Identification of protein markers for the occurrence of defrosted material in milk through a MALDI-TOF-MS profiling approach

Protein Mass Fingerprinting and Antioxidant Power of Hemp Seeds in Relation to Plant Cultivar and Environment

Cannabis sativa (hemp) seeds are considered a functional food for their favorable contents of essential fatty acids, proteins and antioxidants. Beyond phenolics and carotenoids, the bioactivity of proteins has recently been investigated. However, plant genotype and environmental conditions can affect quantity and quality of macronutrients and phytochemicals in seeds, influencing their nutraceutical properties. In this study, the effects of plant variety and seed origin on the protein profile and antioxidant activity of hemp seeds were evaluated. Seeds from two cultivars, Secuieni Jubileu and Finola, were harvested from a mountain field located in Italy and compared with reference seeds used for sowing. Albumin and globulin extracts were obtained using the Osborne method and their antioxidant power was assayed (DPPH and ABTS methods). A matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry method was developed for protein fingerprinting analysis. Albumins from seeds of the mountain site showed higher radical scavenging activity and compounds of lower molecular weight than reference seeds, suggesting a role of proteins in the observed bioactivity. The MALDI-TOF method discriminated samples according to origin and variety, highlighting changes in the protein profile and identifying signals which could be used as markers of hemp cultivars.

Copper inhibits postacidification of yogurt and affects its flavor: A study based on the Cop operon

Yogurt and its related products are popular worldwide. During transportation and storage, Lactobacillus delbrueckii ssp. bulgaricus in yogurt continues to metabolize to form lactic acid, the postacidification phenomenon of yogurt. Postacidification of yogurt is a widespread phenomenon in the dairy industry. Many scholars have done research on controlling the postacidification process, but few report on the molecular mechanisms involved. In this study, we used a molecular-assisted approach to screen food additives that can inhibit postacidification and analyzed its effects on yogurt quality as well as its regulatory mechanism from multi-omics perspectives in combination. The copper ion was found to upregulate the expression of the LDB_RS05285 gene, and the copper transporter-related genes were regulated by copper. Based on the metabolic-level analysis, copper was found to promote lactose hydrolysis, accumulate a large amount of glucose and galactose, inhibit the conversion of glucose to lactic acid, and reduce the production of lactic acid. The significantly greater abundance of l-isoleucine and l-phenylalanine increased the abundance of 3-methylbutyraldehyde (∼1.2 times) and benzaldehyde (∼7.9 times) to different degrees, which contributed to the formation of the overall flavor of yogurt. Copper not only stabilizes the acidity of yogurt, but also it improves the flavor of yogurt. Through this established method involving quantitative and correlation analyses at the transcriptional and metabolic levels, this study provides guidance for the research and development of food additives that inhibit postacidification of yogurt and provide a reference for studying the changes of metabolites during storage of yogurt.

Foodomic-Based Approach for the Control and Quality Improvement of Dairy Products

The food quality assurance before selling is a needed requirement intended for protecting consumer interests. In the same way, it is also indispensable to promote continuous improvement of sensory and nutritional properties. In this regard, food research has recently contributed with studies focused on the use of 'foodomics'. This review focuses on the use of this technology, represented by transcriptomics, proteomics, and metabolomics, for the control and quality improvement of dairy products. The complex matrix of these foods requires sophisticated technology able to extract large amounts of information with which to influence their aptitude for consumption. Thus, throughout the article, different applications of the aforementioned technologies are described and discussed in essential matters related to food quality, such as the detection of fraud and/or adulterations, microbiological safety, and the assessment and improvement of transformation industrial processes (e.g., fermentation and ripening). The magnitude of the reported results may open the door to an in-depth transformation of the most conventional analytical processes, with the introduction of new techniques that allow a greater understanding of the biochemical phenomena occurred in this type of food.

Mass spectrometry-based protein and peptide profiling for food frauds, traceability and authenticity assessment

The ever-growing use of mass spectrometry (MS) methodologies in food authentication and traceability originates from their unrivalled specificity, accuracy and sensitivity. Such features are crucial for setting up analytical strategies for detecting food frauds and adulterations by monitoring selected components within food matrices. Among MS approaches, protein and peptide profiling has become increasingly consolidated. This review explores the current knowledge on recent MS techniques using protein and peptide biomarkers for assessing food traceability and authenticity, with a specific focus on their use for unmasking potential frauds and adulterations. We provide a survey of the current state-of-the-art instrumentation including the most reliable and sensitive acquisition modes highlighting advantages and limitations. Finally, we summarize the recent applications of MS to protein/peptide analyses in food matrices and examine their potential in ensuring the quality of agro-food products.

Detection of Frozen-Thawed Duck Fatty Liver by MALDI-TOF Mass Spectrometry: A Chemometrics Study

The marketing of poultry livers is only authorized as fresh, frozen, or deep-frozen. The higher consumer demand for these products for a short period of time may lead to the marketing of frozen–thawed poultry livers: this constitutes fraud. The aim of this study was to design a method for distinguishing frozen–thawed livers from fresh livers. For this, the spectral fingerprint of liver proteins was acquired using Matrix-Assisted Laser Dissociation Ionization-Time-Of-Flight mass spectrometry. The spectra were analyzed using the chemometrics approach. First, principal component analysis studied the expected variability of commercial conditions before and after freezing–thawing. Then, the discriminant power of spectral fingerprint of liver proteins was assessed using supervised model generation. The combined approach of mass spectrometry and chemometrics successfully described the evolution of protein profile during storage time, before and after freezing-thawing, and successfully discriminated the fresh and frozen–thawed livers. These results are promising in terms of fraud detection, providing an opportunity for implementation of a reference method for agencies to fight fraud.

Rapid Discrimination and Authentication of Korean Farmstead Mozzarella Cheese through MALDI-TOF and Multivariate Statistical Analysis

Geographical origin and authenticity are the two crucial factors that propel overall cheese perception in terms of quality and price; therefore, they are of great importance to consumers and commercial cheese producers. Herein, we demonstrate a rapid, accurate method for discrimination of domestic and import mozzarella cheeses in the Republic of Korea by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The protein profiles' data aided by multivariate statistical analysis successfully differentiated farmstead and import mozzarella cheeses according to their geographical location of origin. A similar investigation within domestic samples (farmsteads/companies) also showed clear discrimination regarding the producer. Using the biomarker discovery tool, we identified seven distinct proteins, of which two (m/z 7407.8 and 11,416.6) were specific in farmstead cheeses, acting as potential markers to ensure authentication and traceability. The outcome of this study can be a good resource in building a database for Korean domestic cheeses. This study also emphasizes the combined utility of MALDI-TOF MS and multivariate analysis in preventing fraudulent practices, thereby ensuring market protection for Korean farmstead cheeses.

MALDI-TOF Mass Spectrometry Applications for Food Fraud Detection

Chemical analysis of food products relating to the detection of the most common frauds is a complex task due to the complexity of the matrices and the unknown nature of most processes. Moreover, frauds are becoming more and more sophisticated, making the development of reliable, rapid, cost-effective new analytical methods for food control even more pressing. Over the years, MALDI-TOF MS has demonstrated the potential to meet this need, also due to a series of undeniable intrinsic advantages including ease of use, fast data collection, and capability to obtain valuable information even from complex samples subjected to simple pre-treatment procedures. These features have been conveniently exploited in the field of food frauds in several matrices, including milk and dairy products, oils, fish and seafood, meat, fruit, vegetables, and a few other categories. The present review provides a comprehensive overview of the existing MALDI-based applications for food quality assessment and detection of adulterations.

Monitoring aging of hen egg by integrated quantitative peptidomic procedures

Environmental conditions and timing of egg storage highly affect raw material quality. Aging and endogenous processing of constituent proteins can determine important changes in specific functions and technological properties of inner egg compartments. We here used integrated peptidomic procedures to identify peptide markers of egg freshness. At first, peptides extracted from egg white and yolk plasma taken from eggs stored for different times were subjected to a label-free untargeted quantitation procedure based on nanoLC-ESI-Q-Orbitrap-MS/MS, which identified 836 and 1974 unique variable molecules, respectively. By applying stringent criteria for filtering data, 30 and 66 putative egg aging markers were selected for egg white and yolk plasma, respectively. Proposed molecules were then validated through a targeted label-free parallel reaction monitoring procedure based on nanoLC-ESI-Q-Orbitrap-MS/MS, confirming quantitative trends for 19 and 25 peptides in egg white and yolk plasma, respectively, and generating a robust panel of egg storage markers. Quantitative results reflected physico-chemical phenomena occurring in egg compartments during storage and offered essential information for the development of novel control procedures to assess quality features of fresh/stored raw material.

Fluorescent Protein Variants Generated by Reassembly between Skeleton and Chromophore

Fluorescent proteins (FPs) can be used as intrinsic molecular tags to track the dynamic activity in live cells. To obtain variants in an available and massive manner is always a challenge. Here, we adopted a computer-based microarray synthesis method to realize the reassembly between the chromophore and the skeleton. DNAWorks was used to segment the input FP templates into a set of overlapping oligonucleotides (20-43 mer) with a balanced annealing temperature, G + C content, and codon frequency. The constitution of the chromophore was kept in the same section by switching the divided sites during segmentation and the codon was optimized to further keep the balanced parameters. The designed oligonucleotides were synthesized on photo-programmable microfluidic arrays. Sequence analysis and the subsequent conditional induced expression of FPs revealed that oligonucleotides were highly reassembled. Spectra, photostability, and molecular size detection of randomly selected variants showed that they were distinct monomeric proteins that preserved photoactivity. Our study provides an effective means of obtaining FP variants based on a computer-designed parallel synthesis.

Advances in Analysis of Milk Proteases Activity at Surfaces and in a Volume by Acoustic Methods

This review is focused on the application of surface and volume-sensitive acoustic methods for the detection of milk proteases such as trypsin and plasmin. While trypsin is an important protein of human milk, plasmin is a protease that plays an important role in the quality of bovine, sheep and goat milks. The increased activity of plasmin can cause an extensive cleavage of β-casein and, thus, affect the milk gelation and taste. The basic principles of surface-sensitive acoustic methods, as well as high-resolution ultrasonic spectroscopy (HR-US), are presented. The current state-of-the-art examples of the application of acoustic sensors for protease detection in real time are discussed. The application of the HR-US method for studying the kinetics of the enzyme reaction is demonstrated. The sensitivity of the acoustics biosensors and HR-US methods for protease detection are compared.

Novel Biomarkers of Mastitis in Goat Milk Revealed by MALDI-TOF-MS-Based Peptide Profiling

Mastitis is the most common infection of dairy goats impairing milk production and quality, which is usually recognized by mammary gland visual inspection and palpation. Subclinical forms of the disease are also widely represented, which lack the typical signs of the clinical ones but are still associated with reduced production and safety for human consumption of milk, generally presenting a high bacterial count. In order to obtain novel analytical tools for rapid and non-invasive diagnosis of mastitis in goats, we analyzed milk samples from healthy, subclinical and clinical mastitic animals with a MALDI-TOF-MS-based peptidomic platform, generating disease group-specific spectral profiles whose signal intensity and mass values were analyzed by statistics. Peculiar spectral signatures of mastitis with respect to the control were identified, while no significant spectral differences were observed between clinical and subclinical milk samples. Discriminant signals were assigned to specific peptides through nanoLC-ESI-Q-Orbitrap-MS/MS experiments. Some of these molecules were predicted to have an antimicrobial activity based on their strong similarity with homolog bioactive compounds from other mammals. Through the definition of a panel of peptide biomarkers, this study provides a very rapid and low-cost method to routinely detect mastitic milk samples even though no evident clinical signs in the mammary gland are observed.

Food authentication in real life: How to link nontargeted approaches with routine analytics?

In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and, thus, the safety of food is one of the central questions for actors from science, politics, and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis. In the past 5 years, nontargeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further nontargeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding high-resolution laboratory infrastructure, and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of nontargeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.

A non-canonical phosphorylation site in β-casein A from non-Mediterranean water buffalo makes quantifiable the adulteration of Italian milk with foreign material by combined isoelectrofocusing-immunoblotting procedures

The need of controlling illegal addition of water buffalo (WB) milk from foreign countries to the Italian counterpart devoted to the production of Protected Denomination of Origin (PDO) Mozzarella di Bufala Campana (MBC) cheese has promoted the development of simple, fast and cheap isoelectrofocusing (IEF) methods for evaluating the nature of the raw material to be used according to a high-throughput sample multiplexing format, avoiding the use of dedicated mass spectrometry-based procedures. Thus, combined proteomic methods were here integrated with optimized western blotting protocols in solving the complex IEF pattern of casein (CN) mixtures observed when Italian and foreign WB milk are mixed together. Identification of internally deleted α_s1-CN hepta-phosphorylated species as well as of still unknown β-CN A hexa-phosphorylated and N-terminally-nicked β-CN A phosphorylated forms present uniquely in foreign WB milk samples, allowed recognizing these molecules as adulteration markers to be assayed in combined IEF-immunoblotting procedures; the latter ones showing optimal migration characteristics to be used in routine assays. A linear relationship between detected area of specific immunorecognized gel bands and percentage of international WB milk added to the Italian counterpart was verified, demonstrating that this method has an adulteration detection limit close to 3% v/v. Based on these results, this analytical procedure is here proposed as optimal one for evaluating the authenticity of PDO MBC cheese products.

Foodomics for human health: current status and perspectives

INTRODUCTION

In the post-genomic era, the opportunity to combine and integrate cutting-edge analytical platforms and data processing systems allowed the birth of foodomics, 'a discipline that studies the Food and Nutrition domains through the application of advanced omics technologies to improve consumer's well-being, health, and confidence'. Since then, this discipline has rapidly evolved and researchers are now facing the daunting tasks to meet consumers' needs in terms of food traceability, sustainability, quality, safety and integrity. Most importantly, today it is imperative to provide solid evidence of the mechanisms through which food can promote human health and well-being. Areas covered: In this review, the complex relationships connecting food, nutrition and human health will be discussed, with emphasis on the relapses for the development of functional foods and nutraceuticals, personalized nutrition approaches, and the study of the interplay among gut microbiota, diet and health/diseases. Expert commentary: Evidence has been provided supporting the role of various omic platforms in studying the health-promoting effects of food and customized dietary interventions. However, although associated to major analytical challenges, only the proper integration of multi-omics studies and the implementation of bioinformatics tools and databases will help translate findings from clinical practice into effective personalized treatment strategies.

Simultaneously tracing the geographical origin and presence of bovine milk in Italian water buffalo Mozzarella cheese using MALDI-TOF data of casein signature peptides

Water buffalo (WB) casein (CN) and curd samples from indigenous Italian and international breeds were examined with the objective of identifying signature peptides that could function as an indicator to determine the origin of their milk products. CN in complex mixtures were digested with trypsin, and peptide fragments were subsequently identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The unique presence of a β-CN A variant and an internally deleted αs1-CN (f35-42) variant in international WB milk samples was ascertained by identifying signature tryptic peptides from either dephosphorylated or native CN. Four signature unphosphorylated peptides derived from β-CN A, i.e. (f49-68) Asn(68) (2223.6 Da), (f1-28) Ser(10) (3169.4 Da), (f1-29) Ser(10) (3297.4 Da) and (f33-48) Thr(41) (1982 Da) and two from αs1-CN (f35-42) deleted fragments, i.e. (f23-34) Met(31) (1415.7 Da) and (f43-58) Val(44) (1752.7 Da), were identified. Two signature casein phosphopeptides (CPPs), i.e. β-CN (f1-28) 4P (3489.1 Da) and β-CN (f33-48) 1P (2062.0 Da), were identified in the tryptic hydrolysate of native casein or curd and cheese samples using in-batch hydroxyapatite (HA) chromatography. All these fragments functioned as analytical surrogates of two αs1- and β-casein variants that specifically occur in the milk of international WB breeds. Furthermore, the bovine peptide β-CN (f1-28) 4P had a distinct and lower molecular mass compared with the WB counterpart and functioned as a species-specific marker for all breeds of WB. Advantages of this analytical approach are that (i) peptides are easier to separate than proteins, (ii) signature peptide probes originating from specific casein variants allow for the targeting of all international WB milk, curd and cheese samples and (iii) bovine and WB casein in mixtures can be simultaneously determined in protected designation of origin (PDO) "Mozzarella di Bufala Campana" cheese. This analytical method enabled the specific detection of international WB and bovine casein with a sensitivity threshold of 2 and 0.78 %, respectively. Graphical Abstract Monitoring of prototypic tryptic CPPs by MALDI-TOF analysis in Mediterranean (A), Romanian (B), Indian (C), Polish (D) and Canadian (E) curd samples to guarantee the authenticity of the PDO "Mozzarella di Bufala Campana" cheese.