Label-free proteomic analysis reveals freshness-related proteins in sea bass (Lateolabrax japonicus) fillets stored on ice

Carvacrol-loaded nanoemulsions stabilized by soy protein isolate / chitooligosaccharide conjugates inhibited the oxidation and conformational variations of myofibrillar proteins in refrigerated sea bass (Lateolabrax maculatus)

Soy isolate protein / chitooligosaccharide (SPI/COS) glycosylated conjugates was prepared and employed as an emulsifier to stabilize carvacrol-loaded nanoemulsions (CNE-SPI/COS). The effects of CNE-SPI/COS on the oxidation and aggregation of myofibrillar protein (MPs) from sea bass (Lateolabrax maculatus) were investigated. Samples were immersed in sterile water (CK), SPI/COS solution and CNE-SPI/COS solution, respectively, follow by a 15-day refrigerated storage. MPs were extracted from fish fillets at 3-day intervals, then assessed for the oxidation degree and conformational changes in MPs, as well as structural variations in myofibrils. Compared with the CK group, the results obtained from protein oxidation assessment clarified that the oxidation and aggregation of MPs was significantly reduced by the CNE-SPI/COS treatment, as evidenced by the higher total sulfhydryl content and Ca2+-ATPase activity and lower surface hydrophobicity. Conformational analysis of MPs showed that CNE-SPI/COS was effective in maintaining the ordered secondary structure of MPs and reducing the exposure of hydrophobic residues in the hydrophobic core of the tertiary structure. In addition, CNE-SPI/COS was found to be effective in protecting the microstructure of muscle fibers and myofibrils in fish fillets. These results suggest that CNE-SPI/COS can be a promising method to prevent protein oxidation and aggregation in fish.

Role of the intestines on the muscle quality of Pacific white shrimp (Litopenaeus vannamei) during chilled storage: Physicochemical and label-free-based peptidomics analyses

The effect of shrimp deveining on the quality of Pacific white shrimp muscle was investigated by analyzing the protein degradation during chilled storage via physicochemical and label-free peptidomics analyses. In this study, shrimp with intact intestines were in the control group (CS), while deveined shrimp (DS) were in the treatment group. The total viability count (TVC), total volatile base nitrogen (TVB-N) content, and trichloroacetic acid (TCA)-soluble peptide content in all of the shrimp groups gradually increased with prolonged chilled storage. However, in the later stages of chilled storage, the DS samples exhibited significantly lower TVB-N, total bacterial, and TCA-soluble peptide contents than the CS samples, indicating that deveining treatment effectively prolonged shrimp quality. The peptidomics analysis revealed varying degrees of protein hydrolysis in the DS and CS samples during chilled storage. A total of 396 differentially abundant peptides (DAPs) were identified in the DS compared with the CS, comprising 98 upregulated and 298 downregulated segments. This suggests that the removal of the intestine effectively inhibits protein hydrolysis. Gene ontology (GO) analysis suggested that the DAPs were mainly involved in catalytic activity, binding, and metabolic processes. The cluster of orthologous groups of protein (COG) analysis showed that the cytoskeleton dynamics of the muscle proteins underwent considerable alterations influenced by the shrimp's intestines during chilled storage.

Towards a comprehensive understanding of the muscle proteome in Schizothorax labiatus: Insights from seasonal variations, metabolic responses, and reproductive signatures in the River Jhelum

Proteomics is a very advanced technique used for defining correlations, compositions and activities of hundreds of proteins from organisms as well as effectively used in identifying particular proteins with varying peptide lengths and amino acid counts. In the present study, an endeavour has been put forth to create muscle proteome expression of snow trout, Schizothorax labiatus. Liquid chromatography-mass spectrometry (LC-MS) using label free quantification (LFQ) technique has extensively been carried out to explore changes in protein metabolism and its composition to discriminate across species, clarify functions and pinpoint protein biomarkers from organisms. In LFQ technique, the abundances of proteins are determined based on the signal intensities of their corresponding peptides in mass spectrometry. The main benefit of using this method is that it doesn't require pre-labelling proteins with isotopic tags, which streamlines the experimental procedure and gets rid of any bias that might have been caused by the labelling process. LFQ techniques frequently offer a wider dynamic range, making it possible to detect and quantify proteins over a broad range of abundances obtained from the complex biological materials including fish muscle. The results of proteomic analysis could provide an insight in understanding about how various proteins are expressed in response to environmental challenges. For proteomic study, two different weight groups of S. labiatus were taken from River Jhelum based on biological, physiological and logistical factors. These groups corresponded to different life stages, such as younger size and adults/brooders in order to capture potential variations in the muscle proteome related to growth and development. The proteomic analysis of S. labiatus depicted that an overall of 220 proteins in male and 228 in female fish of group 1 were noted. However, when male and female S. labiatus were examined based on spectral count and peptide abundance using ProteinLynx Global Software, a total of 10 downregulated and 32 upregulated proteins were found. In group 2 of S. labiatus, a total of 249 proteins in male and 301 in female fish were documented. When the two genders of S. labiatus were likened to one another by LFQ technique, a total of 41 downregulated and 06 upregulated proteins were identified. The variability in the protein numbers between two fish weight groups reflected biological differences, influenced by factors such as age, developmental stages, physiological condition and reproductive activities. During the study, it was observed that S. labiatus exhibited downregulated levels of proteins that were involved in feeding and growth. The contributing factors to this manifestation could be explained by lower feeding and metabolic activity of fish and decreased food availability during winter in River Jhelum. Contrarily, the fish immune response proteins were found to be significantly over-expressed in S. labiatus, indicating that the environment was more likely to undergo increased microbial infection, pollution load and anthropogenic activities. In addition, it was also discovered that there was an upregulated expression of the reproductive proteins in S. labiatus, which could be linked to the fish's pre-spawning time as the fish used in this study was collected in the winter season which is the pre-spawning period of the fish. Therefore, the present study would be useful in obtaining new insights regarding the molecular makeup of species, methods of adaptation and reactions to environmental stresses. This information contributes to our understanding of basic science and may have applications in environmental monitoring, conservation and preservation of fish species.

The stable co-pigmented roselle anthocyanin active film extended shelf life of Penaeus vannamei better: Mechanism revealed by the TMT-labeled proteomic strategy

In order to investigate the influences of modified RAE-based film on shrimp quality, the proteomic approach was performed to elucidate preservation mechanism. Results showed that the modified RAE-based film kept better shrimp quality compared with natural RAE-based film in terms of determined biochemical parameters and estimated shelf-life. Totally, 49 differentially abundance proteins (DAPs) were identified compared with shrimp without packaging. Bioinformatics analysis demonstrated that the modified RAE-based film could maintain functional DAPs which were mainly distributed in the binding, catalytic activity, etc., and metabolic signaling pathways like melanogenesis signaling pathway were remarkably enriched. Meanwhile, there were 25 DAPs showing close relationship with quality traits, and some of them, such as myosin chains, troponin I and heat shock protein were considered as the potential biomarkers to evaluate shrimp quality deterioration. In conclusion, this study revealed the preservation mechanism of modified RAE-based active film on shrimp quality at the protein molecular level.

Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass (Dicentrarchus Labrax): Data Fusion Applications

Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.

Effect of vacuum and modified atmosphere packaging on moisture state, quality, and microbial communities of grouper (Epinephelus coioides) fillets during cold storage

The study aimed to assess the impact of different packaging methods on the moisture state, quality, and microbial composition of grouper fillets. The grouper fillets were packaged under the following four conditions: vacuum packaging (VP), 70% CO2/30% N2 (MAP1); 60% CO2/30% N2/10% O2 (MAP2); 40% CO2/30% N2/30% O2 (MAP3). Physicochemical and microbiological parameters were evaluated during 21 days of cold storage. The result demonstrated that MAP was effective in inhibiting microbial growth and accumulation of total volatile basic nitrogen (TVB-N), while also maintaining the water-holding capacity (WHC) of grouper fillets. Additionally, MAP1 effectively inhibited lipid and protein oxidation and protected the secondary structure of myofibrils compared to MAP2 and MAP3, with MAP1 samples having the lowest thiobarbituric acid reactive substances (TBARS) value (0.009-0.04 MDA/kg) and carbonyl content (0.20-0.26 μmol/g) and the highest sulfhydryl content (0.25-0.49 μmol/g) during cold storage. The results of high-throughput sequencing revealed that the presence of oxygen in the packaging system significantly influenced bacterial succession. Over time, Carnobacterium gradually became the dominant genera of fillets stored in MAP, and the presence of oxygen in MAP2 and MAP3 accelerated this transition by 9 days, compared to MAP1. In contrast, Enterobacteriaceae and Carnobacterium were the main dominant genera in VP. Remarkably, Enterobacteriaceae were virtually absent in MAP2 and MAP3 during storage, suggesting that the presence of oxygen exerted a significant inhibitory effect on Enterobacteriaceae. This study provides valuable insights into the application of MAP in the preservation of grouper fillets.

Integrated volatile compounds and non-targeted metabolomics analysis reveal the characteristic flavor formation of proteins in grouper (Epinephelus coioides) during cold storage

Microorganisms, lipids, and proteins always interact in a complex way in the fish matrix, which becomes a hindrance to evaluate the quality of the individual factors affecting them. In order to investigate the relationship between protein deterioration and volatile compounds (VOCs) in grouper during cold storage, the myofibril protein (MP) was used as a single-factor study to exclude microorganisms and lipids effects. The oxidation and degradation of MP during storage at 4 ℃ were evaluated, including MP content, total sulfhydryl content, carbonyl content, spatial structure and microstructure. Headspace-solid phase microextraction- gas chromatography-mass spectrometry (HS-SPME-GC-MS) was used to analyze the VOCs of grouper MP, and a total of 7 key VOCs were selected, including three ketones (2-nonanone, 2-undecanone and 2-tridecanone), three esters (methyl butyrate, methyl palmitate and methyl ester 9-octadecenoic acid) and one alcohol (3-methyl-1-butanol). At the same time, a non-targeted metabolomics method based on UPLC-Q-Extractive Orbitrap was used to investigate the changes in metabolites during MP storage. A total of 107 up-regulated differential metabolites and 7 down-regulated metabolites were annotated, and 6 metabolic pathways highly related to proteins were screened. Spearman correlation analysis showed that 7 key VOCs are associated with the biosynthesis and metabolism of ornithine and lysine. And a possible solution to protein deterioration in grouper was proposed, which provided a reference for improving protein quality and regulating flavor formation during cold storage of grouper at source.

Degradation and evaluation of myofibril proteins induced by endogenous protease in aquatic products during storage: a review

Myofibril proteins degradation constitutes an important factor in quality deterioration, procedural activation or inhibition of endogenous protease potential regulates autolytic proteolysis-induced softening of post mortem fish muscle. Based on the brief introduction of myofibril proteins degradation in fish skeletal muscle, a detailed description of the main myofibril degradation properties and the distinct role played by endogenous proteases were proposed, which reflects the limitations and challenges of the current research on myofibril hydrolysis mechanisms based on the varied surrounding conditions. In addition, the latest researches on the evaluation method of myofibril proteins degradation were comprehensively reviewed. The potential use of label-free proteomics combined with bioinformatics was also emphasized and has become an important means to in-depth understand protein degradation mechanism.

Quality changes and indicator proteins of Litopenaeus vannamei based on label-free proteomics analysis during partial freezing storage

Litopenaeus vannamei are known to deteriorate in quality during low-temperature storage. This study demonstrated the potential protein indicators of partial freezing of stored shrimp by traditional quality parameters and label-free based proteomic techniques. The carbonyl content and myofibril fragmentation index (MFI) of shrimp increased from 0.56 ± 0.03 to 2.14 ± 0.03 nmol/mg and 13.09 ± 0.14 to 54.93 ± 0.96, respectively. Within the extension of storage, the trichloroacetic acid (TCA), cooking loss and whiteness significantly increased. A total of 240 proteins changed in abundance at 10, 20, and 30 days compared to fresh samples. Projectin, ribosomal protein and histone were potential biomarkers for protein denaturation and oxidation in shrimp muscle. Myosin heavy chain and glyceraldehyde-3-phosphate dehydrogenase corresponded with the degradation of muscle proteins. Myosin light chain, tubulin alpha chain, and heat shock protein correlated with tenderness and water holding capacity; meantime, malate dehydrogenase and hemocyanin can serve as color indicators. Further study of the properties of these indicator proteins can inform their exploitation as quality indicator proteins during partial freezing storage.

Unraveling the effect of the combination of modified atmosphere packaging and ε-polylysine on the physicochemical properties and bacterial community of greater amberjack (Seriola dumerili)

The combined effect of ε-polylysine (PL) and modified atmosphere packaging (MAP; 60% CO2/40% N2) on the bacterial community of greater amberjack filets and their physicochemical properties was evaluated at 4°C. The total viable counts (TVC), psychrotrophic bacterial count, sensory index, texture analysis, and total volatile basic nitrogen (TVB-N) revealed that PL, MAP, and MAP + PL treatment delayed the deterioration of greater amberjack filets. These treatment groups also showed decreased accumulation of biogenic amines. High-throughput 16S rRNA gene sequencing results indicated that these treatments suppressed the growth of Pseudomonas in greater amberjack filets. Furthermore, the MAP + PL treatment group was observed to be more effective than the PL and MAP groups, extending the shelf life of greater amberjack filets by 6 days. This investigation showed that the combination of PL and MAP has the potential to retain the quality and extend the shelf life of greater amberjack.

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.

Bioinformatic Prediction and Characterization of Proteins in Porphyra dentata by Shotgun Proteomics

Porphyra dentata is an edible red seaweed with high nutritional value. It is widely cultivated and consumed in East Asia and has vast economic benefits. Studies have found that P. dentata is rich in bioactive substances and is a potential natural resource. In this study, label-free shotgun proteomics was first applied to identify and characterize different harvest proteins in P. dentata. A total of 13,046 different peptides were identified and 419 co-expression target proteins were characterized. Bioinformatics was used to study protein characteristics, functional expression, and interaction of two important functional annotations, amino acid, and carbohydrate metabolism. Potential bioactive peptides, protein structure, and potential ligand conformations were predicted, and the results suggest that bioactive peptides may be utilized as high-quality active fermentation substances and potential targets for drug production. Our research integrated the global protein database, the first time bioinformatic analysis of the P. dentata proteome during different harvest periods, improves the information database construction and provides a framework for future research based on a comprehensive understanding.

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

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

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

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

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Membrane and cytoskeletal proteins were vulnerable to damage during storage.

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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.

Photosynthetic Protein-Based Edible Quality Formation in Various Porphyra dentata Harvests Determined by Label-Free Proteomics Analysis

The influence of harvest time on the photosynthetic protein quality of the red alga Porphyra dentata was determined using label-free proteomics. Of 2716 differentially abundant proteins that were identified in this study, 478 were upregulated and 374 were downregulated. The top enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) pathways were metabolic processes and biosynthetic pathways such as photosynthesis, light harvesting, and carbon fixation in photosynthetic organisms. Nine important photosynthetic proteins were screened. Correlations among their expression levels were contrasted and verified by western blotting. PSII D1 and 44-kDa protein levels increased with later harvest time and increased light exposure. Specific photoprotective protein expression accelerated P. dentata growth and development. Biological processes such as photosynthesis and carbon cycling increased carbohydrate metabolism and decreased the total protein content. The results of the present study provide a scientific basis for the optimization of the culture and harvest of P. dentata.