Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra

Multi-omics characterization of NIST seafood reference materials and alternative matrix preparations

The National Institute of Standards and Technology (NIST) has prepared four seafood reference materials (RMs) for use in food safety and nutrition studies: wild-caught and aquacultured salmon (RM 8256 and RM 8257) and wild-caught and aquacultured shrimp (RM 8258 and RM 8259). These materials were characterized using genetic, metabolomic (1H-NMR, nuclear magnetic resonance and LC-HRMS/MS, liquid chromatography high-resolution tandem mass spectrometry), lipidomic, and proteomic methods to explore their use as matrix-matched, multi-omic differential materials for method development towards identifying product source and/or as quality control in untargeted omics studies. The results from experimental replicates were reproducible for each reference material and analytical method, with the most abundant features reported. Additionally, differences between the materials could be detected, where wild-caught and aquacultured seafood could be distinguished using untargeted metabolite, lipid, and protein analyses. Further processing of the fresh-frozen RMs by freeze-drying revealed the freeze-dried seafoods could still be reliably discerned. These results demonstrate the usefulness of these reference materials as tools for omics instrument validation and measurement harmonization in seafood-related studies. Furthermore, their use as differential quality control (QC) materials, regardless of preparation method, may also provide a tool for laboratories to demonstrate proficiency at discriminating between products based on source/species.

compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets

It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.

Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics

Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a “gem” at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.

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.

Protein Signatures to Trace Seafood Contamination and Processing

This review presents some applications of proteomics and selected spectroscopic methods to validate certain aspects of seafood traceability. After a general introduction to traceability and the initial applications of proteomics to authenticate traceability information, it addresses the application of proteomics to trace seafood exposure to some increasingly abundant emergent health hazards with the potential to indicate the geographic/environmental origin, such as microplastics, triclosan and human medicinal and recreational drugs. Thereafter, it shows the application of vibrational spectroscopy (Fourier-Transform Infrared Spectroscopy (FTIR) and Fourier-Transform Raman Spectroscopy (FT Raman)) and Low Field Nuclear Magnetic Resonance (LF-NMR) relaxometry to discriminate frozen fish from thawed fish and to estimate the time and temperature history of frozen fillets by monitoring protein modifications induced by processing and storage. The review concludes indicating near future trends in the application of these techniques to ensure seafood safety and traceability.

Identification of peptide biomarkers for authentication of Atlantic salmon and rainbow trout with untargeted and targeted proteomics approaches and quantitative detection of adulteration

Atlantic salmon is often adulterated or substituted by rainbow trout with much lower price and quality. However, it is extremely difficult to distinguish Atlantic salmon and rainbow trout due to their similar appearance and close relationship in species. In the present work, untargeted and targeted proteomics approaches were both implemented to identify species-specific peptide biomarkers of Atlantic salmon and rainbow trout. Potential peptide biomarkers were obtained through matching HRMS data with UniProt database, screened by BLAST and then verified with real samples. Five peptide biomarkers were identified each for Atlantic salmon and rainbow trout. MRM method was established for quantitative measurement of rainbow trout Adulteration in Atlantic salmon, showing high sensitivity and repeatability. The biomarker peptide GDPGPGGPQGEQGVVGPAGISGDK was used for quantification. The limit of the detection (LOD) of adulteration of rainbow trout is 0.19%, and the limit of quantitation (LOQ) is 0.62%. Furthermore, this method was successfully applied to analyze a number of Atlantic salmon and Rainbow trout samples from different regions and different batches, as well as commercially available processed products.

Proteomics in Non-model Organisms: A New Analytical Frontier

For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.

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.

Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture

Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.

Differentiation and authentication of fishes at the species level through analysis of fish skin by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

RATIONALE

Authentication of fish is of importance in the view of toxins, allergen warnings and economic fraud control. Traditional methods in the authentication of fish, e.g. morphological, genetic and proteomic analysis, are either at low throughput or at high-cost.

METHODS

A high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS)-based approach was developed to analyze biomaterials from fish skin, and mass spectra from different fish species were compared by chemometric methods to differentiate fish species.

RESULTS

A total of 51 fish samples were used to generate more than 150 fingerprinting mass spectra. The fish belonging to the same genus can be identified at species level. A mass spectral database of different fishes can be built as reference for authentication. The analysis can be performed based on micrograms of fish-skin sample and accomplished in 1-3 hours.

CONCLUSIONS

The developed strategy holds potential to be applied to fish authentication in the fishing industry and as a scientific method to avoid mislabeling. It has promise to be practically used for fast and effective identification of closely related fish species to guarantee the quality of fishery products to consumers.

Species-Specific Discrimination of Insect Meals for Aquafeeds by Direct Comparison of Tandem Mass Spectra

Insect protein has the potential to become a sustainable feed ingredient for the rapidly growing aquaculture industry. In the European Union, insect derived protein is placed under the same legislation as processed animal proteins (PAP). It is therefore of interest to develop methods for regulatory use, which unambiguously identify the species origin of insect-based ingredients. We performed (i) total protein quantification of insect samples using the traditional nitrogen-to-protein conversion factor of 6.25 and the sum of anhydrous amino acids, (ii) quantitative amino acid profiling and (iii) high-throughput tandem mass spectrometry to describe and differentiate 18 different commercial-grade insect meal samples derived from Hermetia illucens (8), Tenebrio molitor (5), Alphitobius diaperinus (3) and Acheta domesticus (2). In addition, we investigated and compared different protein extraction and digestion protocols for proteomic analysis. We found that irrespective of sample preparation, shotgun proteomics in combination with direct spectral comparison were able to differentiate insect meal according to their taxonomic classification. The insect specific spectral libraries created in the present work can in future be used to develop more sensitive targeted methods of insect PAP identification and quantification in commercial feed mixtures.

Overview on Untargeted Methods to Combat Food Frauds: A Focus on Fishery Products

Authenticity and traceability of food products are of primary importance at all levels of the production process, from raw materials to finished products. Authentication is also a key aspect for accurate labeling of food, which is required to help consumers in selecting appropriate types of food products. With the aim of guaranteeing the authenticity of foods, various methodological approaches have been devised over the past years, mainly based on either targeted or untargeted analyses. In this review, a brief overview of current analytical methods tailored to authenticity studies, with special regard to fishery products, is provided. Focus is placed on untargeted methods that are attracting the interest of the analytical community thanks to their rapidity and high throughput; such methods enable a fast collection of “fingerprinting signals” referred to each authentic food, subsequently stored into large database for the construction of specific information repositories. In the present case, methods capable of detecting fish adulteration/substitution and involving sensory, physicochemical, DNA-based, chromatographic, and spectroscopic measurements, combined with chemometric tools, are illustrated and commented on.

Tandem mass spectral libraries of peptides and their roles in proteomics research

Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis. This review describes the historical development of spectral libraries in proteomics, details the computational procedures behind library building and searching, surveys the current applications of spectral libraries, and discusses the outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:634-648, 2017.

Review on proteomics for food authentication

Consumers have the right to know what is in the food they are eating. Accordingly, European and global food regulations require that the provenance of the food can be guaranteed from farm to fork. Many different instrumental techniques have been proposed for food authentication. Although traditional methods are still being used, new approaches such as genomics, proteomics, and metabolomics are helping to complement existing methodologies for verifying the claims made about certain food products. During the last decade, proteomics (the large-scale analysis of proteins in a particular biological system at a particular time) has been applied to different research areas within food technology. Since proteins can be used as markers for many properties of a food, even indicating processes to which the food has been subjected, they can provide further evidence of the foods labeling claim. This review is a comprehensive and updated overview of the applications, drawbacks, advantages, and challenges of proteomics for food authentication in the assessment of the foods compliance with labeling regulations and policies.

SIGNIFICANCE

This review paper provides a comprehensive and critical overview of the application of proteomics approaches to determine the authenticity of several food products updating the performances and current limitations of the applied techniques in both laboratory and industrial environments.

Species and tissues specific differentiation of processed animal proteins in aquafeeds using proteomics tools

The rapidly growing aquaculture industry drives the search for sustainable protein sources in fish feed. In the European Union (EU) since 2013 non-ruminant processed animal proteins (PAP) are again permitted to be used in aquafeeds. To ensure that commercial fish feeds do not contain PAP from prohibited species, EU reference methods were established. However, due to the heterogeneous and complex nature of PAP complementary methods are required to guarantee the safe use of this fish feed ingredient. In addition, there is a need for tissue specific PAP detection to identify the sources (i.e. bovine carcass, blood, or meat) of illegal PAP use. In the present study, we investigated and compared different protein extraction, solubilisation and digestion protocols on different proteomics platforms for the detection and differentiation of prohibited PAP. In addition, we assessed if tissue specific PAP detection was feasible using proteomics tools. All work was performed independently in two different laboratories. We found that irrespective of sample preparation gel-based proteomics tools were inappropriate when working with PAP. Gel-free shotgun proteomics approaches in combination with direct spectral comparison were able to provide quality species and tissue specific data to complement and refine current methods of PAP detection and identification.

SIGNIFICANCE

To guarantee the safe use of processed animal protein (PAP) in aquafeeds efficient PAP detection and monitoring tools are required. The present study investigated and compared various proteomics workflows and shows that the application of shotgun proteomics in combination with direct comparison of spectral libraries provides for the desired species and tissue specific classification of this heat sterilized and pressure treated (≥133°C, at 3bar for 20min) protein feed ingredient.

Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching

Proteomics methodology has seen increased application in food authentication, including tandem mass spectrometry of targeted species-specific peptides in raw, processed, or mixed food products. We have previously described an alternative principle that uses untargeted data acquisition and spectral library matching, essentially spectral counting, to compare and identify samples without the need for genomic sequence information in food species populations. Here, we present an interlaboratory comparison demonstrating how a method based on this principle performs in a realistic context. We also increasingly challenge the method by using data from different types of mass spectrometers, by trying to distinguish closely related and commercially important flatfish, and by analyzing heavily contaminated samples. The method was found to be robust in different laboratories, and 94-97% of the analyzed samples were correctly identified, including all processed and contaminated samples.

Differentiating samples and experimental protocols by direct comparison of tandem mass spectra

RATIONALE

Peptide tandem mass spectra can be analyzed by a number of means. They can be compared against predicted spectra of peptides derived from genome sequences, compared against previously acquired and identified spectra, or - sometimes - sequenced de novo. We recently introduced another method which compares spectra between liquid chromatography/tandem mass spectrometry (LC/MS/MS) datasets to determine the shared spectral content, and demonstrated how this can be applied in a molecular phylogenetic study using sera from human and non-human primates. We will here explore if such a method have other, serendipitous uses.

METHODS

We used the existing compareMS2 algorithm without modification on a diverse set of experiments.

RESULTS

First we conducted a small phylogenetic study, using (mammalian) bone samples to study old material, and human pathogens aiming to distinguish clinically important strains. Although not as straightforward as primate sera analysis, the method shows significant promise for all these applications. We also used the algorithm to compare 24 different protocols for extraction of proteins from muscle tissue. The results provided useful information in comparing protocols. Finally, we applied compareMS2 aiming for quality control of two traceable protein reference standards (troponin) used in clinical chemistry assays, by analysing the effect of storage conditions.

CONCLUSIONS

The results illustrate a broad applicability of the metric based on shared tandem mass spectra between LC/MS/MS datasets for analysing protein digests in different types of experiments. There is no reason to assume that our instance of this method is optimal in any of these situations, as it makes limited or no use of accurate mass and chromatographic retention time. We propose that with further improvement and refinement, this type of analysis can be applied as a simple but informative first step in many pipelines for bottom-up tandem mass spectrometry data analysis in proteomics and other fields, comparing or analysing large numbers of samples or datasets.

Proteomics for the authentication of fish species

Assessment of seafood authenticity and origin, mainly in the case of processed products (fillets, sticks, baby food) represents the crucial point to prevent fraudulent deceptions thus guaranteeing market transparency and consumers health. The most dangerous practice that jeopardies fish safety is intentional or unintentional mislabeling, originating from the substitution of valuable fish species with inferior ones. Conventional analytical methods for fish authentication are becoming inadequate to comply with the strict regulations issued by the European Union and with the increase of mislabeling due to the introduction on the market of new fish species and market globalization. This evidence prompts the development of high-throughput approaches suitable to identify unambiguous biomarkers of authenticity and screen a large number of samples with minimal time consumption. Proteomics provides suitable and powerful tools to investigate main aspects of food quality and safety and has given an important contribution in the field of biomarkers discovery applied to food authentication. This report describes the most relevant methods developed to assess fish identity and offers a perspective on their potential in the evaluation of fish quality and safety thus depicting the key role of proteomics in the authentication of fish species and processed products.

BIOLOGICAL SIGNIFICANCE

The assessment of fishery products authenticity is a main issue in the control quality process as deceptive practices could imply severe health risks. Proteomics based methods could significantly contribute to detect falsification and frauds, thus becoming a reliable operative first-line testing resource in food authentication.

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.