How processing affects marker peptide quantification - A comprehensive estimation on bovine material relevant for food and feed control

Processing food and feed challenges official control e.g. by modifying proteins, which leads to significant underestimation in targeted, MS-based protein quantification. Whereas numerous studies identified processing-induced changes on proteins in various combinations of matrices and processing conditions, studying their impact semi-quantitatively on specific protein sequences might unveil approaches to improve protein quantification accuracy. Thus, 335 post-translational modifications (e.g. oxidation, deamidation, carboxymethylation, Amadori, acrolein adduction) were identified by bottom-up proteomic analysis of 37 bovine materials relevant in food and feed (meat, bone, blood, milk) with varying processing degrees (raw, spray-dried, pressure-sterilized). To mimic protein recovery in a targeted analysis, peak areas of marker and reference peptides were compared to those of their modified versions, which revealed peptide-specific recoveries and variances across all samples. Detailed analysis suggests that incorporating two modified versions additionally to the unmodified marker may significantly improve quantification accuracy in targeted MS-based food and feed control in processed matrices.

The effect of heat treatment on the lactosylation of milk proteins

Protein lactosylation is a significant modification that occurs during the heat treatment of dairy products, causing changes in proteins' physical-chemical and nutritional properties. Knowledge of the detailed lactosylation information on milk proteins under various heat treatments is important for selecting appropriate thermo-processing and identifying markers to monitor heat load in dairy products. In the present study, we used proteomics techniques to investigate lactosylated proteins under different heating temperatures. We observed a total of 123 lactosylated lysines in 65 proteins, with lactosylation even occurring in raw milk. The number of lactosylated lysines and proteins increased moderately at 75°C to 130°C, but dramatically at 140°C. We found that 6 out of 10, 9 out of 16, 6 out of 12, and 5 out of 15 lysine residues in κ-casein, β-lactoglobulin, α-lactalbumin, and αS1-casein, respectively, were lactosylated under the applied heating treatment. Moreover, different lactosylation states of individual lysines and proteins can indicate the intensity of heating processes. Lactosylation of K14 in β-lactoglobulin could distinguish pasteurized and UHT milk, while lactosylation of lactotransferrin can reflect moderate heat treatment of products.

Cross-linking reactions in food proteins and proteomic approaches for their detection

Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.

Online trypsin digestion coupled with LC-MS/MS for detecting of A1 and A2 types of β-casein proteins in pasteurized milk using biomarker peptides

Bovine A1-or A2-type β-caseins have attracted a growing interest due to their variation in beta-casomorphin-7 (BCM-7) formation, which may affect health. In the present work, identification and quantification of A1 and A2 types of β-casein proteins at the peptide level was achieved for the first time. An automated and online immobilized trypsin digestion system was employed for high throughput digesting of proteins into peptides. Tryptic peptides were separated and analyzed subsequently by liquid chromatography coupled to mass spectrometry platform. Two specific peptides ranging from the position of 49 to 97 in the peptide chain were selected for the identification and quantification of A1 and A2 β-casein, which covered the different amino acids between them. Synthetic isotopically labeled winged peptides were used for absolute quantification. Compared with traditional in-solution digestion, online digestion shortens digestion times from 2 to 24 h to 4 min. The limits of quantification (LOQ) of A1 and A2 β-casein in pasteurized milk are 0.8 and 2.4 µg/g, respectively. To further demonstrate the applicability of the proposed method, commercial pasteurized milk tests were performed with satisfactory results.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13197-022-05376-6.

Comprehensive Profiling of the Native and Modified Peptidomes of Raw Bovine Milk and Processed Milk Products

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from α_S- and β-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of β-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from α_S-caseins. The numbers of lactosylated peptides increased with harsher processing.

Profiling of Low-Molecular-Weight Carbonyls and Protein Modifications in Flavored Milk

Thermal treatments of dairy products favor oxidations, Maillard reactions, and the formation of sugar or lipid oxidation products. Additives including flavorings might enhance these reactions or even induce further reactions. Here we aimed to characterize protein modifications in four flavored milk drinks using samples along the production chain—raw milk, pasteurization, mixing with flavorings, heat treatment, and the commercial product. Therefore, milk samples were analyzed using a bottom up proteomics approach and a combination of data-independent (MS^E) and data-dependent acquisition methods (DDA). Twenty-one small carbonylated lipids were identified by shotgun lipidomics triggering 13 protein modifications. Additionally, two Amadori products, 12 advanced glycation end products (AGEs), and 12 oxidation-related modifications were targeted at the protein level. The most common modifications were lactosylation, formylation, and carboxymethylation. The numbers and distribution of modification sites present in raw milk remained stable after pasteurization and mixing with flavorings, while the final heat treatment significantly increased lactosylation and hexosylation in qualitative and quantitative terms. The processing steps did not significantly affect the numbers of AGE-modified, oxidized/carbonylated, and lipid-carbonylated sites in proteins.

Influence of ultrasound pretreatment on the subsequent glycation of dietary proteins

The influence of ultrasound treatment on the subsequent glycation process of proteins is controversial. Glycation behaviors of bovine serum albumin (BSA), β-lactoglobulin (β-Lg) and β-casein (β-CN) after ultrasound pretreatment (UP) were compared by both evaluating glycation kinetics and analyzing structural changes of proteins. UP resulted in both unfolding and aggregation behavior in protein samples, which altered the accessibility of the Lys and Arg. Five cycles of UP up-regulated the glycation degree of BSA and β-Lg, possibly due to the unfolding behavior induced by UP, which exposed additional glycation sites. In contrast, 30 cycles of UP induced a dramatic increase (by 97.9 nm) in particle size of BSA, thus burying portions of glycation sites and suppressing the glycation process. Notably, UP had minimal influence on glycation kinetics of β-CN, due to its intrinsic disordered structure. Based on proteomics analysis, the preference of Lys and Arg during glycation was found to be changed by UP in BSA and β-Lg. Four, 3 and 3 unique carboxyethylated lysine residues were identified in glycated BSA after 0, 5 and 30 cycles of UP, respectively. This study suggests that the protein glycation can be affected by UP, depending on the ultrasonication duration and native structure of the protein.

Reduced IgE/IgG binding capacities of bovine α-Lactalbumin by glycation after dynamic high-pressure microfluidization pretreatment evaluated by high resolution mass spectrometry

Dynamic high-pressure microfluidization (DHPM) pretreatment and glycation with lactose were employed to modify α-Lactalbumin (α-LA) with respect to the IgE/IgG binding capacities. No significant difference on incorporation ratio value of glycated α-LA was observed with and without DHPM pretreatment. However, IgE/IgG binding capacities of α-LA were decreased after glycation and DHPM pretreatment promoted the reduction. The lowest IgE/IgG binding capacities of glycated α-LA were obtained by DHPM pretreatment at 110 MPa. Native α-LA was mainly glycated at K62, K94, K98, whereas glycation sites and degree of substitution per peptide (DSP) were added after DHPM treatment. Therefore, the reduced IgE/IgG binding capacities of α-LA was attributed to the characteristics of glycated sites, including the amount, location, and DSP values. Interestingly, K98 played the most important role in decreasing IgE/IgG binding capacities of α-LA. The study revealed that glycation combined with DHPM was a promising way to decrease the allergenicity of proteins.

Digestibility of glycated milk proteins and the peptidomics of their in vitro digests

BACKGROUND

Milk proteins are widely used in food production and are often glycated by reducing sugar. Although many studies have reported the digestibility of glycated milk protein, most have focused on measuring degree of hydrolysis (DH), showing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) image of digests. Detailed information on the changes in peptide composition of digests has seldom been revealed. Therefore, in addition to measuring the DH and showing the SGS-PAGE images of digests, we also analyzed the peptidomics in digests using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) and Mascot database in this work to further reveal the influence of glycation on protein nutrition.

RESULTS

Compared with β-lactoglobulin and bovine serum albumin (BSA), DH of β-casein was suppressed to a lesser extent by glycation in both gastric and intestinal stages. Aggregates of glycated BSA were less sensitive to the action of digestive enzymes throughout gastrointestinal digestion according to SDS-PAGE images. Changes in the peptide composition of digests induced by glycation were distinctly displayed, showing both absence of peptides and occurrence of new peptides, based on the results obtained from LC-ESI-MS/MS.

CONCLUSIONS

Glycation can greatly change the peptide composition in digests of milk protein. The nutritional impact of the change in the peptide composition requires further investigation, and the impact of MRPs in unabsorbed digests on the gut flora should be an interesting field for further studies. © 2018 Society of Chemical Industry.

The Reduction in the IgE-Binding Ability of β-Lactoglobulin by Dynamic High-Pressure Microfluidization Coupled with Glycation Treatment Revealed by High-Resolution Mass Spectrometry

Our previous study indicated that pretreatment by dynamic high-pressure microfluidization (DHPM) and glycation with galactose was a promising method for decreasing the immunoglobulin E (IgE)-binding ability of β-lactoglobulin (β-LG). In this work, the conformational alteration of β-LG subjected to DHPM and glycation treatment was investigated in relation to IgE-binding ability by orbitrap mass spectrometry. After DHPM pretreatment, lower IgE-binding ability of glycated β-LG was observed with increasing pressures. Prior to DHPM pretreatment, 11 glycated sites were identified, while the number of glycation sites was increased to 12 after pretreatment. However, there was no significant difference of the glycation sites at the pressures of 50, 100, and 200 MPa, respectively. Average degree of substitution per peptide molecule of β-LG (DSP) was investigated to assess the degree of glycation per glycation site. All of the samples pretreated by DHPM exhibited a higher glycation level than those without DHPM pretreatment. The shielding effects of epitopes owing to glycation contributed to the reduction of IgE-binding capacity. Orbitrap mass spectrometry could provide a comprehensive understanding of the nature of protein glycation.

Effects of Wet-Blending on Detection of Melamine in Spray-Dried Lactose

During the development of rapid screening methods to detect economic adulteration, spray-dried milk powders prepared by dissolving melamine in liquid milk exhibited an unexpected loss of characteristic melamine features in the near-infrared (NIR) and Raman spectra. To further characterize this "wet-blending" phenomenon, spray-dried melamine and lactose samples were produced as a simplified model and investigated by NIR spectroscopy, Raman spectroscopy, proton nuclear magnetic resonance (¹H NMR), and direct analysis in real time Fourier transform mass spectrometry (DART-FTMS). In contrast to dry-blended samples, characteristic melamine bands in NIR and Raman spectra disappeared or shifted in wet-blended lactose-melamine samples. Subtle shifts in melamine ¹H NMR spectra between wet- and dry-blended samples indicated differences in melamine hydrogen-bonding status. Qualitative DART-FTMS analysis of powders detected a greater relative abundance of lactose-melamine condensation product ions in the wet-blended samples, which supported a hypothesis that wet-blending facilitates early Maillard reactions in spray-dried samples. Collectively, these data indicated that the formation of weak, H bonded complexes and labile, early Maillard reaction products between lactose and melamine contribute to spectral differences observed between wet- and dry-blended milk powder samples. These results have implications for future evaluations of adulterated powders and emphasize the important role of sample preparation methods on adulterant detection.

Influence of storage and heating on protein glycation levels of processed lactose-free and regular bovine milk products

Thermal treatment preserves the microbiological safety of milk, but also induces Maillard reactions modifying for example proteins. The purpose of this study was evaluating the influence of consumer behaviors (storage and heating) on protein glycation degrees in bovine milk products. Lactosylation and hexosylation sites were identified in ultra-high temperature (UHT), lactose-free pasteurized, and lactose-free UHT milk (ULF) and infant formula (IF) using tandem mass spectrometry (electron transfer dissociation). Overall, 303 lactosylated and 199 hexosylated peptides were identified corresponding to 170 lactosylation (31 proteins) and 117 hexosylation sites (25 proteins). In quantitative terms, storage increased lactosylation up to fourfold in UHT and IF and hexosylation up to elevenfold in ULF and threefold in IF. These levels increased additionally twofold when the stored samples were heated (40°C). In conclusion, storage and heating appear to influence protein glycation levels in milk at similar or even higher degrees than industrial processing.

Dairy products and the Maillard reaction: A promising future for extensive food characterization by integrated proteomics studies

Heating of milk and dairy products is done using various technological processes with the aim of preserving microbiological safety and extending shelf-life. These treatments result in chemical modifications in milk proteins, mainly generated as a result of the Maillard reaction. Recently, different bottom-up proteomic methods have been applied to characterize the nature of these structural changes and the modified amino acids in model protein systems and/or isolated components from thermally-treated milk samples. On the other hand, different gel-based and shotgun proteomic methods have been utilized to assign glycation, oxidation and glycoxidation protein targets in diverse heated milks. These data are essential to rationalize eventual, different nutritional, antimicrobial, cell stimulative and antigenic properties of milk products, because humans ingest large quantities of corresponding thermally modified proteins on a daily basis and these molecules also occur in pharmaceuticals and cosmetics. This review provides an updated picture of the procedures developed for the proteomic characterization of variably-heated milk products, highlighting their limits as result of concomitant factors, such as the multiplicity and the different concentration of the compounds to be detected.

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.

Identification and quantification of bovine protein lactosylation sites in different milk products

The microbiological safety of milk is typically guaranteed by thermal treatments, such as pasteurization and ultra high temperature (UHT) treatment, whereas infant formula (IF) is often produced at even harsher conditions including a drying process. Thermal treatments have raised concerns, as they may denature proteins and initiate protein modifications. Previous studies identified already many lactosylation sites in milk and showed that the lactosylation degree of some proteins correlates to thermal treatment conditions. Here, we studied the glycation degrees of 124 lactosylation sites in 28 bovine milk proteins in raw milk, three brands of pasteurized milk, three brands of UHT milk, and five brands of IF. Whereas, the glycation degree of many lactosylation sites increased from raw milk, to pasteurized milk, UHT milk, and IF, several modification sites showed a different behavior indicating that global measures do not correctly reflect the reactivity of distinct sites. Interestingly, the glycation degrees varied considerably among the brands of UHT milk and IF indicating that specific production processes of a company have to be considered and not only the classification of milk as pasteurized or UHT. Thus, proper adjustments of the technical processes should allow reducing the lactosylation levels in both UHT milk and IF.

SIGNIFICANCE

It is well established that thermal treatment of milk triggers protein modifications, such as lactosylation of lysine residues in several proteins, although the extent of lactosylation has not been quantitatively compared for a broad panel of protein lactosylation sites among different commercial products. The current study extends previous reports by relatively quantifying 124 confirmed lactosylation sites in 28 bovine milk proteins including several low abundant proteins. Whereas, glycation is generally assumed to be an unspecific chemical reaction with the modification degrees depending on the protein and sugar concentrations, we could show that each protein and even each lactosylation site in a given protein is differently affected by thermal processes indicating that the global lactosylation degrees will not allow predicting the influence of a technical process on individual proteins and lactosylation sites. Additionally, we could show that brands of each milk product differ significantly in their glycation degrees with UHT milk brands for example spanning the whole range from the relatively low lactosylation degree of pasteurized milk to the rather high lactosylation degree of IF. Similar differences were obtained for IF that generally showed the highest glycation degree. The targeted quantification approach established and validated here will be useful to reveal technical processing steps that trigger individual lactosylation sites and thus can help to prevent such unwanted reactions. Even slight changes of the technical processes might allow reducing the lactosylation degree of milk proteins significantly without challenging the microbiological safety or affecting consumer behavior.

MALDI-TOF-MS Platform for Integrated Proteomic and Peptidomic Profiling of Milk Samples Allows Rapid Detection of Food Adulterations

Adulteration of ovine, caprine, and buffalo milks with more common bovine material occurs for economic reasons and seasonal availability. Frauds are also associated with the use of powdered milk instead of declared, fresh material. In this context, various analytical methods have been adapted to dairy science applications with the aim to evaluate adulteration of milk samples, although time-consuming, suitable only for speciation or thermal treatment analysis, or useful for a specific fraud type. An integrated MALDI-TOF-MS platform for the combined peptidomic and proteomic profiling of milk samples is here presented, which allows rapid detection of illegal adulterations due to the addition of either nondeclared bovine material to water buffalo, goat, and ovine milks or of powdered bovine milk to the fresh counterpart. Peptide and protein markers of each animal milk were identified after direct analysis of a large number of diluted skimmed and/or enriched diluted skimmed filtrate samples. In parallel, markers of thermal treatment were characterized in different types of commercial milks. Principal components scores of ad hoc prepared species- or thermal treatment-associated adulterated milk samples were subjected to partial least-squares regression, permitting a fast accurate estimate of the fraud extents in test samples at either protein and peptide level. With respect to previous reports on MALDI-TOF-MS protein profiling methodologies for milk speciation, this study extends that approach to the analysis of the thermal treatment and introduces an independent, complementary peptide profiling measurement, which integrates protein data with additional information on peptides, validating final results and ultimately broadening the method applicability.

Proteomic characterization of intermediate and advanced glycation end-products in commercial milk samples

The Maillard reaction consists of a number of chemical processes affecting the structure of the proteins present in foods. We previously accomplished the proteomic characterization of the lactosylation targets in commercial milk samples. Although characterizing the early modification derivatives, this analysis did not describe the corresponding advanced glycation end-products (AGEs), which may be formed from the further oxidation of former ones or by reaction of oxidized sugars with proteins, when high temperatures are exploited. To fill this gap, we have used combined proteomic procedures for the systematic characterization of the lactosylated and AGE-containing proteins from the soluble and milk fat globule membrane fraction of various milk products. Besides to confirm all lactulosyl-lysines described previously, 40 novel lactosylation sites were identified. More importantly, 308 additional intermediate and advanced glyco-oxidation derivatives (including cross-linking adducts) were characterized in 31 proteins, providing the widest qualitative inventory of modified species ascertained in commercial milk samples so far. Amadori adducts with glucose/galactose, their dehydration products, carboxymethyllysine and glyoxal-, 3-deoxyglucosone/3-deoxygalactosone- and 3-deoxylactosone-derived dihydroxyimidazolines and/or hemiaminals were the most frequent derivatives observed. Depending on thermal treatment, a variable number of modification sites was identified within each protein; their number increased with harder food processing conditions. Among the modified proteins, species involved in assisting the delivery of nutrients, defense response against pathogens and cellular proliferation/differentiation were highly affected by AGE formation. This may lead to a progressive decrease of the milk nutritional value, as it reduces the protein functional properties, abates the bioavailability of the essential amino acids and eventually affects food digestibility. These aspects are of particular importance in products intended for infant diet, such as milk powders and infant formulas.

BIOLOGICAL SIGNIFICANCE

We used combined shotgun proteomic procedures for the systematic characterization of intermediate and advanced glycoxidation protein products in various raw and commercial milk samples. Several hundreds of modified species were characterized as deriving from 31 milk proteins, providing the widest qualitative inventory of assigned components in this fluid. Amadori adducts with glucose/galactose, their dehydration products, carboxymethyl-lysine, and glyoxal-, 3-deoxyglucosone/3-deoxygalactosone- and 3-deoxylactosone-derived dihydroxyimidazolines and/or hemiaminals were the most frequent derivatives observed. Proteins involved in nutrient delivery, defense response against pathogens and cellular proliferation/differentiation were highly subjected to intermediate and advanced glyco-oxidation modification. This may lead to a progressive decrease of the milk nutritional value, as it reduces the protein functional properties, diminishes the bioavailability of the essential amino acids, eventually affects food digestibility and determines a potential increase of specific allergens. These information are important points of interest to connect the extent of the Maillard reaction present in different commercial samples with the potential nutritional aspects mentioned above. These themes have to be fully evaluated in a next future for a complete estimation of the nutritional and toxicological properties of the dairy products deriving from severe heat processing.

Modified peptides as indicators for thermal and nonthermal reactions in processed milk

Site-specific relative quantification of β-lactoglobulin modifications in heated milk and dairy products was performed to determine their thermal and nonthermal origins and to evaluate marker candidates for milk processing. Therefore, formation kinetics of 19 different structures at 26 binding sites were analyzed by ultrahigh-performance liquid chromatography-tandem mass spectrometry with multiple reaction monitoring (UHPLC-MS/MS/MRM) after specific protein hydrolysis. The results indicate that (i) site-specific analysis of lactulosyllysine may be a more sensitive marker for mild heat treatment than its overall content; (ii) N(ε)-carboxymethyllysine, N-terminal ketoamide, and asparagine deamidation are of thermal origin and may be good markers for rather intensive heat treatment, whereas N(ε)-carboxyethyllysine reflects thermal and nonthermal processes; (iii) the relevance of methylglyoxal-derived arginine modifications is low compared to that of other modifications; (iv) oxidation of methionine and cysteine is a rather weak indicator of thermal impact; and (v) the tryptophan modifications formylkynurenine and kynurenine are of nonthermal origin and further degraded during processing.

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.

Effects of different industrial heating processes of milk on site-specific protein modifications and their relationship to in vitro and in vivo digestibility

Heating processes are applied to milk and dairy products to ensure their microbiological safety and shelf lives. However, how differences in "industrial" thermal treatments affect protein digestibility is still equivocal. In this study, raw milk was subjected to pasteurization, three kinds of ultra-high-temperature (UHT) treatment, and in-can sterilization and was investigated by in vitro and in vivo digestion and proteomic methods. In-can sterilized milk, followed by UHT milk samples, showed a rapid decrease in protein bands during the course of digestion. However, protein digestibility determined by a Kjeldahl procedure showed insignificant differences. Proteomic analysis revealed that lactulosyllysine, which reflects a decrease in protein digestibility, in α-lactalbumin, β-lactoglobulin, and caseins was higher in in-can sterilized milk, followed by UHT milk samples. Thus, industrial heating may improve the digestibility of milk proteins by denaturation, but the improvement is likely to be offset by heat-derived modifications involved in decreased protein digestibility.

Non-enzymatic glycation and glycoxidation protein products in foods and diseases: an interconnected, complex scenario fully open to innovative proteomic studies

The Maillard reaction includes a complex network of processes affecting food and biopharmaceutical products; it also occurs in living organisms and has been strictly related to cell aging, to the pathogenesis of several (chronic) diseases, such as diabetes, uremia, cataract, liver cirrhosis and various neurodegenerative pathologies, as well as to peritoneal dialysis treatment. Dozens of compounds are involved in this process, among which a number of protein-adducted derivatives that have been simplistically defined as early, intermediate and advanced glycation end-products. In the last decade, various bottom-up proteomic approaches have been successfully used for the identification of glycation/glycoxidation protein targets as well as for the characterization of the corresponding adducts, including assignment of the modified amino acids. This article provides an updated overview of the mass spectrometry-based procedures developed to this purpose, emphasizing their partial limits with respect to current proteomic approaches for the analysis of other post-translational modifications. These limitations are mainly related to the concomitant sheer diversity, chemical complexity, and variable abundance of the various derivatives to be characterized. Some challenges to scientists are finally proposed for future proteomic investigations to solve main drawbacks in this research field.

Characterisation of Maillard reaction products derived from LEKFD--a pentapeptide found in β-lactoglobulin sequence, glycated with glucose--by tandem mass spectrometry, molecular orbital calculations and gel filtration chromatography coupled with continuous photodiode array

Maillard reaction peptides (MRPs) contribute to taste, aroma, colour, texture and biological activity. However, peptide degradation or the cross-linking of MRPs in the Maillard reaction has not been investigated clearly. A peptide of LEKFD, a part of β-lactoglobulin, was heated at 110 °C for 24h with glucose and the reaction products were analysed by HPLC with ODS, ESI-MS, ESI-MS/MS and HPLC with gel-filtration column and DAD detector. In the HPLC fractions, an imminium ion of LEK*FD, a pyrylium ion or a hydroxymethyl furylium ion of LEK*FD, and KFD and EK were detected by ESI-MS. Therefore, those products may be produced by the Maillard reaction. The molecular orbital of glycated LEKFD at the lysine epsilon-amino residue with Schiff base form was calculated by MOPAC. HPLC with gel-filtration column showed cross-linking and degradation of peptides.

Quantification of allergenic bovine milk α(S1)-casein in baked goods using an intact ¹⁵N-labeled protein internal standard

Intact bovine ¹⁵N-α(S1)-casein was used as an internal standard in a selected reaction monitoring (SRM) assay for milk protein in baked food samples containing fats, sugar, and gums. Effects on SRM results of sample matrix composition in two biscuit recipes containing nonfat dry milk (NFDM) were studied, including samples from a milk allergen ELISA proficiency trial. Following extraction of defatted samples with carbohydrate-degrading enzymes and acid precipitation of casein, the SRM assay exhibited an LOQ of <3 ppm NFDM with 60-80% recovery. NFDM levels measured by the SRM assay were 1.7-2.5 times greater than median levels determined by ELISA. Differences were observed in the α(S1)-casein interpeptide SRM ion abundance profile between recipes and after baking. ¹⁵N-α(S1)-Casein increases SRM analysis accuracy by correcting for extraction recovery but does not eliminate underestimation of allergen concentrations due to baking-related milk protein transformation (modifications).

Quantification of lactosylation of whey proteins in stored milk powder using multiple reaction monitoring

Lactosylation in stored milk powder was quantified by multiple reaction monitoring (MRM), a mass spectrometry-based quantification method. The MRM method was developed from a knowledge of peptide fragmentation. The neutral losses of 162Da (cleavage of galactose) and 216Da (the formation of furylium ion) which were representative of lactosylated peptides were specifically selected as MRM transitions. Quantification of lactosylated protein was based on the peak areas of these fragmentation ions. The MRM results showed an increase in peak areas of the two transition fragments from tryptic digests of whey proteins in stored milk protein concentrate powder. A good correlation between the MRM and furosine results indicated that MRM based on tryptic digests of whole products was a feasible method for quantification of modified milk proteins.

Proteomic approach based on MALDI-TOF MS to detect powdered milk in fresh cow's milk

Milk and cheese are expensive foodstuffs, and their consumption is spread among the population because of their high nutritional value; for this reason they are often subjected to adulterations. Among the common illegal practices, the addition of powdered derivatives seems very difficult to detect because the adulterant materials have almost the same chemical composition of liquid milk. However, the high temperatures (180-200 °C) used for milk powder production could imply the occurrence of some protein modifications (e.g., glycation, lactosylation, oxidation, deamidation, dehydration). The modified proteins or peptides could then be used as markers for the presence of powdered milk. In this work, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed to analyze tryptic digests relevant to samples of raw liquid (without heat treatment), commercial liquid, and powdered cow's milk. Samples were subjected to two-dimensional gel electrophoresis (2-DE); differences among liquid and powder milk were detected at this stage and eventually confirmed by MALDI analysis of the in gel digested proteins. Some diagnostic peptides of powdered milk, attributed to modified whey proteins and/or caseins, were identified. Then, a faster procedure was optimized, consisting of the separation of caseins from milk whey and the subsequent in-solution digestion of the two fractions, with the advantage of obtaining almost the same information in a limited amount of time. Finally, analyses were carried out with the fast procedure on liquid milk samples adulterated with powdered milk at different percentages, and diagnostic peptides were detected down to 1% of adulteration level.

Nucleolar accumulation of APE1 depends on charged lysine residues that undergo acetylation upon genotoxic stress and modulate its BER activity in cells

The functional importance of APE1 nucleolar accumulation is described. It is shown that acetylation of Lys27–35, affecting local conformation, regulates APE1 function by 1) controlling its interaction with NPM1 and rRNA and its nucleolar accumulation, 2) modulating K6/K7 acetylation status, and 3) promoting APE1 BER activity in cells.

Apurinic/apyrimidinic endonuclease 1 (APE1) is the main abasic endonuclease in the base excision repair (BER) pathway of DNA lesions caused by oxidation/alkylation in mammalian cells; within nucleoli it interacts with nucleophosmin and rRNA through N-terminal Lys residues, some of which (K²⁷/K³¹/K³²/K³⁵) may undergo acetylation in vivo. Here we study the functional role of these modifications during genotoxic damage and their in vivo relevance. We demonstrate that cells expressing a specific K-to-A multiple mutant are APE1 nucleolar deficient and are more resistant to genotoxic treatment than those expressing the wild type, although they show impaired proliferation. Of interest, we find that genotoxic treatment induces acetylation at these K residues. We also find that the charged status of K²⁷/K³¹/K³²/K³⁵ modulates acetylation at K⁶/K⁷ residues that are known to be involved in the coordination of BER activity through a mechanism regulated by the sirtuin 1 deacetylase. Of note, structural studies show that acetylation at K²⁷/K³¹/K³²/K³⁵ may account for local conformational changes on APE1 protein structure. These results highlight the emerging role of acetylation of critical Lys residues in regulating APE1 functions. They also suggest the existence of cross-talk between different Lys residues of APE1 occurring upon genotoxic damage, which may modulate APE1 subnuclear distribution and enzymatic activity in vivo.

Farm animal milk proteomics

Milk is one of the most important nutrients for humans during lifetime. Farm animal milk in all its products like cheese and other fermentation and transformation products is a widespread nutrient for the entire life of humans. Proteins are key molecules of the milk functional component repertoire and their investigation represents a major challenge. Proteins in milk, such as caseins, contribute to the formation of micelles that are different from species to species in dimension and casein-type composition; they are an integral part of the MFGM (Milk Fat Globule Membrane) that has being exhaustively studied in recent years. Milk proteins can act as enzymes or have an antimicrobial activity; they could act as hormones and, last but not least, they have a latent physiological activity encoded in their primary structure that turns active when the protein is cleaved by fermentation or digestion processes. In this review we report the last progress in proteomics, peptidomics and bioinformatics. These new approaches allow us to better characterize the milk proteome of farm animal species, to highlight specific PTMs, the peptidomic profile and even to predict the potential nutraceutical properties of the analyzed proteins.

Proteomic analysis of temperature-dependent changes in stored UHT milk

Molecular changes in milk proteins during storage of UHT-treated milk have been investigated using two-dimensional electrophoresis (2-DE) coupled to MALDI-TOF mass spectrometry. UHT-treated samples were stored at three different temperatures, 4 °C, 28 °C, and 40 °C, for two months. Three main changes could be observed on 2-DE gels following storage. They were (1) the appearance of diffuse staining regions above the position of the monomeric caseins caused by nondisulfide cross-linking of α and β-caseins; (2) the appearance of additional acidic forms of proteins, predominantly of α(S1)-casein, caused by deamidation; and (3) the appearance of "stacked spots" caused by lactosylation of whey proteins. The extent of the changes increased with increased storage temperature. Mass spectrometric analysis of in-gel tryptic digests showed that the cross-linked proteins were dominated by α(S1)-casein, but a heterogeneous population of cross-linked forms with α(S2)-casein and β-casein was also observed. Tandem MS analysis was used to confirm deamidation of N(129) in α(S1)-casein. MS analysis of the stacked spots revealed lactosylation of 9/15 lysines in β-lactoglobulin and 8/12 lysines in α-lactalbumin. More extensive analysis will be required to confirm the nature of the cross-links and additional deamidation sites in α(S1)-casein as the highly phosphorylated nature of the caseins makes them challenging prospects for MS analysis.

Redox proteomics of fat globules unveils broad protein lactosylation and compositional changes in milk samples subjected to various technological procedures

The Maillard reaction between lactose and proteins occurs during thermal treatment of milk and lactosylated β-lactoglobulin, α-lactalbumin and caseins have widely been used to monitor the quality of dairy products. We recently demonstrated that a number of other whey milk proteins essential for nutrient delivery, defense against bacteria/virus and cellular proliferation become lactosylated during milk processing. The extent of their modification is associated with the harshness of product manufacturing. Since fat globule proteins are also highly important for the health-beneficial properties of milk, an evaluation of their lactosylation is crucial for a complete understanding of aliment nutritional characteristics. This is more important when milk is the unique dietary source, as in the infant diet. To this purpose, a sequential proteomic procedure involving an optimized milk fat globule (MFG) preparation/electrophoretic resolution, shot-gun analysis of gel portions for protein identification, selective trapping of lactosylated peptides by phenylboronate chromatography and their analysis by nanoLC-ESI-electron transfer dissociation (ETD) tandem MS was used for systematic characterization of fat globule proteins in milk samples subjected to various manufacturing procedures. Significant MFG protein compositional changes were observed between samples, highlighting the progressive adsorption of caseins and whey proteins on the fat globule surface as result of the technological process used. A significant lactosylation of MFG proteins was observed in ultra-high temperature sterilized and powdered for infant nutrition milk preparations, which well paralleled with the harshness of thermal treatment. Globally, this study allowed the identification of novel 157 non-redundant modification sites and 35 MFG proteins never reported so far as being lactosylated, in addition to the 153 ones ascertained here as present on other 21 MFG-adsorbed proteins whose nature was already characterized. Novel MFG proteins include components involved in nutrient delivery, defense response against pathogens and cellular proliferation/differentiation. Nutritional, biological and toxicological consequences of these findings are here discussed, highlighting their possible impact on children's diet.

Review: applications of mass spectrometry techniques in the investigation of milk proteome

The introduction of "soft" desorption/ionization methods such as electrospray ionization and matrix-assisted laser desorption/ionization has determined a breakthrough in the application of mass spectrometry to the structural analysis of proteins. The contemporary advancement of bioinformatics, together with the possibility to combine these mass spectrometric methods with electrophoretic or chromatographic separation techniques has opened up the new field of proteome analysis and, more generally, has established these approaches as indispensable tools for protein and peptide analysis in complex mixtures, such as milk and milk- derived foods. Here, a necessarily not exhaustive series of current applications of mass spectrometry-based techniques for the characterization of milk proteins will be summarized. These include the characterization of milk protein polymorphism, determination of the structural modifications induced on milk proteins by industrial processes, investigation of milk adulterations and characterization of milk allergens.