LC MS/MS identification of large structural proteins from bull muscle and their degradation products during post mortem storage

Proteomic analysis of wild boar meat: Effect of storage method and time on muscle protein stability

Oxidation processes affect proteins from various molecular pathways and are crucial for wild boar meat quality, shelf life and human health. This study investigated the effects of different storage methods on the formation and composition of oxygen-induced protein aggregates in the muscles of European wild boar (Sus scrofa scrofa). Vacuum packaging (VAC), modified atmosphere packaging (MAP) and dry-ageing (DA) were compared over a 21-day storage period. The results showed significant differences in protein aggregation depending on the method and storage time. The most intense protein aggregation occurred in the MAP (80 % O2), while air DA (20.9 % O2) resulted in intermediate levels of protein aggregation. Crucial myofibrillar proteins involved in aggregate formation were titin, myosin isoforms (MYH1, MYH2 and MYH7) and nebulin, which were cross-linked with small sarcoplasmic enzymes, such as muscle creatine kinase, isocitrate dehydrogenase and ATPase 1. High‑oxygen storage conditions also promoted the oxidation of ATP synthase, beta-enolase 3, ADP/ATP translocase and myoglobin.

Unveils key proteins in Xinjiang goat muscle linked to post-mortem meat quality: A TMT-based proteomic analysis

An extensive proteomic analysis utilizing the tandem mass tag (TMT) method was conducted to investigate the changes in protein expression in the longissimus dorsi muscle of Xinjiang goats over various post-mortem intervals: immediately after death within 0 h, 12 h, 24 h and 48 h. The investigation carefully identified around 108 proteins that showed significant changes in expression during these intervals. Among these proteins, six were highlighted for their crucial roles in muscle growth and differentiation of muscle fibers post-mortem. These proteins, namely COL12A1, MRPL46, CTNNB1, MYH1, CAPZA1, and MYL9, have a direct effect on the meat's quality attributes, such as tenderness and color. Further discuss observed a progressive increase in the expression of proteins linked with oxidative metabolism (MSRB2, ENOX1, LOC102170282, GSTM1, and AOC3) as the post-mortem aging period extended, particularly between 24 h to 48 h. These proteins are instrumental in defining the color and flavor profiles of goat meat, underscoring the importance of precise processing and storage conditions to preserve meat quality during the critical aging phase. This enhanced understanding of protein expression dynamics offers significant implications for optimizing meat quality and provides a scientific basis for post-mortem handling practices in the goat meat industry.

Quantitative Analysis of Deer Bone Hydroethanolic Extract Using Label-Free Proteomics: Investigating Its Safety and Promoting Effect on Mouse Embryonic Osteoblastic Progenitor Cell Proliferation

BACKGROUND

Deer bone is rich in proteins and free amino acids, offering high nutritional value and benefits such as strengthening bones and antioxidant properties. However, the development and utilization of deer bone resources are limited, and the safety evaluation of health foods is incomplete.

METHODS

We established a hydrogen ethanol extraction method for deer bone and analyzed the components of the deer bone hydroethanolic extract (DBHE) using liquid chromatography-tandem mass spectrometry (LC-MS/MS), gas chromatography-mass spectrometry (GC-MS), and inductively coupled plasma mass spectrometry (ICP-MS).

RESULTS

Using Label-free proteomics technology, we identified 69 proteins and 181 peptides. We also quantified 16 amino acids, 22 fatty acids, and 17 inorganic elements. Finally, we evaluated the safety of DBHE both in vitro and in vivo. The results indicated that DBHE did not exhibit any toxic effects at the doses we tested and can promote the proliferation of mouse embryonic osteoblastic progenitor cells (MC3T3-E1), demonstrating potential efficacy against osteoporosis and arthritis.

CONCLUSIONS

This study provides a theoretical basis for the quality control, processing, and resource development of deer bone.

Preparation of Complementary Food for Infants and Young Children with Beef Liver: Process Optimization and Storage Quality

In this study, fuzzy mathematics and response surface modeling were applied to optimize the preparation process of beef liver paste and characterize the proximate composition, sensory and physicochemical qualities, and in vitro simulated digestive properties while refrigerated at 0-4 °C (0, 3, 7, 15, 30, 45, and 60 days). The results showed that the optimal preparation process was 4.8% potato starch, 99.4% water, 10.2% olive oil, and a 3:2 ratio of chicken breast and beef liver. The beef liver paste prepared contained essential amino acids for infants and children, with a protein content of 10.29 g/100 g. During storage, the pH of the beef liver paste decreased significantly (p < 0.05) on day 7, texture and rheological properties decreased significantly after 30 days, a* values increased, L* and b* values gradually decreased, and TVB-N and TBARS values increased significantly (p < 0.05) on day 7 but were below the limit values during the storage period (TVB-N value ≤ 15 mg/100 g, TBARS value ≤ 1 mg/Kg). In vitro simulated digestion tests showed better digestibility and digestive characteristics in the first 15 days. The results of this study provide a reference for the development of beef liver products for infant and child supplementation.

Identification of novel serum autoantibody biomarkers for early esophageal squamous cell carcinoma and high-grade intraepithelial neoplasia detection

BACKGROUND

Early diagnosis of esophageal squamous cell carcinoma (ESCC) is critical for effective treatment and optimal prognosis; however, less study on serum biomarkers for the early ESCC detection has been reported. The aim of this study was to identify and evaluate several serum autoantibody biomarkers in early ESCC.

METHODS

We initially screened candidate tumor-associated autoantibodies (TAAbs) associated with ESCC by serological proteome analysis (SERPA) combined with nanoliter-liquid chromatography combined with quadrupole time of flight tandem mass spectrometry (nano-LC-Q-TOF-MS/MS), and the TAAbs were further subjected to analysis by Enzyme-linked immunosorbent assay (ELISA) in a clinical cohort (386 participants, including 161 patients with ESCC, 49 patients with high-grade intraepithelial neoplasia [HGIN] and 176 healthy controls [HC]). Receiver operating characteristic (ROC) curve was plotted to evaluate the diagnostic performance.

RESULTS

The serum levels of CETN2 and POFUT1 autoantibodies which were identified by SERPA were statistically different between ESCC or HGIN patients and HC in ELISA analysis with the area under the curve (AUC) values of 0.709 (95%CI: 0.654-0.764) and 0.741 (95%CI: 0.689-0.793), 0.717 (95%CI: 0.634-0.800) and 0.703 (95%CI: 0.627-0.779) for detection of ESCC and HGIN, respectively. Combining these two markers, the AUCs were 0.781 (95%CI: 0.733-0.829), 0.754 (95%CI: 0.694-0.814) and 0.756 (95%CI: 0.686-0.827) when distinguishing ESCC, early ESCC and HGIN from HC, respectively. Meanwhile, the expression of CETN2 and POFUT1 was found to be correlated with ESCC progression.

CONCLUSIONS

Our data suggest that CETN2 and POFUT1 autoantibodies have potential diagnostic value for ESCC and HGIN, which may provide novel insights for early ESCC and precancerous lesions detection.

iTRAQ-based proteomic analysis reveals the underlying mechanism of postmortem tenderization of refrigerated porcine Longissimus thoracis et lumborum muscle

The isobaric tags for relative and absolute quantitation (iTRAQ) technology was used for differential proteomic analysis of refrigerated porcine Longissimus thoracis et lumborum (LTL) muscle at different time points postmortem (45 min, 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h) to mechanistically elucidate the postmortem tenderization. Compared with the proteins identified in porcine LTL muscle at 45 min postmortem (control), 862 proteins were significantly expressed at 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h postmortem. Moreover, clustering and path analysis showed that the quality traits of porcine LTL muscle, including pH, shear force, myofibril fragmentation index, correlated significantly with 2, 6 and 6 differentially expressed proteins, respectively, with the lowest or highest expression at 8 h or 12 h postmortem. Overall, the tenderness of refrigerated porcine LTL muscle might be significantly affected by changes in quality traits at 8 h and 12 h postmortem.

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.

Proteomics and Metabolomics Profiling of Pork Exudate Reveals Meat Spoilage during Storage

Previous studies have evaluated pork quality by omics methods. However, proteomics coupled with metabolomics to investigate pork freshness by using pork exudates has not been reported. This study determined the changes in the profiles of peptides and metabolites in exudates from pork stored at different temperatures (25, 10, 4, and −2 °C). Multivariate statistical analysis revealed similar changes in profiles in exudates collected from pork stored at −2 and 4 °C, and additional changes following storage at higher temperatures. We identified peptides from 7 proteins and 30 metabolites differing in abundance between fresh and spoiled pork. Significant correlations between pork quality and most of the peptides from these 7 proteins and 30 metabolites were found. The present study provides insight into changes in the peptide and metabolite profiles of exudates from pork during storage at different temperatures, and our analysis suggests that such changes can be used as markers of pork spoilage.

New Insights on the Impact of Cattle Handling on Post-Mortem Myofibrillar Muscle Proteome and Meat Tenderization

This study investigated the effect of different cattle management strategies at farm (Intensive vs. Extensive) and during transport and lairage (mixing vs. non-mixing with unfamiliar animals) on the myofibrillar subproteome of Longissimus thoracis et lumborum (LTL) muscle of "Asturiana de los Valles" yearling bulls. It further aimed to study the relationships with beef quality traits including pH, color, and tenderness evaluated by Warner-Bratzler shear force (WBSF). Thus, comparative proteomics of the myofibrillar fraction along meat maturation (from 2 h to 14 days post-mortem) and different quality traits were analyzed. A total of 23 protein fragments corresponding to 21 unique proteins showed significant differences among the treatments (p < 0.05) due to any of the factors considered (Farm, Transport and Lairage, and post-mortem time ageing). The proteins belong to several biological pathways including three structural proteins (MYBPC2, TNNT3, and MYL1) and one metabolic enzyme (ALDOA) that were affected by both Farm and Transport/Lairage factors. ACTA1, LDB3, and FHL2 were affected by Farm factors, while TNNI2 and MYLPF (structural proteins), PKM (metabolic enzyme), and HSPB1 (small Heat shock protein) were affected by Transport/Lairage factors. Several correlations were found between the changing proteins (PKM, ALDOA, TNNI2, TNNT3, ACTA1, MYL1, and CRYAB) and color and tenderness beef quality traits, indicating their importance in the determination of meat quality and their possible use as putative biomarkers.

The Extent and Rate of the Appearance of the Major 110 and 30 kDa Proteolytic Fragments during Post-Mortem Aging of Beef Depend on the Glycolysing Rate of the Muscle and Aging Time: An LC-MS/MS Approach to Decipher Their Proteome and Associated Pathways

Post-mortem (p-m) muscle undergoes a myriad of complex physical and biochemical changes prior to its conversion to meat, which are influential on proteolysis and hence tenderization. A more in-depth understanding of the mechanisms underpinning these dynamics is a key to consistently providing tender beef. Using an LC-MS/MS approach, with state-of-art mass spectrometry Q Exactive HF-X, the proteome and associated pathways contributing to the appearance of the proteolytic breakdown products appearing over 14 days p-m, at two important molecular weights (110 and 30 kDa) on 1D SDS-PAGE gels, have been investigated in beef longissimus thoracis et lumborum muscles exhibiting four rates of pH decline differentiated on the basis of time at pH 6 (fast glycolysing, <3 h; medium, 3-5 h; slow, 5-8 h; and very slow, 8+ h). Both 110 and 30 kDa bands appeared during aging and increased in intensity as a function of p-m time in a pH decline-dependent manner. The 110 kDa band appeared as early as 3 h p-m and displayed an incremental increase in all groups through to 14 days p-m. From 2 days p-m, this increase in abundance during aging was significantly (P < 0.001) influenced by the glycolytic rate: fast > or = medium > slow > very slow. The day 2 p-m appearance of the 30 kDa band was most evident for the fast glycolysing muscle with little or no evidence of appearance in slow and very slow. For days 7 and 14 p-m, the strength of appearance was dependent on glycolysing groups fast > medium > or = slow > very slow. LC-MS/MS analysis yielded a total of 22 unique proteins for the 110 kDa fragment and 13 for the 30 kDa, with 4 common proteins related to both the actin and fibrinogen complex. The Gene Ontology analysis revealed that a myriad of biological pathways are influential with many related to proteins involved primarily in muscle contraction and structure. Other pathways of interest include energy metabolism, apoptotic mitochondrial changes, calcium and ion transport, and so on. Interestingly, most of the proteins composing the fragments were so far identified as biomarkers of beef tenderness and other quality traits.

In-Bag Dry- vs. Wet-Aged Lamb: Quality, Consumer Acceptability, Oxidative Stability and In Vitro Digestibility

The aim of this study was to produce in-bag dry-aged lamb and compare its meat quality, consumer acceptability, oxidative stability and in vitro digestibility to the wet-aged equivalents. Significantly higher pH, weight loss and reduced cook loss were observed in dry-aged lamb compared to the wet-aged (p < 0.0001). Dry-aged lamb had harder and chewier texture profiles and lower colour attributes (L*, a* and b*) than the wet-aged (p < 0.001). The dry-aged and wet-aged lamb were equally preferred (around 40% each) by the consumer panel, underpinning the niche nature of dry-aged meat. Significantly (p < 0.05) higher yeast and thiobarbituric acid reactive substances (TABRS) levels were observed in dry-aged lamb compared to the wet-aged. There was no difference in fatty acid profile, protein carbonyl content and pattern of proteolysis between ageing regimes (p > 0.05). Ageing regimes had no impact on overall digestibility; however, a greater gastric digestibility was observed in dry-aged lamb through the increased release of free amino acids (FAAs) compared to the wet-aged. Outcomes of this study demonstrated for the first time the possibility of producing dry-aged lamb legs of acceptable quality, oxidative stability and superior digestibility compared to the equivalent wet-aged lamb.

Effects of protein posttranslational modifications on meat quality: A review

Meat quality plays an important role in the purchase decision of consumers, affecting producers and retailers. The formation mechanisms determining meat quality are intricate, as several endogenous and exogenous factors contribute during antemortem and postmortem periods. Abundant research has been performed on meat quality; however, unexpected variation in meat quality remains an issue in the meat industry. Protein posttranslational modifications (PTMs) regulate structures and functions of proteins in living tissues, and recent reports confirmed their importance in meat quality. The objective of this review was to provide a summary of the research on the effects of PTMs on meat quality. The effects of four common PTMs, namely, protein phosphorylation, acetylation, S-nitrosylation, and ubiquitination, on meat quality were discussed, with emphasis on the effects of protein phosphorylation on meat tenderness, color, and water holding capacity. The mechanisms and factors that may affect the function of protein phosphorylation are also discussed. The current research confirms that meat quality traits are regulated by multiple PTMs. Cross talk between different PTMs and interactions of PTMs with postmortem biochemical processes need to be explored to improve our understanding on factors affecting meat quality.

Meat color is determined not only by chromatic heme pigments but also by the physical structure and achromatic light scattering properties of the muscle

Meat color is important for consumer acceptability, with excessively dark meat often associated with consumer rejection. It is determined chromatically by pigment content (measured by hue and chroma) and achromatically by scattering of light by the microstructure (measured by lightness), the latter of which has received minimal research focus. This review discusses the individual components of the meat microstructure that cause differences in achromatic contributions to color. Differences in achromatic light scattering between light and dark extremes of meat color are most likely explained by structural attributes within the muscle cell. These differences are proposed to arise from variations in (a) transverse shrinkage of the structural lattice of the myofilaments, myofibrils, and muscles fibers, (b) longitudinal shrinkage of the sarcomere, and (c) different protein composition of the surrounding medium (sarcoplasm and extracellular space). These are discussed at a mechanistic level, in relation to six parameters of the muscle cell: (a) protein surface charge altering the myofilament spacing, (b) protein solubility, (c) sarcoplasmic protein binding to myofilaments and myofibrils, (d) integrity of the cytoskeleton and cell adhesion proteins, (e) sarcomere integrity and myofibrillar proteins, and (f) myosin denaturation and rigor bond modification. New data are presented to support the proposed role of structural elements in muscle causing achromatic light scattering and their contribution to the surface color of meat. In addition, the relationships between lightness and water holding capacity and pH are explored and the economic impact of dark meat for the meat industry is discussed.

LC⁻Q⁻TOF⁻MS/MS Identification of Specific Non-Meat Proteins and Peptides in Beef Burgers

Beef burgers are a popular food choice, due to their taste and convenience. The extensive range of beef burgers with different flavours currently offered on the market is adding to their growing consumption. This study detected and identified specific non-meat proteins and peptide markers originating from functional preparations, i.e., powdered mixes of protein additives and spices, used as meat substitutes in the production of ready-to-cook beef burgers. Twenty-eight soy proteins, including isoforms (nine milk-, three pea- and one beetroot-specific protein) were found concurrently with a set of peptide markers unique to soy glycinin and β-conglycinin, pea vicilin and provicilin, milk α_S1-casein, β-lactoglobulin, as well as beetroot elongation factor 2. Soy and beetroot proteins and peptides were observed in all burgers containing additives. Milk and pea proteins were included in powdered mixes but were not detected in burgers, indicating that their content was below the limit of detection. The study demonstrates that the proposed method can be implemented to analyse protein additives in cooked burgers; however, the presence of low amounts of additives, below 1–2%, should be further confirmed by using a more sensitive triple quadrupole instrument.

Reverse phase protein arrays for the identification/validation of biomarkers of beef texture and their use for early classification of carcasses

The validation of biomarkers and tools for the prediction of beef texture remains a challenging task. In this study, reverse phase protein arrays (RPPA) quantified 29 protein biomarkers in the m. Longissimus thoracis of Charolais cattle sampled early post-mortem. Myosin heavy chain 1 (MHC1, slow-oxidative fibers) and Retinal dehydrogenase 1 (ALDH1A1, oxidative enzyme) discriminated between tender and juicy vs. tough meat with residues classes and are validated as prime biomarkers of beef texture. Several proteins belonging to energy metabolism, heat shock and oxidative stress, cytoskeletal, cell signaling and apoptosis were related with tenderness. Among the unusual proteins, Four and a half LIM domains 1 (FHL1) and Tripartite motif protein 72 (TRIM72) correlated respectively negatively and positively with beef tenderness. Principal component regression was used for the first time to explain beef texture traits using biomarkers. The results are very promising as they revealed sophisticated mechanisms behind the tenderizing process.

Proteomic Investigation of Protein Profile Changes and Amino Acid Residue Level Modification in Cooked Lamb Meat: The Effect of Boiling

Hydrothermal treatment (heating in water) is a common method of general food processing and preparation. For red-meat-based foods, boiling is common; however, how the molecular level effects of this treatment correlate to the overall food properties is not yet well-understood. The effects of differing boiling times on lamb meat and the resultant cooking water were here examined through proteomic evaluation. The longer boiling time was found to result in increased protein aggregation involving particularly proteins such as glyceraldehyde-3-phosphate dehydrogenase, as well as truncation in proteins such as in α-actinin-2. Heat-induced protein backbone cleavage was observed adjacent to aspartic acid and asparagine residues. Side-chain modifications of amino acid residues resulting from the heating, including oxidation of phenylalanine and formation of carboxyethyllysine, were characterized in the cooked samples. Actin and myoglobin bands from the cooked meat per se remained visible on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, even after significant cooking time. These proteins were also found to be the major source of observed heat-induced modifications. This study provides new insights into molecular-level modifications occurring in lamb meat proteins during boiling and a protein chemistry basis for better understanding the effect of this common treatment on the nutritional and functional properties of red-meat-based foods.

Postmortem degradation of skeletal muscle proteins: a novel approach to determine the time since death

Estimating the time since death is a very important aspect in forensic sciences which is pursued by a variety of methods. The most precise method to determine the postmortem interval (PMI) is the temperature method which is based on the decrease of the body core temperature from 37 °C. However, this method is only useful in the early postmortem phase (~0-36 h). The aim of the present work is to develop an accurate method for PMI determination beyond this present limit. For this purpose, we used sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting, and casein zymography to analyze the time course of degradation of selected proteins and calpain activity in porcine biceps femoris muscle until 240 h postmortem (hpm). Our results demonstrate that titin, nebulin, desmin, cardiac troponin T, and SERCA1 degraded in a regular and predictable fashion in all samples investigated. Similarly, both the native calpain 1 and calpain 2 bands disintegrate into two bands subsequently. This degradation behavior identifies muscular proteins and enzymes as promising substrates for future molecular-based PMI determination technologies.

The in vitro digestibility of beef varies with its inherent ultimate pH

Animal carcasses and cuts of meat are usually differentiated and valued according to size and compositional attributes. An indicator of meat quality that is invisible to consumers is the inherent ultimate pH (pH_u), which affects organoleptic and processing characteristics.