Changes in glycolytic and mitochondrial protein profiles regulates postmortem muscle acidification and oxygen consumption in dark-cutting beef

Sequential window acquisition of all theoretical mass spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers

Recent advances in "omics" technologies have enabled the identification of new beef quality biomarkers and have also allowed for the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef. However, most of the studies conducted were carried out on a small number of animals and mostly applied gel-based proteomics. The present study proposes for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteome of DFD (pH24 ≥ 6.2) and CONTROL (5.4 ≤ pH24 ≤ 5.6) beef samples within the largest database of DFD/CONTROL beef samples to date (26 pairs of the Longissimus thoracis muscle samples of young bulls from Asturiana de los Valles breed, n = 52). The pairwise comparison yielded 35 proteins that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA revealed 31 and 36 proteins with VIP > 2.0, respectively. The combination of different statistical methods these being Volcano plot, PLS-DA and OPLS-DA allowed us to propose 16 proteins as good candidate biomarkers of DFD beef. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef condition.

In-depth exploration of the high and normal pH beef proteome: First insights emphasizing the dynamic protein changes in Longissimus thoracis muscle from pasture-finished Nellore bulls over different postmortem times

This study aimed to evaluate for the first time the temporal dynamic changes in early postmortem proteome of normal and high ultimate pH (pHu) beef samples from the same cattle using a shotgun proteomics approach. Ten selected carcasses classified as normal (pHu < 5.8; n = 5) or high (pHu ≥ 6.2; n = 5) pHu beef from pasture-finished Nellore (Bos taurus indicus) bulls were sampled from Longissimus thoracis muscle at 30 min, 9 h and 44 h postmortem for proteome comparison. The temporal proteomics profiling quantified 863 proteins, from which 251 were differentially abundant (DAPs) between high and normal pHu at 30 min (n = 33), 9 h (n = 181) and 44 h (n = 37). Among the myriad interconnected pathways regulating pH decline during postmortem metabolism, this study revealed the pivotal role of energy metabolism, cellular response to stress, oxidoreductase activity and muscle system process pathways throughout the early postmortem. Twenty-three proteins overlap among postmortem times and may be suggested as candidate biomarkers to the dark-cutting condition development. The study further evidenced for the first time the central role of ribosomal proteins and histones in the first minutes after animal bleeding. Moreover, this study revealed the disparity in the mechanisms underpinning the development of dark-cutting beef condition among postmortem times, emphasizing multiple dynamic changes in the muscle proteome. Therefore, this study revealed important insights regarding the temporal dynamic changes that occur in early postmortem of high and normal muscle pHu beef, proposing specific pathways to determine the biological mechanisms behind dark-cutting determination.

The importance of including metmyoglobin levels in reflectance-based oxygen consumption measurements

Reflectance-based oxygen consumption measurement utilizes changes in oxymyoglobin levels between bloomed and vacuum-packaged meat, assuming that oxymyoglobin is converted to deoxymyoglobin. However, the interconversion of oxymyoglobin to deoxymyoglobin depends on the age of the meat and the length of display; hence, oxygen consumption calculations might yield inaccurate interpretations if deoxymyoglobin is not the final form. The objective was to evaluate the effectiveness of determining metmyoglobin levels during oxygen consumption analysis and its relationship to beef color stability. Seven psoas major (color labile) and longissimus (color stable) were displayed in retail for 6 d and evaluated for oxygen consumption on the retail (oxygen exposed) and interior (non‑oxygen exposed) surfaces. The retail surface had greater (P < 0.05) metmyoglobin formed during oxygen consumption than the interior surface on d 6 of the display. Furthermore, the psoas major muscle exhibited greater (P < 0.05) metmyoglobin content during oxygen consumption than the longissimus on the retail surface paralleling with the decline in color stability. Therefore, the study indicates that sampling location and including metmyoglobin content in oxygen consumption calculations, along with changes in oxymyoglobin, will better explain meat color stability.

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

Effects of Premortem Stress on Protein Expression, Steak Color, Oxidation, and Myofibrillar Fragmentation Index in the Longissimus Lumborum

Forty castrated Holstein calves underwent an adrenocorticotropic hormone (ACTH) challenge to assess the effects of premortem stress on the longissimus lumborum (LL) following harvest. LL biopsies were collected before the challenge, at different harvest times (2, 12, 24, and 48 h; n = 10), and after 14 d aging. The expression of small heat shock proteins (SHSPs), deglycase 1 (DJ-1), and troponin were analyzed. Blood was analyzed throughout the ACTH challenge and at harvest for cortisol, oxidative stress, and complete blood count (CBC). Color and myofibrillar fragmentation index (MFI) were measured in aged samples. Unexpectedly, calves from different harvest times differed (p = 0.05) in cortisol response. Calves were divided into two different cortisol response groups (high or low; n = 20). Statistical analysis assessed the effects of cortisol response (n = 20), harvest time (n = 10), and their interaction. Harvest time altered SHSPs (p = 0.03), DJ-1 (p = 0.002), and troponin (p = 0.02) expression. Harvest time and cortisol response impacted steak color (p < 0.05), and harvest time altered steak pH (p < 0.0001). Additionally, various CBCs were changed (p < 0.05) by harvest time. Harvest time changed (p = 0.02) MFI. These data demonstrate that the protein expression, color, and MFI of the LL may be influenced by premortem stress.

The effect of succinate on color stability of Bos indicus bull meat: pH-dependent effects during the 14-day aging period

Bos taurus indicus bulls are very susceptible to pre-slaughter stress, which directly impacts the decline in muscle pH, leading to darker meat. The aim was to investigate the effect of succinate and atmosphere on the color stability of Nellore (Bos taurus indicus) Longissimus lumborum steaks classified by ultimate pH (pHu): normal pHu (5.40 ≤ pHu ≤ 5.79) and high pHu (pHu ≥ 5.80). The experimental treatment systems were: (i) vacuum packaging without succinate injection, (ii) HiOx-MAP (80 % O2 + 20 % CO2), and (iii) HiOx-MAP (80 % O2 + 20 % CO2) enhanced with sodium succinate injection (pH 5.4). Steaks from all treatment systems were stored at 4 °C for 14 days and tested for instrumental color, myoglobin content, oxygen consumption (OC), metmyoglobin-reducing activity (MRA), lipid oxidation, and microbiological analysis. High and normal pHu vacuum-packaged steaks exhibited greater color stability due to higher MRA. High and normal pHu steaks packaged with HiOx-MAP or HiOx-MAP enhanced with succinate showed improved color due to lower deoxymyoglobin content (%DMb) and OC up to the eighth day of storage. Still, succinate injection promoted increased (P < 0.05) lipid oxidation in normal pHu steaks and reduced MRA after 14 days. These findings emphasize the intricate interplay between pHu and packaging systems on Bos taurus indicus meat quality. Further research in this area could contribute to a better understanding of meat color abnormalities and provide insights into potential meat preservation and enhancement strategies.

Muscle of dark and normal beef differs metabolically

Reduction in muscle glycogen triggered by adverse antemortem handling events alters postmortem energy metabolism and results in a high ultimate pH and dark, firm and dry beef, often referred to as 'dark-cutting'. However, the relationship between atypical dark (AT) beef, postmortem energy metabolism and underlying tissue characteristics remains somewhat unclear. Cattle harvested in the US and Canada representing normal (pH < 5.6), AT dark (pH 5.6-5.8) and dark cutting (DC; pH > 5.8) beef were analyzed for tissue characteristics related to energy metabolism. Results show AT dark beef is more oxidative but similar to normal beef in glycolytic potential and nucleotide abundance. Mitochondria DNA content (P < 0.05, Canada; P < 0.005, US) and oxidative enzymes for DC and AT dark beef were greater (P < 0.01; Canada and US) compared to normal beef. Myoglobin tracked (P < 0.01) with color classification. These findings show both DC and AT beef are inherently more oxidative and raise the possibility that more oxidative muscle may be more prone to develop dark beef.

Contribution of mitochondria to postmortem muscle tenderization: a review

Postmortem meat tenderization is a process mediated by a series of biochemical reactions related to muscle cell death. Cell death is considered a sign that muscle has started to transform into meat. Mitochondria play a significant role in regulating and executing cell death, as they are an aggregation point for many cell death signals and are also the primary target organelle damaged by tissue anoxia. Mitochondrial damage is likely to have an expanded role in postmortem meat tenderization. This review presents current findings on mitochondrial damage induced by the accumulation of reactive oxygen species during postmortem anaerobic metabolism and on the impact of mitochondrial damage on proteolysis and discusses how this leads to improved tenderness during aging. The underlying mechanisms of mitochondrial regulation of postmortem muscle tenderization likely focus on the mitochondria's role in postmortem cell death and energy metabolism. The death process of postmortem skeletal muscle cells may exhibit multiple types, possibly involving transformation from autophagy to apoptosis and, ultimately, necroptosis or necrosis. Mitochondrial characteristics, especially membrane integrity and ATP-related compound levels, are closely related to the transformation of multiple types of dead postmortem muscle cells. Finally, a possible biochemical regulatory network in postmortem muscle tenderization is proposed.

Metabolomics Analysis Provides Novel Insights into the Difference in Meat Quality between Different Pig Breeds

The Chuanzang black (CB) pig is a new crossbred between Chinese local breeds and modern breeds. Here, we investigated the growth performance, plasma indexes, carcass traits, and meat quality characteristics of conventional DLY (Duroc × Landrace × Yorkshire) crossbreed and CB pigs. The LC-MS/MS-based metabolomics of pork from DLY and CB pigs, as well as the relationship between the changes in the metabolic spectrum and meat quality, were analyzed. In this study, CB pigs presented lower final body weight, average daily gain, carcass weight, and eye muscle area than DLY pigs (p ˂ 0.05). Conversely, the ratio of feed to gain, marbling score, and meat color score of longissimus dorsi (LD) were higher in CB than DLY pigs (p ˂ 0.05). Moreover, psoas major (PM) showed a higher meat color score and a lower cooking loss in CB than DLY pigs (p ˂ 0.05). Interestingly, CB pigs showed lower myofiber diameter and area but higher myofiber density than DLY pigs (p ˂ 0.05). Furthermore, the mRNA expression levels of MyHC I, PPARδ, MEF2C, NFATC1, and AMPKα1 were higher in CB than DLY pigs (p ˂ 0.05). Importantly, a total of 753 metabolites were detected in the two tissues (e.g., psoas major and longissimus dorsi) of CB and DLY pigs, of which the difference in metabolite profiles in psoas major between crossbreeds was greater than that in longissimus dorsi. Specifically, palmitic acid, stearic acid, L-aspartic acid, corticosterone, and tetrahydrocorticosterone were the most relevant metabolites of psoas major meat quality, and tetrahydrocorticosterone, L-Palmitoylcarnitine, arachidic acid, erucic acid, and 13Z,16Z-docosadienoic acid in longissimus dorsi meat were positively correlated with meat quality. The most significantly enriched KEGG pathways in psoas major and longissimus dorsi pork were galactose metabolism and purine metabolism, respectively. These results not only indicated improved meat quality in CB pigs as compared to DLY pigs but may also assist in rational target selection for nutritional intervention or genetic breeding in the swine industry.

Effects of mitochondria on postmortem meat quality: characteristic, isolation, energy metabolism, apoptosis and oxygen consumption

Meat quality holds significant importance for both consumers and meat producers. Various factors influence meat quality, and among them, mitochondria play a crucial role. Recent studies have indicated that mitochondria can sustain their functions and viability for a certain duration in postmortem muscles. Consequently, mitochondria have an impact on oxygen consumption, energy metabolism, and apoptotic processes, which in turn affect myoglobin levels, oxidative stress, meat tenderness, fat oxidation, and protein oxidation. Ultimately, these factors influence the color, tenderness, and flavor of meat. However, there is a dearth of comprehensive summaries addressing the effects of mitochondria on postmortem muscle physiology and meat quality. Therefore, this review aims to describe the characteristics of muscle mitochondria and their potential influence on muscle. Additionally, a suitable method for isolating mitochondria is presented. Lastly, the review emphasizes the regulation of oxygen consumption, energy metabolism, and apoptosis by postmortem muscle mitochondria, and provides an overview of relevant research and recent advancements. The ultimate objective of this review is to elucidate the underlying mechanisms through which mitochondria impact meat quality.

Molecular Changes of Meat Proteins During Processing and Their Impact on Quality and Nutritional Values

Meats are rich in lipids and proteins, exposing them to rapid oxidative changes. Proteins are essential to the human diet, and changes in the structure and functional attributes can greatly influence the quality and nutritional value of meats. In this article, we review the molecular changes of proteins during processing, their impact on the nutritional value of fresh and processed meat, the digestibility and bioavailability of meat proteins, the risks associated with high meat intake, and the preventive strategies employed to mitigate these risks. This information provides new research directions to reduce or prevent oxidative processes that influence the quality and nutritional values of meat.

Integrative proteomics and metabolomics profiling to understand the biochemical basis of beef muscle darkening at a slightly elevated pH

Previous studies investigated the biochemical basis of dark-cutting conditions at elevated muscle pH (above 6), but the molecular basis at slightly above normal pH (between 5.6 and 5.8) is still unclear. The objective was to determine protein and metabolite profiles to elucidate postmortem muscle darkening at slightly elevated pH. Loins were selected based on the criteria established in our laboratory before sample collections, such as pH less than 5.8, L* values (muscle lightness) less than 38, and not discounted by the grader (high-pH beef with dark color are discounted and not sold in retail stores). Six bright red loins (longissimus lumborum) at normal-pH (average pH = 5.57) and six dark-colored strip loins at slightly elevated pH (average pH = 5.70) from A maturity carcasses were obtained within 72-h postmortem from a commercial beef purveyor. Surface color, oxygen consumption, metmyoglobin reducing activity, protein, and metabolite profiles were determined on normal-pH and dark-colored steaks at slightly elevated pH. Enzymes related to glycogen metabolism and glycolytic pathways were more differently abundant than metabolites associated with these pathways. The results indicated that oxygen consumption and metmyoglobin reducing activity were greater (P < 0.05) in darker steaks than normal-pH steaks. Enzymes involved with glycogen catabolic pathways and glycogen storage disease showed lower abundance in dark beef. The tricarboxylic acid metabolite, aconitic acid, was overabundant in darker-colored beef than normal-pH beef, but glucose derivative metabolites were less abundant. The majority of glycogenolytic proteins and metabolites reported as overabundant in the previous dark-cutting studies at high pH (>6.4) also did not show significant differences in the current study. Therefore, our data suggest enzymes involved in glycogen metabolism, in part, create a threshold for muscle darkening than metabolites.

Effects of altitude on meat quality difference and its relationship with HIF-1α during postmortem maturation of beef

This study investigated the differences in meat quality during postmortem aging of yak meat from different altitudes as well as the relationship between the release of hypoxic factor HIF-1α and meat quality. The results showed that the HIF-1α increased with altitude but during aging process, there was an initial increase before a subsequent decrease (p < .05). Moreover, significant increases were showed in glycolytic potential, a* value, pH, HIF-1α mRNA expression, HIF-1α protein expression and shear force with altitude (p < .05). Additionally, the b* value, L* value, water holding power and MFI decreased significantly (p < .05). HIF-1α was shown, by PLS-DA method analysis, to be the main protein marker for differences in the quality during aging time of meat from three altitude groups. HIF-1α protein expression was high correlated with glycolytic potential, pH value, meat color, tenderness and water holding capacity during postmortem aging. The results demonstrated that HIF-1α is a novel marker protein that influences meat quality in yak from different altitudes and that HIF-1α-mediated glycolytic pathway was key to the meat quality during postmortem aging. PRACTICAL APPLICATIONS: Yak meat has the advantages of high protein, low fat, good amino acid and fatty acid composition, so the nutritional value of yak meat is in line with the current best-selling beef with less fat in domestic and foreign markets. But consumers often think that the meat tenderness of yak meat is worse than that of beef and improving the quality of yak meat was worthy of attention specifically. This study investigated the differences in meat quality during postmortem aging of yak meat at different altitudes and the relationship between hypoxic factor HIF-1α release and meat quality.

Exploratory lipidome and metabolome profiling contributes to understanding differences in high and normal ultimate pH beef

The aim of this work was to compare the lipidome and metabolome profiling in the Longissimus thoracis muscle early and late postmortem from high and normal ultimate pH (pHu) beef. Lipid profiling discriminated between high and normal pHu beef based on fatty acid metabolism and mitochondrial beta-oxidation of long chain saturated fatty acids at 30 min postmortem, and phospholipid biosynthesis at 44 h postmortem. Metabolite profiling also discriminated between high and normal pHu beef, mainly through glutathione, purine, arginine and proline, and glycine, serine and threonine metabolisms at 30 min postmortem, and glycolysis, TCA cycle, glutathione, tyrosine, and pyruvate metabolisms at 44 h postmortem. Lipid and metabolite profiles showed reduced glycolysis and increased use of alternative energy metabolic processes that were central to differentiating high and normal pHu beef. Phospholipid biosynthesis modification suggested high pHu beef experienced greater oxidative stress.

Study on the HIF-1α regulated by glycolytic pathways and mitochondrial function in yaks of different altitudes during postmortem aging

The study investigated the glycolysis pathway mediated by hypoxia-inducible factor-1α (HIF-1α) and the mechanism of its regulation. The results indicated that HIF-1α expression initially increased before subsequently decreasing with aging time during postmortem (p < .01). Glucose transporter-1 (GLUT-1), lactate dehydrogenase (LDH), and hexokinase (HK) displayed a similar trend with aging time (p < .01) while pyruvate dehydrogenase kinase 1 (PDK-1) increased gradually within the first 12 hr before decreasing at 24-120 hr. However, after treatment with a HIF-1α inhibitor, no significant differences were observed in the mitochondrial morphology. Furthermore, lactate content decreased, along with LDH, HK, and F0F1-ATP activities as well as GLUT-1 and PDK-1 expression (p < .01). The shear force for all groups also increased during postmortem aging (p < .01), with that of the controls being significantly higher compared with the treatment groups (p < .01). These findings confirmed that, after slaughter, the hypoxic environment within the muscles provided essential conditions for HIF-1α expression, which, in turn, activated the glycolysis pathway by mediating changes in the activities of glycolytic enzymes and mitochondrial function. Moreover, in accelerating glycolysis rate, the expression of HIF-1α further played a negative role in meat tenderization during postmortem aging. This, it was concluded that HIF-1α expression plays a significant role in postmortem yak meat tenderization by regulating the glycolysis pathway. PRATICAL APPLICATIONS: While converting muscle into meat through hypoxic glycolysis during postmortem aging is undeniable, the biochemical mechanism of this process mediated remains quite obscure. However, the meat quality difference which impact muscle regulation mechanism during postmortem aging has not been reported. The study investigated the HIF-1α played a major role in both the glycolytic pathway and as well as meat tenderness during the postmortem aging of yak meat. The glycolysis pathway is mediated by hypoxia-inducible factor-1α (HIF-1α), the mechanism of its regulation, and meat tenderness during the postmortem aging of yak meat.

Untargeted Metabolomics Reveals the Effect of Selective Breeding on the Quality of Chicken Meat

The selection for improved body weight is an effective approach in animal breeding. Guangxi Partridge chickens have differentiated into two lines under selective breeding, which include line S and line D that have shown statistically significant differences in body weight. However, the meat quality analysis in our study indicated that the quality of breast and thigh muscles in line S chickens changed, which included increased values of L*, b*, and drip loss and decreased a* value, pH, and shear force in skeletal muscles. To illuminate the effect of selection on skeletal muscles, LC-MS/MS metabolomics was performed to explore differentiated metabolites in divergent tissues from the two chicken lines. The results of principal component analysis and orthogonal projection to latent structures discriminant analysis suggested that metabolites of different groups were separated, which suggested that selective breeding certainly affected metabolism of skeletal muscles. KEGG analysis identified that valine, leucine, and isoleucine biosynthesis, glycerophospholipid metabolism, and glutathione metabolism noteworthily changed in breast muscle. Amino sugars and nucleotide sugar metabolism, ascorbate and aldarate metabolism, the pentose phosphate pathway, pentose and glucuronate interconversions, fructose and mannose metabolism, and glycerophospholipid metabolism were remarkedly identified in thigh muscle. These screened pathways suggested oxidative stress in breast and thigh muscles, which corresponded with our previous results. Therefore, this study determined that glycerophospholipid metabolism conservatively functioned in muscle flavor and development but exhibited different anti-oxidative patterns in different skeletal muscles. Overall, the present study identified several differentiated metabolites and pathways for exploring differences in meat quality between different broiler populations.

Metabolites Analysis on Water-Holding Capacity in Beef Longissimus lumborum Muscle during Postmortem Aging

Currently, the metabolomic research on water-holding capacity (WHC) of beef during postmortem aging is still insufficient. In this paper, the kit method was adopted for energy metabolites testing, the ultra-high-performance liquid chromatography (UHPLC) system was used for sample separation, and the mass spectrometer was applied to collect the primary and secondary spectra of the samples. The results showed that lactic acid reached saturation at day 2 postmortem, while energy metabolites changed significantly within day 2 postmortem (p < 0.05). Based on these findings, it was suggested that the energy metabolism qualities of the beef had already achieved a largely stable state at around day 2 postmortem. Then, through metabolomic analysis, 25 compounds were differentially abundant at days 0, 0.5, 1, and 2 during postmortem aging. Within the period of day 0−2 postmortem, the purine metabolism in beef was relatively active until 0.5 d postmortem, while glycolysis metabolism remained active until day 2 postmortem. The functions of the identified metabolites contribute to a more detailed molecular view of the processes behind WHC and are a valuable resource for future investigations into the flavor of postmortem beef.

Are muscle fiber types different between normal and dark-cutting beef?

Muscle fiber (MF) characteristics of Longissimus thoracis (LT) muscles from heifer (n = 11) and steer (n = 12) carcasses graded Canada AA (AA, normal, n = 4/sex) or dark-cutting (Canada B4) were examined and related to beef quality. Atypical (AB4, pH < 5.9, n = 4/sex) and typical (TB4, pH > 5.9, n = 3 and 4 for heifers and steers, respectively) dark-cutting carcasses were represented. Muscle fiber type proportions did not differ between AA, AB4 and TB4 muscles, although type I and IIB muscle fiber diameters were greater in TB4 than in AA LT. That AB4 muscle fiber proportions were not different from AA and TB4 muscles suggests that the increased MF diameter of TB4 muscle was due to water retained by muscle proteins at high ultimate pH, as evidenced by decreased cooking loss. Dark-cutting was therefore unrelated to muscle fiber proportions, and increased Type I and IIB diameters in dark cutting LT were likely driven by elevated intramuscular ultimate pH.

Impact of stunning before slaughter on expression of skeletal muscles proteome in sheep

The commercial production of halal and kosher meat and controversy surrounding the slaughter without stunning is rapidly growing across the globe. Huge global market for halal and kosher meat warrants conciliation of religious practices and animal welfare for the betterment of meat industry. In the present study, we investigated changes in muscle proteome of sheep (Ovis aries) subjected to either electrical stunning and slaughtering or slaughter without any stunning (halal). The 2DE gel analysis detected approximately 377 protein spots in which 243 (119 up regulated and 124 down regulated) protein spots were significantly (p ≤ 0.05) differentially expressed with a fold change ratio ≥1.5/≤1.5. The in-gel digestion and MALDI-TOF/TOF MS analysis of statistically significant protein spots revealed 35 differentially abundant proteins out of which 26 were up-regulated and 9 were down-regulated. The study demonstrated that slaughtering of sheep without stunning resulted in changes in the abundance of proteins involved in catalytic, structural, and stress related processes. This understanding of protein alterations in sheep slaughtered with and without stunning have the potential to act as possible signature for animal welfare index.

Protein Biomarkers of Bovine Defective Meats at a Glance: Gel-Free Hybrid Quadrupole-Orbitrap Analysis for Rapid Screening

An understanding of biological mechanisms that could be involved in the stress response of animal cattle prior to slaughter is critical to create effective strategies aiming at the production of high-quality meat. The sarcoplasmic proteome of directly extracted samples from normal and high ultimate pH (pHu) meat groups was studied through a straightforward gel-free strategy supported by liquid chromatography hybrid quadrupole-Orbitrap high-resolution mass spectrometry (LC-HRMS) analysis. A stepped proteomic pipeline combining rapid biomarker hunting supported by qualitative protein Mascot scores followed by targeted label-free peptide quantification revealed 26 descriptors that characterized meat groups assayed. The functional study of the proposed biomarkers suggested their relevant role in metabolic, chaperone/stress-related, muscle contractility/fiber organization, and transport activities. The efficiency, flexibility, rapidity, and easiness of the methodology proposed can positively contribute to the creation of innovative proteomic alternatives addressing meat quality assessment.

Dark-cutting beef: A brief review and an integromics meta-analysis at the proteome level to decipher the underlying pathways

Comprehensive characterization of the post-mortem muscle proteome defines a fundamental goal in meat proteomics. During the last decade, proteomics tools have been applied in the field of foodomics to help decipher factors underpinning meat quality variations and to enlighten us, through data-driven methods, on the underlying mechanisms leading to meat quality defects such as dark-cutting meat known also as dark, firm and dry (DFD) meat. In cattle, several proteomics studies have focused on the extent to which changes in the post-mortem muscle proteome relate to dark-cutting beef development. The present data-mining study firstly reviews proteomics studies which investigated dark-cutting beef, and secondly, gathers the protein biomarkers that differ between dark-cutting versus beef with normal-pH in a unique repertoire. A list of 130 proteins from eight eligible studies was curated and mined through bioinformatics for Gene Ontology annotations, molecular pathways enrichments, secretome analysis and biological pathways comparisons to normal beef color from a previous meta-analysis. The major biological pathways underpinning dark-cutting beef at the proteome level have been described and deeply discussed in this integromics study.

Proteomic pipeline for biomarker hunting of defective bovine meat assisted by liquid chromatography-mass spectrometry analysis and chemometrics

A wide variety of factors prior to slaughter may affect the stress status of beef cattle, giving rise to well-known 'dark-cutting' defective meats characterised by a high ultimate pH (pHu). To understand the underlying mechanisms of pHu fluctuations in beef cattle there was studied the proteome changes caused by pre-slaughter stress through a gel-free proteomic approach. Comparative peptidomic analysis was carried out on 12 loin samples at 24 h post-mortem from Longissimus thoracis et lumborum bovine muscle of crossbred animals, previously sorted into two different groups according to their pHu values: normal (pHu < 6.0) and high (pHu ≥ 6.0). Tryptic peptides from direct protein extracts were approached by combining untargeted (intact mass, MS¹) and targeted (Selected Reaction Monitoring, SRM) quantitative LC-MS assays followed by chemometric analysis. Seventeen peptide biomarkers belonging to 10 different proteins appropriately discriminated sample groups assayed. Results may promote the use of this simple and effective methodology towards the creation of new insights in meat quality research. SIGNIFICANCE: The significance of this study was the optimization of an affordable straightforward gel-free proteomic approach addressing the differentiation of the muscle sub-proteome of normal and high pHu meat samples. This strategy allowed the study of tryptic peptides from direct meat protein extracts by combining untargeted MS¹ and targeted SRM quantitative assays performed by conventional LC-MS detection. Affordability, simplicity and robustness of this methodology can facilitate its readily implementation in routine protocols for quality assessment of meat.