Two-dimensional gel and shotgun proteomics approaches to distinguish fresh and frozen-thawed curled octopus (Eledone cirrhosa)

Shotgun proteomics reveals changes in the pectoralis major muscle of broilers supplemented with passion fruit seed oil under cyclic heat stress conditions

The aim of this study was to characterize the proteins differentially expressed in the pectoralis major muscle of broilers supplemented with passion fruit seed oil (PFSO) under cyclic heat stress conditions. Ninety one-day-old male chicks were housed in cages arranged in a climatic chamber, where they were kept under cyclic heat stress for eight hours a day from the beginning to the end of the experiment. The birds were divided into two experimental groups, one group supplemented with 0.9% PFSO and a control group (CON) without PFSO supplementation. At 36 days of age, 18 birds were slaughtered to collect muscle samples. From pools of breast fillet samples from each group, proteolytic cleavage of the protein extracts was performed, and later, the peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The 0.9% PFSO supplementation revealed the modulation of 57 proteins in the pectoralis major muscle of broilers exposed to cyclic heat stress. Among them, four proteins were upregulated, and 46 proteins were downregulated. In addition, seven proteins were expressed only in the CON group. These results suggest that PFSO may increase heat tolerance, with a possible reduction in oxidative stress, activation of neuroprotective mechanisms, protection against apoptosis, decrease in inflammatory responses, and regulation of energy metabolism.

A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection

Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.

Cold-induced denaturation of muscle proteins in hairtail (Trichiurus lepturus) during storage: Physicochemical and label-free based proteomics analyses

Physicochemical, proteomics, and bioinformatics analyses were conducted to investigate protein profiles in Trichiurus haumela under frozen (120 d) and chilled (6 d) storage. Springiness, chewiness, myofibrillar active sulfhydryl content, and Ca²⁺-ATPase activity significantly decreased, suggesting that cold stress altered muscle proteins. Compared with fresh hairtail (FH), 66 common differentially abundant proteins (DAPs) had lower abundances in chilled (3 d; CSH) and frozen (120 d; FSH) hairtail, including myosin binding proteins, filamins, actinin, troponin, and muscle-restricted coiled-coil protein. Gene Ontology (GO) annotation showed DAPs were mainly involved in cellular process, cellular anatomical entity, intracellular, and binding items. Eukaryotic orthologous group (KOG) analysis revealed that changes in cytoskeleton and energy production and conversion functions dominated during cold storage, degrading the myofibril and connective tissue structures and the physicochemical performance of muscle tissues. This study presents deep insights into the protein alternation mechanisms in hairtail muscle under cold stress.

Label-free based proteomics revealed the specific changes of muscle proteins in pike eel (Muraenesox cinereus) under cold stress

•

Changes in protein profiles were investigated in pike eel during cold storage.

•

Cold storage decreased the springiness and MP content in muscle tissues.

•

137 and 148 DAPs were identified in the CPE and FPE compared with the PE samples.

•

Membrane and cytoskeletal proteins were vulnerable to damage during storage.

•

Proteomics revealed significant protein alterations in fresh and stored fish comparisons.

Chemical- and liquid chromatography coupled with mass spectrometry (LC–MS) based proteomics strategies were executed to investigate the alterations of protein profiles in pike eel (Muraenesox cinereus) muscle during chilling (CPE) and frozen (FPE) storage. Chemical results indicated that springiness and myofibrillar protein (MP) content of muscle tissues decreased significantly during 6 days of chilled and 120 days of frozen storage. LC–MS-based proteomics analysis suggested that great alterations occurred in muscle proteins mainly induced by cold stress. The differentially abundant proteins (DAPs) with low abundances in CPE and FPE samples included the annexins, fibronectin, ribosomal proteins, T-complex proteins, tubulin beta chain, and histones, which were mostly associated with the membrane structural constituents, cytoskeleton, and binding functional proteins. Results of eukaryotic cluster of orthologous group (KOG) verified that these identified DAPs were mainly converged in the cytoskeleton function resulting from cold conditions, which in turn affected the physical structure and chemical performances of muscle tissues.

Shotgun analysis to identify differences in protein expression between granulocytes and hyalinocytes of the European flat oyster Ostrea edulis

Recovery of wild populations of the European flat oyster Ostrea edulis is important for ecosystem health and conservation of this species, because native oyster populations have dramatically declined or disappeared in most European waters. Diseases have contributed to oyster decline and are important constrains for oyster recovery. Understanding oyster immune system should contribute to design effective strategies to fight oyster diseases. Haemocytes play a pivotal role in mollusc immune responses protecting from infection. Two main types of haemocytes, granulocytes and hyalinocytes, are distinguished in O. edulis. A study aiming to explore differential functions between both haemocyte types and, thus, to enrich the knowledge of Ostrea edulis immune system, was performed by comparing the proteome of the two haemolymph cell types, using a shotgun approach through liquid chromatography (LC) coupled to mass spectrometry (MS). Cells from oyster haemolymph were differentially separated by Percoll density gradient centrifugation. Shotgun LC-MS/MS performance allowed the identification of 145 proteins in hyalinocytes and 138 in the proteome of granulocytes. After a comparative analysis, 55 proteins with main roles in defence were identified, from which 28 were representative of granulocytes and 27 of hyalinocytes, plus 11 proteins shared by both cell types. Different proteins involved in signal transduction, apoptosis, oxidative response, processes related with the cytoskeleton and structure, recognition and wound healing were identified as representatives of each haemocyte type. Important signalling pathways in the immune response such as MAPK, Ras and NF-κβ seemed to be more relevant for granulocytes, while the Wnt signalling pathway, particularly relevant for wound healing, more relevant in hyalinocytes. The differences in proteins involved in recognition and in cytoskeleton and structure suggest differential specialisation in processes of phagocytosis and internalisation of pathogens between haemocyte types. Apoptosis seemed more active in granulocytes. The differences in proteins involved in oxidative response also suggest different redox processes in each cell type.

Effects of ultrasound on the thawing of quick-frozen small yellow croaker (Larimichthys polyactis) based on TMT-labeled quantitative proteomic

The effect of dual-frequency sequential ultrasonic thawing (DUT) on the quality of quick-frozen small yellow croaker was studied by TMT-labeled quantitative proteomic method. A total number of 75 proteins were identified as differentially abundant proteins (DAPs) in fish meat treated by DUT, while 72 DAPs were in flow water thawing (FWT). The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that the DAPs in the significant enrichment pathway of DUT group were enzymes. Compared with FWT, DUT had a significant effect on the enzyme content. The correlation analyses indicated that 40 DAPs were related with the quality traits. The 11 highly correlated DAPs are expected to be used as potential protein markers for texture profile analyses, color, thawing loss, water-holding capacity, and pH of thawed small yellow croaker quality. These results provide a further understanding of the quality stability of quick-frozen small yellow croaker treated by the DUT.

Differentiation between Fresh and Thawed Cephalopods Using NIR Spectroscopy and Multivariate Data Analysis

The sale of frozen–thawed fish and fish products, labeled as fresh, is currently one of the most common and insidious commercial food frauds. For this reason, the demand of reliable tools to identify the storage conditions is increasing. The present study was performed on two species, commonly sold in large-scale distribution: Cuttlefish (Sepia officinalis) and musky octopus (Eledone spp.). Fifty fresh cephalopod specimens were analyzed at refrigeration temperature (2 ± 2 °C), then frozen at −20 °C for 10 days and finally thawed and analyzed again. The performance of three near-infrared (NIR) instruments in identifying storage conditions were compared: The benchtop NIR Multi Purpose Analyzer (MPA) by Bruker, the portable MicroNIR by VIAVI and the handheld NIR SCiO by Consumer Physics. All collected spectra were processed and analyzed with chemometric methods. The SCiO data were also analyzed using the analytical tools available in the online application provided by the manufacturer to evaluate its performance. NIR spectroscopy, coupled with chemometrics, allowed discriminating between fresh and thawed samples with high accuracy: Cuttlefish between 82.3–94.1%, musky octopus between 91.2–97.1%, global model between 86.8–95.6%. Results show how food frauds could be detected directly in the marketplace, through small, ultra-fast and simplified handheld devices, whereas official control laboratories could use benchtop analytical instruments, coupled with chemometric approaches, to develop accurate and validated methods, suitable for regulatory purposes.

The use of the so-called 'superchilling' technique for the transport of fresh fishery products

Superchilling entails lowering the fish temperature to between the initial freezing point of the fish and about 1-2°C lower. The temperature of superchilled fresh fishery products (SFFP) in boxes without ice was compared to that of products subject to the currently authorised practice in boxes with ice (CFFP) under the same conditions of on-land storage and/or transport. A heat transfer model was developed and made available as a tool to identify under which initial configurations of SFFP the fish temperature, at any time of storage/transport, is lower or equal to CFFP. A minimum degree of superchilling, corresponding to an ice fraction in the fish matrix of SFFP equal or higher than the proportion of ice added per mass of fish in CFFP, will ensure with 99-100% certainty (almost certain) that the fish temperature of SFFP and the consequent increase of relevant hazards will be lower or equal to that of CFFP. In practice, the degree of superchilling can be estimated using the fish temperature after superchilling and its initial freezing point, which are subject to uncertainties. The tool can be used as part of 'safety-by-design' approach, with the reliability of its outcome being dependent on the accuracy of the input data. An evaluation of methods capable of detecting whether a previously frozen fish is commercially presented as 'superchilled' was carried out based on, amongst others, their applicability for different fish species, ability to differentiate fresh fish from fish frozen at different temperatures, use as a stand-alone method, ease of use and classification performance. The methods that were considered 'fit for purpose' are Hydroxyacyl-coenzyme A dehydrogenase (HADH) test, α-glucosidase test, histology, ultraviolet-visible-near-infrared (UV-VIS/NIR) spectroscopy and hyperspectral imaging. These methods would benefit from standardisation, including the establishment of threshold values or classification algorithms to provide a practical routine test.

Peptide markers for distinguishing guinea fowl meat from that of other species using liquid chromatography-mass spectrometry

The inability to easily identify the animal species in highly processed meat products makes them highly susceptible to adulterations. Reliable methods for detecting the species origin of meat used in processed food are required to ensure adequate labelling and minimize food fraud and allergenic potential. Liquid chromatography high resolution mass spectrometry was employed to identify new heat-stable guinea-fowl-specific peptide markers that can differentiate guinea fowl meat from other commonly consumed animal species, including closely related poultry species, in highly processed food products. We identified 26 unique guinea-fowl-specific markers. The high stability of guinea-fowl-specific peptides was confirmed by analysing food products with guinea fowl meat content ranging from 4% to 100%. The findings indicate that sensitive and reliable LC-MS/MS methods can be developed for the targeted detection and quantification of guinea fowl meat in highly processed meat products.

Emerging Techniques for Differentiation of Fresh and Frozen-Thawed Seafoods: Highlighting the Potential of Spectroscopic Techniques

Fish and other seafood products have a limited shelf life due to favorable conditions for microbial growth and enzymatic alterations. Various preservation and/or processing methods have been developed for shelf-life extension and for maintaining the quality of such highly perishable products. Freezing and frozen storage are among the most commonly applied techniques for this purpose. However, frozen–thawed fish or meat are less preferred by consumers; thus, labeling thawed products as fresh is considered a fraudulent practice. To detect this kind of fraud, several techniques and approaches (e.g., enzymatic, histological) have been commonly employed. While these methods have proven successful, they are not without limitations. In recent years, different emerging methods have been investigated to be used in place of other traditional detection methods of thawed products. In this context, spectroscopic techniques have received considerable attention due to their potential as being rapid and non-destructive analytical tools. This review paper aims to summarize studies that investigated the potential of emerging techniques, particularly those based on spectroscopy in combination with chemometric tools, to detect frozen–thawed muscle foods.

Mass Spectrometry for Analysis of Changes during Food Storage and Processing

Many physicochemical changes occur during food storage and processing, such as rancidity, hydrolysis, oxidation, and aging, which may alter the taste, flavor, and texture of food products and pose risks to public health. Analysis of these changes has become of great interest to many researchers. Mass spectrometry is a promising technique for the study of food and nutrition domains as a result of its excellent ability in molecular profiling, food authentication, and marker detection. In this review, we summarized recent advances in mass spectrometry techniques and their applications in food storage and processing. Furthermore, current technical challenges associated with these methodologies were discussed.

The Discovery of Proteins Associated with Freshness of Coregonus Peled Muscle During Refrigerated Storage

The aim of this study is to identify the protein indicator of freshness of Coregonus peled using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) methods. Samples were obtained prior to (control group) and 2, 4, 6, and 8 days after refrigerated storage for quality and proteomics analysis. Three proteins were found to have significant differential abundance in sample groups during the refrigerated storage, including l-lactate dehydrogenase, adenylate kinase isoenzyme 1, and myosin heavy chain, which were associated with freshness changes of C. peled. The freshness of C. peled fish during the refrigerated storage can be differentiated from the comparison of the specific proteins. PRACTICAL APPLICATION: The changes of food quality pose not only the relative economical loses but also the potential implications on consumer's health. Proteomics can represent a powerful tool to explore potential biomarkers that may be related to meat quality defects. The identification of key protein biomarkers linked to freshness of Coregonus peled allows to monitor the response of the food matrix during storage and try to minimizes these defects.