An assessment of the impact of extraction and digestion protocols on multiplexed targeted protein quantification by mass spectrometry for egg and milk allergens

Quantifying allergenic proteins using antibody-based methods or liquid chromatography-mass spectrometry/mass spectrometry: A review about the influence of food matrix, extraction, and sample preparation

Accurate quantification of allergens in food is crucial for ensuring consumer safety. Pretreatment steps directly affect accuracy and efficiency of allergen quantification. We systematically reviewed the latest advances in pretreatment steps for antibody-based methods and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) protein quantification methods in food. For antibody-based methods, the effects induced by food matrix like decreased allergen solubility, epitope masking, and nonspecific binding are of the upmost importance. To mitigate interference from the matrix, effective and proper extraction can be used to obtain the target allergens with a high protein concentration and necessary epitope exposure. Removal of interfering substances, extraction systems (buffers and additives), assistive technologies, and commercial kits were discussed. About LC-MS/MS quantification, the preparation of the target peptides is the crucial step that significantly affects the efficiency and results obtained from the MS detector. The advantages and limitations of each method for pre-purification, enzymatic digestion, and peptide desalting were compared. Additionally, the application characteristics of microfluidic-based pretreatment devices were illustrated to improve the convenience and efficiency of quantification. A promising research direction is the targeted development of pretreatment methods for complex food matrices, such as lipid-based and carbohydrate-based matrices.

Food allergen analysis: Considerations for establishing a reference measurement system to implement EU legislation

Inconsistent quantification results obtained from various analytical methods for food allergen testing hamper an accurate quantitative risk assessment and its regulatory implementation. In order to overcome such problems, a concept aiming at ensuring the comparability of quantitative food allergen measurement results is presented here. It is based on an approach called reference measurement system for food allergens, which uses a commonly agreed reference, namely the 'mass fraction of total protein of the allergenic ingredient in food'. The necessary system components are outlined, consisting of a primary reference measurement method, a certified reference material and a reference laboratory. This metrology-based concept can be applied to quantify various food allergens determined with different analytical procedures. The example of 'milk in cookies' is used to demonstrate the approach.

Quality Control—A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome

Proteomic studies using mass spectrometry (MS)-based quantification are a main approach to the discovery of new biomarkers. However, a number of analytical conditions in front and during MS data acquisition can affect the accuracy of the obtained outcome. Therefore, comprehensive quality assessment of the acquired data plays a central role in quantitative proteomics, though, due to the immense complexity of MS data, it is often neglected. Here, we address practically the quality assessment of quantitative MS data, describing key steps for the evaluation, including the levels of raw data, identification and quantification. With this, four independent datasets from cerebrospinal fluid, an important biofluid for neurodegenerative disease biomarker studies, were assessed, demonstrating that sample processing-based differences are already reflected at all three levels but with varying impacts on the quality of the quantitative data. Specifically, we provide guidance to critically interpret the quality of MS data for quantitative proteomics. Moreover, we provide the free and open source quality control tool MaCProQC, enabling systematic, rapid and uncomplicated data comparison of raw data, identification and feature detection levels through defined quality metrics and a step-by-step quality control workflow.

Discovery of marker peptides of spirulina microalga proteins for allergen detection in processed foodstuffs

Spirulina (Arthrospira platensis) proteins were extracted, digested, and analyzed by LC-ESI-FTMS/MS to find highly conserved peptides as markers of the microalga occurrence in foodstuffs. Putative markers were firstly chosen after in silico digestion of allergenic proteins, according to the FAO and WHO criteria, after assuring their presence in food supplements and in (un)processed foodsuffs. Parameters such as sensitivity, sequence size, and uniqueness for spirulina proteins were also evaluated. Three peptides belonging to C-phycocyanin beta subunit (P72508) were designated as qualifiers (ETYLALGTPGSSVAVGVGK and YVTYAVFAGDASVLEDR) and quantifier (ITSNASTIVSNAAR) marker peptides and used to validate the method for linearity, recovery, reproducibility, matrix effects, processing effects, LOD, and LOQ. The main aim was to determine spirulina in commercial foodstuffs like pasta, crackers, and homemade bread incurred with the microalga. The possible inclusion of the designated peptides in a standardized method, based on multiple reaction monitoring using a linear ion trap MS, was also demonstrated.

Assignment of a Reference Value of Total Cow’s Milk Protein Content in Baked Cookies Used in an Interlaboratory Comparison

Interlaboratory comparisons (ILC) in the food allergens field mainly rely on the use of consensus values per applied methodology or even per type of an ELISA test kit. Results suggest good reproducibility; however, possible biases may not be recognized since metrological traceability to an independent reference is lacking. The work presented here utilizes isotope dilution mass spectrometry (IDMS) to assign a reference value of the total cow’s milk protein (TCMP) content in a baked cookie and its associated uncertainty. TCMP consists of several individual proteins, of which five (representing 92%) served us as markers for TCMP. Per marker, one to four proteotypic peptides were selected for the quantification. These were synthesized, and the mass fractions of respective reference solutions were determined with peptide-impurity-corrected amino acid analysis to establish traceability to SI units. Stable isotope labelled (“heavy”) analogues of the proteotypic peptides were also synthesized and blended with extracts of the test material or the reference solutions for IDMS. Through careful measurement design minimizing biases, well-defined model equations were developed, allowing appropriate estimation of the associated uncertainty. The determined reference value of 11.8 ± 1.1 mg TCMP/kg cookie was used for scoring of a novel ILC.

Up-regulation of ribosomal and carbon metabolism proteins enhanced pyrene biodegradation in fulvic acid-induced biofilm system

The polycyclic aromatic hydrocarbons (PAHs) that enter the aqueous phase usually coexist with fulvic acid (FA). Therefore, we initiated this investigation to explore the influences of FA on bacterial biofilm formation and its potential to biodegrade pyrene (PYR), using electron microscopic techniques and isobaric tags for relative and absolute quantification (iTRAQ). Our results revealed that FA stimulated biofilm formation and enhanced the biodegradation of PYR. First, FA favored the three-dimensional proliferation of bacteria, with an OD590/OD600 value of up to 14.78, and the extracellular surfaces covered by a layer of biomaterials. Distinctive intracellular morphologies of texture and organization were accompanied by reduced inter-bacterial distances of less than 0.31 μm. The biofilms formed displayed interactions between FA and surficial proteins, as noted by band shifts for the C-O and CO groups. Strikingly, FA triggered the upregulation of 130 proteins that were either operational in biofilm formation or in metabolic adjustments; with the changes supported by the increasing intensity of free amino acids and the newly generated N-O bonds. The results above revealed that the enhanced biodegradation was related to the up-regulation of the proteins functioned for ribosomal and carbon metabolism, and the ultra-structural changes in FA-induced biofilm system.

Monitoring the carryover of egg proteins in pasta making to support allergen risk management

Egg proteins are among the major food allergens. Very often, the same pasta-making plants are used for industrial production of egg-based pasta (EBP) and semolina-only pasta (SP), so that residual egg proteins may be present in SP. This calls for defining the amount of semolina pasta that should be discarded when switching production lines. In this study, the egg proteins content was measured in pasta samples taken at various times after switching production lines from EBP to SP Both long and short pasta shapes were sampled before and after a drying step. Protocols meant to circumvent the difficulties associated with detecting egg proteins in a complex matrix after processing were set up for using commercial ELISA kits to monitor the disappearance of egg proteins from the products. The use of both denaturants and disulphide reductants to solubilise egg proteins was found to be mandatory, as verified by ovalbumin detection by ELISA and by using mass spectrometry to assess residual egg white lysozyme. Appropriate sample preparation protocols were used to monitor the progressive disappearance of egg proteins in the products when shifting production lines in an industrial pasta plant, providing a basis for credible, reliable, and consistent self-control procedures. For lines with a production capacity of 2200-2400 kg h^-1, the amount of material to be discarded to ensure that products meet the strictest analytical requirements has been found to be around 2000-3000 kg (for long pasta) and 3000-4000 kg (for short pasta).

Milk Ingredients in Meat Products: Can Autoclaving and In Vitro Gastroduodenal Digestion Mitigate Their IgE-Binding Capacity?

The food industry commonly uses milk ingredients as technological aids in an uncounted number of products. On the other hand, milk contains allergenic proteins causing adverse allergic reactions in sensitized/allergic individuals. This work intends to evaluate the effect of autoclaving and in vitro digestion on the allergenicity of milk proteins incurred in meat products. Protein profiles of raw and autoclaved sausages without and with the addition of 10% of milk protein concentrates were analyzed by gel electrophoresis and liquid chromatography–mass spectrometry. Additionally, residual IgE-reactivity was evaluated by immunoblot analysis using pooled sera of cow’s-milk-allergic individuals followed by bioinformatic analysis. Results showed that autoclaving led to an increase in protein fragmentation (higher number of short peptides) and consequently to a higher digestion rate, that was found to be more pronounced in β-casein. The IgE-binding capacity of milk proteins seems to be reduced after autoclaving prior to digestion, with a residual reactivity in caseins, but was eliminated following digestion. This study highlights the importance of autoclaving as a processing strategy to produce hypoallergenic formulas.

Development of a sample preparation approach for the analysis of fining agents in wines by liquid chromatography with tandem mass spectrometry

During winemaking a wide variety of processing aids such as albumin, caseinates and lysozyme are often used. These proteins are considered allergenic and could become a human health risk in susceptible individuals. In our knowledge, there are no methods published for the analysis of these three proteins simultaneously by liquid chromatography with tandem mass spectrometry, with electrospray ionization. Therefore, in this work, a sample preparation approach for the analysis of α-casein, β-casein, albumin and lysozyme, in a single run, was performed and compared with published data. Through a pH adjustment, combining the use of cellulose ester membranes, a precipitation with organic solvents and a final concentration/clean-up, we achieved recovery values from 90.7 to 108.6%. The method was validated, showing determination coefficients R² ≥ 0.99. This method was able to quantify proteins even at lower levels (limits of quantification from 0.01 to 0.25 mg/L) than the current legal limits.

A reference method for determining the total allergenic protein content in a processed food: the case of milk in cookies as proof of concept

The establishment of a reference method for the determination of the allergen protein content in a processed food material has been explored. An analytical approach was developed to enable the comparability of food allergen measurement results expressed in a decision-relevant manner. A proof of concept is here presented, resulting in quantity values for the common measurand, namely 'mass of total allergen protein per mass of food'. The quantities are determined with SI traceability to enable the comparability of reported results. A method for the quantification of total milk protein content in an incurred baked food at a concentration level clinically relevant is presented. The strategy on how to obtain the final analytical result is outlined. Challenges associated with this method are discussed, in particular the optimal extraction of the marker proteins, the complete digestion and release of the peptides in an equimolar fashion, the use of conversion factors to translate the amount of measured proteins into total milk protein and the estimation of the uncertainty contributions as well as of the combined uncertainty of the final result. The implementation of such a reference method for the determination of the total allergen content in a processed food is an important step, which will provide comparable measurement data of relevance to risk assessors. Graphical abstract.

Discovery based high resolution MS/MS analysis for selection of allergen markers in chocolate and broth powder matrices

Peptide marker identification is an important step in development of a mass spectrometry method for multiple allergen detection, since specificity, robustness and sensitivity of the overall analytical method will depend on the reliability of the proteotypic peptides. As part of the development of a multi-analyte reference method, discovery analysis of two incurred food matrices has been undertaken to select the most reliable peptide markers. Six allergenic ingredients (milk, egg, peanut, soybean, hazelnut, and almond) were incurred into either chocolate or broth powder matrix. Different conditions of protein extraction and purification were tested and the tryptic peptide pools were analysed by untargeted high resolution tandem mass spectrometry and the resulting fragmentation spectra were processed via a commercial software for sequence identification. The analysis performed on incurred foods provides both a prototype effective and straightforward sample preparation protocol and delivers reliable peptides to be included in a standardized selected reaction monitoring method.

Comparative study of concatemer efficiency as an isotope-labelled internal standard for allergen quantification

Mass spectrometry-based methods coupled with stable isotope dilution have become effective and widely used methods for the detection and quantification of food allergens. Current methods target signature peptides resulting from proteolytic digestion of proteins of the allergenic ingredient. The choice of appropriate stable isotope-labelled internal standard is crucial, given the diversity of encountered food matrices which can affect sample preparation and analysis. We propose the use of concatemer, an artificial and stable isotope-labelled protein composed of several concatenated signature peptides as internal standard. With a comparative analysis of three matrices contaminated with four allergens (egg, milk, peanut, and hazelnut), the concatemer approach was found to offer advantages associated with the use of labelled proteins, ideal but unaffordable, and circumvent certain limitations of traditionally used synthetic peptides as internal standards. Although used in the proteomic field for more than a decade, concatemer strategy has not yet been applied for food analysis.

LC-HRMS/MS for the simultaneous determination of four allergens in fish and swine food products

The inclusion on the label of packed foods of any ingredient or technological adjuvant causing allergies is required by EU food legislation. In this study a targeted proteomics method for detecting four allergens in animal-derived food matrices was developed. Liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS/MS) was used to select marker peptides from four allergens and develop a quantitative method able to simultaneously detect the presence of milk, egg, crustaceans and soy. The method was validated on fish or swine processed food products contaminated at 5 μg g^-1 for milk and egg and 10 μg g^-1 for soy and crustaceans. The method was tested by analyzing commercial food products with high protein content and was compared to the ELISA technique. Our results indicated the presence of soy not reported on the food label of some products, pointing out the need for efficient controls to protect allergic consumers.