1 (MICs range 3–6 μM). The antimicrobial mechanism of membrane permeabilisation was detected, and in general, the antifungal activity of Sin a 1 seemed to be expressed in a dose-dependent manner. Data collected confirmed Sin a 1 to be a stable and compact protein, as it displayed resistance to α-chymotrypsin digestion, heat denaturation and insensitivity to pH variations and the presence of salts. In addition, the protein did not show cytotoxicity towards mammalian cells.

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Simple purification of an antiyeast protein from white mustard seeds.

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Identification of the protein as the mustard Napin also classified as Allergen Sin a 1.

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Description of Sin a 1 antimicrobial spectrum and mode of actions against yeasts.

New applications of advanced instrumental techniques for the characterization of food allergenic proteins

Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Identification, characterization and epitope mapping of proteins encoded by putative allergenic napin genes from Brassica rapa

BACKGROUND

Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans.

OBJECTIVE

To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins.

METHODS

To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity.

RESULTS

Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens.

CONCLUSION

Napin is thought to be responsible for a  high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.

Identification and characterization of major IgE binding of purified allergenic protein (11 kDa) from Buchanania lanzan

Tree nut along with peanut are among the most potent food allergens, responsible for frequently inducing the IgE-mediated hypersensitivity reaction. Our aim was identification, purification of Buchanania lanzan (Bl-11 kDa) protein along with characterization and assessment of allergenic potential of clinically relevant allergen. Further study was executed in clinical samples of sensitive patients, BALB/c mice, and in-vitro. A major IgE binding 11-kDa protein from Buchanania lanzan was purified by anion exchange chromatography, reverse phase high pressure liquid chromatography (RP-HPLC) and characterized using peptide mass fingerprinting (PMF). Buchanania lanzan (Bl-11 kDa) protein shows the pepsin resistance and depicts IgE interacting capacity to Buchanania lanzan allergic patient's sera as well as sensitized mice sera. It also showed increase in the allergic mediator's like IgE, IgG1, histamine levels in sensitized mice sera. Further study was carried out in-vitro (RBL-2H3 cells) and increased release mast cell degranulation mediators such as β-hexosaminidase, histamine, CysL and PGD2 in the culture supernatant was found. The activation of Th2 cytokines/transcription factors and expression of molecular markers in the downstream of mast cell signaling were up-regulated while the Th1 transcriptional factor (T-bet) was decreased in Bl-11 kDa protein treated mice. Conclusively, our study demonstrates Buchanania lanzan purified protein to be potential allergen that may generate an allergic reaction in sensitized individuals, and one of the most important IgE binding protein responsible for its allergenicity.

Detection and identification of allergens from Canadian mustard varieties of Sinapis alba and Brassica juncea

Currently, information on the allergens profiles of different mustard varieties is rather scarce. Therefore, the objective of this study was to assess protein profiles and immunoglobulin E (IgE)-binding patterns of selected Canadian mustard varieties. Optimization of a non-denaturing protein extraction from the seeds of selected mustard varieties was first undertaken, and the various extracts were quantitatively and qualitatively analyzed by means of protein recovery determination and protein profiling. The IgE-binding patterns of selected mustard seeds extracts were assessed by immunoblotting using sera from mustard sensitized and allergic individuals. In addition to the known mustard allergens—Sin a 2 (11S globulins), Sin a 1, and Bra j 1 (2S albumins)—the presence of other new IgE-binding protein bands was revealed from both Sinapis alba and Brassica juncea varieties. Mass spectrometry (MS) analysis of the in-gel digested IgE-reactive bands identified the unknown ones as being oleosin, β-glucosidase, enolase, and glutathione-S transferase proteins. A bioinformatic comparison of the amino acid sequence of the new IgE-binding mustard proteins with those of know allergens revealed a number of strong homologies that are highly relevant for potential allergic cross-reactivity. Moreover, it was found that Sin a 1, Bra j 1, and cruciferin polypeptides exhibited a stronger IgE reactivity under non-reducing conditions in comparison to reducing conditions, demonstrating the recognition of conformational epitopes. These results further support the utilization of non-denaturing extraction and analysis conditions, as denaturing conditions may lead to failure in the detection of important immunoreactive epitopes.

Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.

Characterization and Detection of Food Allergens Using High-Resolution Mass Spectrometry: Current Status and Future Perspective

Allergic reactions to food are among the major food safety concerns in industrialized countries, and it is estimated that approximately 5% of the population suffers from immunoglobulin-E-mediated food allergy. High-resolution mass spectrometry has become one of the most important techniques for the molecular characterization of allergens, including structural modification, degradation in the gastrointestinal environment, or identification of suitable marker peptides for the development of novel analytical approaches, in the past decade. This perspective aims to briefly summarize the current situation and discuss future developments.

Current (Food) Allergenic Risk Assessment: Is It Fit for Novel Foods? Status Quo and Identification of Gaps

Food allergies are recognized as a global health concern. In order to protect allergic consumers from severe symptoms, allergenic risk assessment for well-known foods and foods containing genetically modified ingredients is installed. However, population is steadily growing and there is a rising need to provide adequate protein-based foods, including novel sources, not yet used for human consumption. In this context safety issues such as a potential increased allergenic risk need to be assessed before marketing novel food sources. Therefore, the established allergenic risk assessment for genetically modified organisms needs to be re-evaluated for its applicability for risk assessment of novel food proteins. Two different scenarios of allergic sensitization have to be assessed. The first scenario is the presence of already known allergenic structures in novel foods. For this, a comparative assessment can be performed and the range of cross-reactivity can be explored, while in the second scenario allergic reactions are observed toward so far novel allergenic structures and no reference material is available. This review summarizes the current analytical methods for allergenic risk assessment, highlighting the strengths and limitations of each method and discussing the gaps in this assessment that need to be addressed in the near future.

Complete Characterization of Cardiac Myosin Heavy Chain (223 kDa) Enabled by Size-Exclusion Chromatography and Middle-Down Mass Spectrometry

Myosin heavy chain (MHC), the major component of the myosin motor molecule, plays an essential role in force production during muscle contraction. However, a comprehensive analysis of MHC proteoforms arising from sequence variations and post-translational modifications (PTMs) remains challenging due to the difficulties in purifying MHC (∼223 kDa) and achieving complete sequence coverage. Herein, we have established a strategy to effectively purify and comprehensively characterize MHC from heart tissue by combining size-exclusion chromatography (SEC) and middle-down mass spectrometry (MS). First, we have developed a MS-compatible SEC method for purifying MHC from heart tissue with high efficiency. Next, we have optimized the Glu-C, Asp-N, and trypsin limited digestion conditions for middle-down MS. Subsequently, we have applied this strategy with optimized conditions to comprehensively characterize human MHC and identified β-MHC as the predominant isoform in human left ventricular tissue. Full sequence coverage based on highly accurate mass measurements has been achieved using middle-down MS combining 1 Glu-C, 1 Asp-N, and 1 trypsin digestion. Three different PTMs: acetylation, methylation, and trimethylation were identified in human β-MHC and the corresponding sites were localized to the N-terminal Gly, Lys34, and Lys129, respectively, by electron capture dissociation (ECD). Taken together, we have demonstrated this strategy is highly efficient for purification and characterization of MHC, which can be further applied to studies of the role of MHC proteoforms in muscle-related diseases. We also envision that this integrated SEC/middle-down MS strategy can be extended for the characterization of other large proteins over 200 kDa.

Structural Characterization of the Allergenic 2S Albumin Cor a 14: Comparing Proteoform Patterns across Hazelnut Cultivars

The hazelnut allergen Cor a 14 belongs to the 2S albumins, a family of heterodimeric seed storage proteins exhibiting a high degree of structural diversity. Given its relevance as an allergen and the potential to elicit severe reactions, elucidation of the sequence heterogeneity of naturally occurring Cor a 14 is essential for the development of reliable diagnostics and risk evaluation. We therefore performed a comprehensive survey on the proteoforms of Cor a 14 and determined their quantitative distribution in three different hazelnut cultivars by a combinatory HPLC-HRMS approach including bottom-up and intact mass analysis. Compared with the Cor a 14 prototype sequence, we identified three sequence polymorphisms, two of the small and one of the large subunit, and elucidated their specific pairing on the protein level. Furthermore, we located a pronounced microheterogeneity on the protein termini and, for the first time, provide data on varying proteoform patterns between different cultivars of an allergenic seed. Together, these data present the basis for a more detailed investigation on the allergenicity of Cor a 14 in different cultivars and constitute, to be best of our knowledge, the largest set of proteoforms so far reported for a 2S albumin.

Progress in Top-Down Proteomics and the Analysis of Proteoforms

From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.

A tripartite approach identifies the major sunflower seed albumins

We have used a combination of genomic, transcriptomic, and proteomic approaches to identify the napin-type albumin genes in sunflower and define their contributions to the seed albumin pool. Seed protein content is determined by the expression of what are typically large gene families. A major class of seed storage proteins is the napin-type, water soluble albumins. In this work we provide a comprehensive analysis of the napin-type albumin content of the common sunflower (Helianthus annuus) by analyzing a draft genome, a transcriptome and performing a proteomic analysis of the seed albumin fraction. We show that although sunflower contains at least 26 genes for napin-type albumins, only 15 of these are present at the mRNA level. We found protein evidence for 11 of these but the albumin content of mature seeds is dominated by the encoded products of just three genes. So despite high genetic redundancy for albumins, only a small sub-set of this gene family contributes to total seed albumin content. The three genes identified as producing the majority of sunflower seed albumin are potential future candidates for manipulation through genetics and breeding.

Simple, Rapid, and Selective Isolation of 2S Albumins from Allergenic Seeds and Nuts

The 2S albumins belong to the group of seed storage proteins present in different seeds and nuts. Due to their pronounced allergenic potential, which is often associated with severe allergic reactions, this protein family is of special interest in the field of allergen research. Here we present a simple, rapid, and selective method for the purification of 2S albumins directly from allergenic seeds and nuts. We systematically optimized the parameters "buffer system", "extraction temperature", "buffer molarity", and "pH " and were able to achieve 2S albumin purities of about 99% without further purification and demonstrate transferability of this method to nine different allergenic food matrices. Compared to conventional isolation routines, significant reduction of hands-on time and required laboratory equipment is achieved, but nonetheless higher protein yields are obtained. The presented method allows for the rapid purification of different 2S albumins including the corresponding isoforms from natural material.