Proteomic biomarkers of beef colour

Electrical stimulation to improve meat quality: Factors at interplay, underlying biochemical mechanisms and a second look into the molecular pathways using proteomics

Ensuring consistent beef eating quality is paramount for meeting consumer demands and sustaining the meat industry. Electrical stimulation (ES) is a post-slaughter intervention used to accelerate post-mortem glycolysis, to avoid cold shortening, to control the tenderization rate of meat through sophisticated physical, chemical and biochemical mechanisms including proteolysis, to improve beef tenderness and to achieve normal pHu that might lead to positive impact on color. This review comprehensively examines the multifaceted effects of ES on beef quality, encompassing factors and settings influencing its efficacy and the underlying biochemical mechanisms revealed using traditional biochemistry methods. It then delves into the molecular pathways modulated by ES, as unveiled by muscle proteomics, aiming to provide a second look and an unprecedented understanding of the underlying biochemical mechanisms through an integrative proteomics analysis of low-voltage ES (LVES) proteomics studies. The proteins changing as a result of ES were gathered in a compendium of 67 proteins, from which 14 were commonly identified across studies. In-depth bioinformatics of this compendium allowed a comprehensive overview of the molecular signatures and interacting biochemical pathways behind electrically stimulated beef muscles. The proteins belong to interconnected molecular pathways including the ATP metabolic process and glycolysis, muscle structure and contraction, heat shock proteins, oxidative stress, proteolysis and apoptosis. Understanding the intricate interplay of molecular pathways behind ES could improve the efficiency of beef production, ensuring consistent meat quality and meeting consumer expectations. The integrative analysis approach performed in this study holds promise for the meat industry's sustainability and competitiveness.

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.

Comparative proteomic analyses to investigate premature browning in high‑oxygen modified atmosphere packaged beef patties

This study compared the proteomics of beef patties under high‑oxygen modified atmosphere packaging (HiOx-MAP) and vacuum packaging (VP) during heating. The color and oxidation stability of fresh patties, and myoglobin denaturation of cooked patties were also measured. The results suggested that HiOx-MAP patties contained more oxymyoglobin in fresh meat and had higher myoglobin denaturation during heating than VP patties, resulting in premature browning (PMB) during cooking. Proteomic analysis found that the overabundance of proteasome subunit beta type-2 (PSMB2) and peroxiredoxin-2 (PRDX2) in HiOx-55 °C, which can remove the damaged proteins and inhibit oxidation respectively, are of benefit to meat color stability during storage, however, this was still insufficient to inhibit the occurrence of PMB during cooking. The high abundance of lamin B1 (LMNB1) in VP-55 °C can maintain the stability of meat color. This research provides greater understanding, based on proteomic perspectives, of the molecular mechanism of PMB.

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 effect of the production system on the proteomics profiles of the Longissimus thoracis muscle in Arouquesa cattle

Arouquesa cattle breed is an autochthonous Portuguese breed produced under a traditional mountain system that need improvement without affecting beef quality. The aim of this work is to compare the proteomics profiles of the Longissimus thoracis muscle from Arouquesa animals produced under different production systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF + S1) with weaning and slaughtering at 9 months, the S1 + S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF + S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative markers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins are involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. We identified specific proteins for each group related to different metabolisms involved in several aspects that affect meat quality parameters. Our results demonstrate the link between production practices and putative meat characteristics, which have the potential to improve the traceability of certified products. SIGNIFICANCE: Arouquesa breed is produced in a sustainable system using natural resources and contributing to the economy of low-populated rural regions in Northern Portugal. Besides their economic relevance, producing autochthonous breeds can counter rural depopulation and maintain local heritage. Additionally, consumer awareness about product quality is increasing and PDO products contribute to satisfying this demand. However, it is necessary to increase production so that it is possible to sell these products outside the production region. To ensure robust traceability and that PDO label characteristics are maintained despite increasing production yield, product analysis is of paramount importance. For this reason, proteomic approaches can provide insight into how production changes will affect beef quality and generate putative biomarkers of certified production systems.

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.

Proteomics and bioinformatics analyses based on two-dimensional electrophoresis and LC-MS/MS for the primary characterization of protein changes in chicken breast meat from divergent farming systems: Organic versus antibiotic-free

Proteomics is a key analytical method in meat research thanks to its potential in investigating the proteins at interplay in post-mortem muscles. This study aimed to characterize for the first time the differences in early post-mortem muscle proteomes of chickens raised under two farming systems: organic versus antibiotic-free. Forty post-mortem Pectoralis major muscle samples from two chicken strains (Ross 308 versus Ranger Classic) reared under organic versus antibiotic-free farming systems were characterized and compared using two-dimensional electrophoresis and LC-MS/MS mass spectrometry. Within antibiotic-free and organic farming systems, 14 and 16 proteins were differentially abundant between Ross 308 and Ranger Classic, respectively. Within Ross 308 and Ranger Classic chicken strains, 12 and 18 proteins were differentially abundant between organic and antibiotic-free, respectively. Bioinformatics was applied to investigate the molecular pathways at interplay, which highlighted the key role of muscle structure and energy metabolism. Antibiotic-free and organic farming systems were found to significantly impact the muscle proteome of chicken breast meat. This paper further proposes a primary list of putative protein biomarkers that can be used for chicken meat or farming system authenticity.

Acetylation and Phosphorylation Regulate the Role of Pyruvate Kinase as a Glycolytic Enzyme or a Protein Kinase in Lamb

Protein post-translational modifications (PTMs) play an essential role in meat quality development. However, the effect of specific PTM sites on meat proteins has not been investigated yet. The characteristics of pyruvate kinase M (PKM) were found to exhibit a close correlation with final meat quality, and thus, serine 99 (S99) and lysine 137 (K137) in PKM were mutated to study their effect on PKM function. The structural and functional properties of five lamb PKM variants, including wild-type PKM (wtPKM), PKM_S99D (S99 phosphorylation), PKM_S99A (PKM S99 dephosphorylation), PKM_K137Q (PKM K137 acetylation), and PKM_K137R (PKM K137 deacetylation), were evaluated. The results showed that the secondary structure, tertiary structure, and polymer formation were affected among different PKM variants. In addition, the glycolytic activity of PKM_K137Q was decreased because of its weakened binding with phosphoenolpyruvate. In the PKM_K137R variant, the actin phosphorylation level exhibited a decrease, suggesting a low kinase activity of PKM_K137R. The results of molecular simulation showed a 42% reduction in the interface area between PKM_K137R and actin, in contrast to wtPKM and actin. These findings are significant for revealing the mechanism of how PTMs regulate PKM function and provide a theoretical foundation for the development of precise meat quality preservation technology.

Data-independent acquisition-based SWATH-MS proteomics profiling to decipher the impact of farming system and chicken strain and discovery of biomarkers of authenticity in organic versus antibiotic-free chicken meat

In the literature, there is a paucity of methods and tools that allow the identification of biomarkers of authenticity to discriminate organic and non-organic chicken meat products. Shotgun proteomics is a powerful tool that allows the investigation of the entire proteome of a muscle and/or meat sample. In this study, a shotgun proteomics approach using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) has been applied for the first time to characterize and identify candidate protein biomarkers of authenticity in post-mortem chicken Pectoralis major muscles produced under organic and non-organic farming systems (antibiotic-free). The proteomics characterization was further performed within two chicken strains, these being Ross 308 and Ranger Classic, which differ in their growth rate. From the candidate protein biomarkers, the bioinformatics enrichment analyses revealed significant differences in the muscle proteome between the two chicken strains, which may be related to their genetic background and rearing conditions. The results further provided novel insights on the potential interconnected pathways at interplay that are associated with the differences as a consequence of farming system of chicken strain, such as muscle contraction and energy metabolism. This study could pave the way to more in-depth investigations in proteomics applications to assess chicken meat authenticity and better understand the impact of farming systems on the chicken muscle and meat quality.

Relationship between peptides and the change in quality characteristics of beef strip loin (M. longissimus lumborum) and tenderloin (M. psoas major)

Peptides in fresh and aged beef strip loin (M. longissimus lumborum) and tenderloin (M. psoas major) were quantified to investigate the relationship between proteolysis-induced peptides and beef quality characteristics. A total of 409 and 450 peptides were quantified from strip loin and tenderloin, respectively, and found to be significantly correlated to beef quality characteristics. Changes in redness and yellowness were significantly correlated to the peptides derived from G3P, ENOB, and KCRM in both muscles during 14 days of storage. The peptides produced from MYG, ENOB, HBA, PGK1, and TPIS were strongly associated with improved tenderness, while those derived from major myofibrillar proteins, such as MYH1, MYH2, ACTS, and DESM, were associated with changes in tenderloin color. These results improve our understanding of the association between peptides and changes in meat quality during cold storage, indicating that proteolysis-induced peptides can be indicators of the quality characteristics of fresh and aged meat.

The color of fresh pork: Consumers expectations, underlying farm-to-fork factors, myoglobin chemistry and contribution of proteomics to decipher the biochemical mechanisms

The color of fresh pork is a crucial quality attribute that significantly influences consumer perception and purchase decisions. This review first explores consumer expectations and discrimination regarding pork color, as well as an overview of the underlying factors that, from farm-to-fork, contribute to its variation. Understanding the husbandry factors, peri- and post-mortem factors and consumer preferences is essential for the pork industry to meet market demands effectively. This review then delves into current knowledge of pork myoglobin chemistry, its modifications and pork discoloration. Pork myoglobin, which has certain peculiarities comparted to other meat species, plays a weak role in determining pork color, and a thorough understanding of the biochemical changes it undergoes is crucial to understand and improve color stability. Furthermore, the growing role of proteomics as a high-throughput approach and its application as a powerful research tool in meat research, mainly to decipher the biochemical mechanisms involved in pork color determination and identify protein biomarkers, are highlighted. Based on an integrative muscle biology approach, the available proteomics studies on pork color have enabled us to provide the first repertoire of pork color biomarkers, to shortlist and propose a list of proteins for evaluation, and to provide valuable insights into the interconnected biochemical processes implicated in pork color determination. By highlighting the contributions of proteomics in elucidating the biochemical mechanisms underlying pork color determination, the knowledge gained hold significant potential for the pork industry to effectively meet market demands, enhance product quality, and ensure consistent and appealing pork color.

Meat Quality Traits in Beef from Heifers: Effect of including Distiller Grains in Finishing Pasture-Based Diets

Distiller grains (DG), which are the by-product from the bioethanol industry, represent an interesting alternative as animal feedstock. To our knowledge, little information is available on the inclusion of DG on the quality of meat from pasture-fed heifers. Thus, the aim of the present study was to evaluate the effect of DG inclusion in pasture-based systems on the main meat quality attributes of Charolais x Aberdeen Angus heifers. For this purpose, meat from heifers fed with a pasture-based diet without supplementation (P) or with 0.75% of live weight DG supplementation (PDG; DG plus dry-rolled corn, 50:50) or with 0.75% of live weight dry-rolled corn supplementation (PRC) was evaluated. Physical (pH, WHC, color, texture), sensory and nutritional (fat content, fatty acid, and amino acid profile) attributes were evaluated in beef samples. No effect of supplementation was observed on meat pH or color (p > 0.05). Meat from PDG heifers showed higher values of WBSF than meat from P heifers (p = 0.039). However, the overall tenderness evaluated by trained panelists showed no differences due to supplementation (p > 0.05). Our results indicate that the inclusion of DG as a partial corn-replacement supplementation for heifers under grazing represents a strategic tool not only related to meat quality, but also as an alternative to reduce food–feed competition.

In-depth characterization of the sarcoplasmic muscle proteome changes in lambs fed with hazelnut skin by-products: Relationships with meat color

This study investigated the effect of agro-industrial hazelnut skin by-products supplementation on lamb meat color variation and the changes in the sarcoplasmic muscle proteome during post-mortem storage (0, 4 and 7 days). Gel-based proteomics and bioinformatics approaches were applied to better understand the potential role of feeding strategies in modulating the mechanisms underpinning meat discoloration and post-mortem changes during storage. Therefore, twenty-two Valle del Belice male lambs were randomly assigned to two dietary treatments: control (C), lambs fed with maize-barley diet, and hazelnut skin (H), lambs fed hazelnut skin by-product as maize partial replacer in the concentrate diet. Hazelnut dietary treatment led to better lamb meat color stability as evidenced by the lowest decrease in redness and saturation index values. Proteomics and bioinformatics results revealed changes in the abundance of 41 proteoforms, which were mainly involved in glycolytic processes, responses to oxidative stress, and immune and endocrine system. The proteins allowed revealing interconnected pathways to be behind meat color variation as a consequence of using hazelnut skin by-products to sustainable feed lamb. The proteins can be used as potential predictors of lamb meat color variation. Accordingly, the regression equations developed in this paper revealed triosephosphate isomerase (TPI1) as a reliable candidate biomarker of color stability in lamb meat. SIGNIFICANCE: The use of agro-industrial by-products in animal feeding can be a potential sustainable strategy to reduce the environmental impacts of the food production chain and consequently improve animal welfare and product quality. The inclusion of hazelnut skin by-products in the animal's diet, due to the high concentration of polyphenols, represents an effective strategy to improve the oxidative stability of meat, with significant implications on color. The use of proteomics combined with bioinformatics on the sarcoplasmic proteome is a powerful approach to decipher the underlying mechanism. Accordingly, this approach allowed in this trial a deeper understanding of the molecular mechanisms involved in the post-mortem processes through the discovery of several biological pathways linked with lamb meat color variation. Glycolysis, followed by responses to oxidative stress, and other proteins involved in the immune and endocrine system were found as the major interconnected pathways that could act as potential predictors of lamb meat color stability. Candidate proteins biomarkers were further revealed in this study to be related with multiple meat color traits.

Towards the discovery of goat meat quality biomarkers using label-free proteomics

This study aimed to identify for the first time protein biomarkers of meat quality traits from Longissimus thoracis (LT) muscle of goats (Capra hircus). Male goats of similar age and weight reared under extensive rearing conditions were used to relate the LT muscle proteome with multiple meat quality traits. The early post-mortem muscle proteome analyzed using label-free proteomics was compared among three texture clusters built using hierarchical clustering analysis. Twenty-five proteins were differentially abundant and their mining using bioinformatics revealed three major biological pathways to be involved: 10 muscle structure proteins (MYL1, MYL4, MYLPF, MYL6B, MYH1, MYH2, ACTA1, ACTBL2, FHL1 and MYOZ1); 6 energy metabolism proteins (ALDOA, PGAM2, ATP5F1A, GAPDH, PGM1 and ATP5IF1), and two heat shock proteins: HSPB1 (small) and HSPA8 (large). Seven other miscellaneous proteins belonging to pathways such as regulation, proteolysis, apoptosis, transport and binding, tRNA processing or calmodulin-binding were further identified to play a role in the variability of goat meat quality. The differentially abundant proteins were correlated with the goat meat quality traits in addition to multivariate regression models built to propose the first regression equations of each quality trait. This study is the first to highlight in a multi-trait quality comparison the early post-mortem changes in the goat LT muscle proteome. It also evidenced the mechanisms underpinning the development of several quality traits of interest in goat meat production along the major biochemical pathways at interplay. SIGNIFICANCE: The discovery of protein biomarkers in the field of meat research is an emerging topic. In the case of goat meat quality, very few studies using proteomics have been conducted with the aim of proposing biomarkers. Therefore, this study is the first to quest for biomarkers of goat meat quality using label-free shotgun proteomics with a focus on multiple quality traits. We identified the molecular signatures underlying goat meat texture variation, which were found to belong to muscle structure and related proteins, energy metabolism and heat shock proteins along with other proteins involved in regulation, proteolysis, apoptosis, transport and binding, tRNA processing or calmodulin-binding. We further evaluated the potential of the candidate biomarkers to explain meat quality using the differentially abundant proteins by means of correlation and regression analyses. The results allowed the explanation of the variation in multiple traits such as pH, color, water-holding capacity, drip and cook losses traits and texture.

Post-mortem muscle proteome of crossbred bulls and steers: Relationships with carcass and meat quality

This study investigated the skeletal muscle proteome of crossbred bulls and steers with the aim of explaining the differences in carcass and meat quality traits. Therefore, 640 post-weaning Angus-Nellore calves were fed a high-energy diet for a period of 180 days. In the feedlot trial, comparisons of steers (n = 320) and bulls (n = 320) showed lower (P < 0.01) average daily gain (1.38 vs. 1.60 ± 0.05 kg/d), final body weight (547.4 vs. 585.1 ± 9.3 kg), which resulted in lower hot carcass weight (298.4 vs. 333.7 ± 7.7 kg) and ribeye area (68.6 vs. 81.0 ± 2.56 cm²). Steers had higher (P < 0.01) carcass fatness, meat color parameters (L*, a*, b*, chroma (C*), hue (h°)) and lower ultimate pH. Moreover, lower (P < 0.01) Warner-Bratzler shear force (WBSF) were observed in steers compared to bulls (WBSF = 3.68 vs. 4.97 ± 0.08 kg; and 3.19 vs. 4.08 ± 0.08 kg). The proteomic approach using two-dimensional electrophoresis, mass spectrometry and bioinformatics procedures revealed several differentially expressed proteins between steers and bulls (P < 0.05). Interconnected pathways and substantial changes were revealed in biological processes, molecular functions, and cellular components between the post-mortem muscle proteomes of the compared animals. Steers had increased (P < 0.05) abundance of proteins related to energy metabolism (CKM, ALDOA, and GAPDH), and bulls had greater abundance of proteins associated with catabolic (glycolysis) processes (PGM1); oxidative stress (HSP60, HSPA8 and GSTP1); and muscle structure and contraction (TNNI2 and TNNT3). The better carcass (fatness and marbling degree) and meat quality traits (tenderness and color parameters) of steers were associated with higher abundance of key proteins of energy metabolism and lower abundance of enzymes related to catabolic processes, oxidative stress, and proteins of muscle contraction SIGNIFICANCE: Sexual condition of cattle is known to be an important factor affecting animal performances and growth as well as the carcass and meat quality traits. The investigation of skeletal muscle proteome help a better understanding of the origin of the differences in quality traits between bulls and steers. The inferior meat quality of bulls was found to be due to the greater expression of proteins associated with primary and catabolic processes, oxidative stress, and muscle contraction. Steers had greater expression of proteins, from which several are known biomarkers of beef quality (mainly tenderness).

First insights into the dynamic protein changes in goat Semitendinosus muscle during the post-mortem period using high-throughput proteomics

Proteomics plays a key and insightful role in meat research in the post-genomic era. This study aimed to unveil using a shotgun proteomics approach the temporal dynamic changes in early post-mortem proteome of goat Semitendinosus muscle. Therefore, the evolution and comparison of the muscle proteome over three post-mortem times (1, 8, and 24 h) was assessed. The temporal proteomics profiling quantified 748 proteins, from which 174 were differentially abundant (DAPs): n = 55 between 1 h versus 8 h, n = 52 between 8 h versus 24 h, and n = 154 between 1 h versus 24 h. The DAPs belong to myriad interconnected pathways. Binding, transport and calcium homeostasis, as well as muscle contraction and structure, exhibited an equivalent contribution during post-mortem, demonstrating their central role. Catalytic, metabolism and ATP metabolic process, and proteolysis were active pathways from the first hours of animal bleeding. Conversely, oxidative stress, response to hypoxia and cell redox homeostasis along chaperones and heat shock proteins accounted for the large proportion of the biochemical processes, more importantly after 8 h post-mortem. Overall, the conversion of muscle into meat is largely orchestrated by energy production as well as mitochondrial metabolism and homeostasis through calcium and permeability transition regulation. The study further evidenced the role of ribosomal proteins in goat post-mortem muscle, signifying that several proteins experiencing changes during storage, also undergo splicing modifications, which is for instance a mechanism known for mitochondrial proteins. Overall, temporal proteomics profiling of early post-mortem muscle proteome offers an unparalleled view of the sophisticated post-mortem biochemical and proteolytic events associated with goat meat quality determination.

Molecular insights into quality and authentication of sheep meat from proteomics and metabolomics

Sheep meat (encompassing lamb, hogget and mutton) is an important source of animal protein in many countries, with a unique flavour and sensory profile compared to other red meats. Flavour, colour and texture are the key quality attributes contributing to consumer liking of sheep meat. Over the last decades, various factors from 'farm to fork', including production system (e.g., age, breed, feeding regimes, sex, pre-slaughter stress, and carcass suspension), post-mortem manipulation and processing (e.g., electrical stimulation, ageing, packaging types, and chilled and frozen storage) have been identified as influencing different aspects of sheep meat quality. However conventional meat-quality assessment tools are not able to elucidate the underlying mechanisms and pathways for quality variations. Advances in broad-based analytical techniques have offered opportunities to obtain deeper insights into the molecular changes of sheep meat which may become biomarkers for specific variations in quality traits and meat authenticity. This review provides an overview on how omics techniques, especially proteomics (including peptidomics) and metabolomics (including lipidomics and volatilomics) are applied to elucidate the variations in sheep meat quality, mainly in loin muscles, focusing on colour, texture and flavour, and as tools for authentication. SIGNIFICANCE: From this review, we observed that attempts have been made to utilise proteomics and metabolomics techniques on sheep meat products for elucidating pathways of quality variations due to various factors. For instance, the improvement of colour stability and tenderness could be associated with the changes to glycolysis, energy metabolism and endogenous antioxidant capacity. Several studies identify proteolysis as being important, but potentially conflicting for quality as the enhanced proteolysis improves tenderness and flavour, while reducing colour stability. The use of multiple analytical methods e.g., lipidomics, metabolomics, and volatilomics, detects a wider range of flavour precursors (including both water and lipid soluble compounds) that underlie the possible pathways for sheep meat flavour evolution. The technological advancement in omics (e.g., direct analysis-mass spectrometry) could make analysis of the proteins, lipids and metabolites in sheep meat routine, as well as enhance the confidence in quality determination and molecular-based assurance of meat authenticity.

Relationships between the abundance of 29 proteins and several meat or carcass quality traits in two bovine muscles revealed by a combination of univariate and multivariate analyses

We aimed to evaluate the relationships between meat or carcass properties and the abundance of 29 proteins quantified in two muscles, Longissimus thoracis and Rectus abdominis, of Rouge des Prés cows. The relative abundance of the proteins was evaluated using a high throughput immunological method: the Reverse Phase Protein array. A combination of univariate and multivariate analyses has shown that small HSPs (CRYAB, HSPB6), fast glycolytic metabolic and structural proteins (MYH1, ENO3, ENO1, TPI1) when assayed both in RA and LT, were related to meat tenderness, marbling, ultimate pH, as well as carcass fat-to-lean ratio or conformation score. In addition to some small HSP, ALDH1A1 and TRIM72 contributed to the molecular signature of muscular and carcass adiposity. MYH1 and HSPA1A were among the top proteins related to carcass traits. We thus shortened the list to 10 putative biomarkers to be considered in future tools to manage both meat and carcass properties. SIGNIFICANCE: In three aspects this manuscript is notable. First, this is the first proteomics study that aims to evaluate putative biomarkers of both meat and carcass qualities that are of economic importance for the beef industry. Second, the relationship between the abundance of proteins and the carcass or meat traits were evaluated by a combination of univariate and multivariate analyses on 48 cows that are representative of the biological variability of the traits. Third, we provide a short list of ten proteins to be tested in a larger population to feed the pipeline of biomarker discovery.

Effect of hazelnut skin by-product supplementation in lambs' diets: Implications on plasma and muscle proteomes and first insights on the underlying mechanisms

This study aimed to evaluate the effect of hazelnut skin by-product supplementation on lamb meat quality characteristics and plasma and muscle proteomes. Twenty-two Valle del Belice male lambs were divided into two experimental groups: control (C), fed a maize-barley diet and hazelnut (H), fed hazelnut skin by-product as maize partial replacer in the concentrate diet. The meat of lambs fed hazelnut skin showed greater values of lightness, redness, yellowness, and chroma color parameters together with the highest myofibril fragmentation index. Two-dimensional electrophoresis and mass spectrometry applied on plasma proteome identified 20 protein spots corresponding to 18 unique gene names to be differently expressed due to hazelnut skin by-product substitution. For the early post-mortem muscle, 23 protein spots (42 unique gene names) were significantly up-regulated due to hazelnut skin by-product supplementation. Four proteins these being APOA1, PHB, ACTG1 and ALB, were found to be common to the two proteomes suggesting that these proteins could be candidate biomarkers to monitor in vita and post-mortem lamb meat quality traits. This study evidenced the main mechanisms involved in the supplementation of hazelnut skin by-product in lambs' diet and confirmed the possibility of using plasma proteome as a non-invasive way to predict lamb meat quality. SIGNIFICANCE: Maximizing the use of agro-industrial by-products as replacers of traditional feedstuff for improving animal products is one of the important challenges to preserving natural resources and guaranteeing environmental sustainability. Hazelnut (Corylus avellana L.) skin, obtained as a results of hazelnut roasting, represents a valuable by-products due to its high content in unsaturated fatty acids, tannins, and vitamins. Thus, including hazelnut skin by-product in small ruminant nutrition could reduce the costs of animal feedings for farmers as well as improve meat nutritional and sensorial characteristics. Additionally, monitoring the meat quality characteristics with fast, accurate, and non-invasive tools to find, before slaughter, animals with desired quality characteristics is of growing interest in the last years. In this regard, the objectives of this study were to assess i) the effect of hazelnut skin supplementation on lamb meat quality characteristics and plasma and muscle proteomes, and ii) whether analyzing plasma proteome by using a gel-based proteomic approach could effectively offer a more readily available option for determining lamb meat quality. Taken together, the proteomic approach applied to plasma and muscle proteomes, allowed us to reveal the pathways and the potential candidate plasma biomarkers to predict lamb meat production in the pre-slaughter phase.

Metabolomics and bioinformatic analyses to determine the effects of oxygen exposure within longissimus lumborum steak on beef discoloration

Meat discoloration starts from the interior and spreads to oxymyoglobin layer on the surface. The effects of oxygen exposure within a steak on the metabolome have not been evaluated. Therefore, the objective of this study was to evaluate the impact of oxygen exposure on the metabolome of the longissimus lumborum muscle. Six United States Department of Agriculture (USDA) Low Choice beef strip loins were sliced into steaks (1.91-cm) and packaged in polyvinyl chloride overwrap trays for 3 or 6 d of retail display. The oxygen exposed (OE) surface was the display surface during retail, and the non-oxygen exposed (NOE) surface was the intact interior muscle. The instrumental color was evaluated using a HunterLab MiniScan spectrophotometer. To analyze the NOE surface on days 3 and 6, steaks were sliced parallel to the OE surface to expose the NOE surface. Metmyoglobin reducing ability (MRA) was determined by nitrite-induced metmyoglobin reduction. A gas chromatography-mass spectrometry was used to identify metabolites. The a* values of steaks decreased (P < 0.05) with display time. MRA was greater (P < 0.05) in the NOE surface compared with the OE surface on days 3 and 6. The KEGG pathway analysis indicated the tricarboxylic acid (TCA) cycle, pentose and glucuronate interconversions, phenylalanine, tyrosine, and tryptophan metabolism were influenced by the oxygen exposure. The decrease in abundance of succinate from days 0 to 6 during retail display aligned with a decline in redness during display. Furthermore, citric acid and gluconic acid were indicated as important metabolites affected by oxygen exposure and retail display based on the variable importance in the projection in the PLS-DA plot. Citric acid was lower in the NOE surface than the OE surface on day 6 of retail display, which could relate to the formation of succinate for extended oxidative stability. Greater alpha-tocopherol (P < 0.05) in the NOE surface supported less oxidative changes compared to the OE surface during retail display. These results indicate the presence of oxygen can influence metabolite profile and promote migration of the metmyoglobin layer from interior to surface.

Proteomics Unveils Post-Mortem Changes in Beef Muscle Proteins and Provides Insight into Variations in Meat Quality Traits of Crossbred Young Steers and Heifers Raised in Feedlot

Proteomics has been widely used to study muscle biology and meat quality traits from different species including beef. Beef proteomics studies allow a better understanding of the biological processes related to meat quality trait determination. This study aimed to decipher by means of two-dimensional electrophoresis (2D-PAGE), mass spectrometry and bioinformatics the changes in post-mortem muscle with a focus on proteins differentially expressed in the Longissimus thoracis (LT) muscle of immunocastrated young heifers and steers. Carcass traits, chemical composition, pH, instrumental color (L*, a*, b*), cooking loss and Warner-Bratzler shear force (WBSF) of meat from F1 Montana-Nellore cattle were also evaluated. Backfat thickness (BFT) and intramuscular fat content (IMF) were 46.8% and 63.6% higher in heifers (p < 0.05), respectively, while evaporation losses (EL) were 10.22% lower compared to steers. No differences (p > 0.05) were observed for tenderness evaluated by WBSF (3, 10, and 17 days post-mortem), pH, and color traits (L*, a* and b*) between the experimental groups. The study revealed several proteins to be differentially expressed proteins in heifers compared steers (p < 0.05). In heifers, proteins involved in nutrient transport (TF, ALB, and MB), energy metabolism (ALDOA, GAPDH, and PKM), and oxidative stress and response to stress (HSPA8 and CA3) were associated with a greater BFT and IMF deposition. The higher expression of these proteins indicated greater oxidative capacity and lower glycolytic activity in the LT muscle of heifers. In steers, there was greater abundance of protein expression related to muscle contraction and proteins of structure (ACTA1, TPM2 and TNNT3), energy metabolism (ENO1, ENO3, PYGM, PGM1 and TPI1) and ATP metabolism (ATP5F1B, PEBP1 and AK1), indicating greater glycogenolysis in LT muscle, suggesting a shift in the glycolytic/oxidative fibers of steers.

Metabolic, proteomic and microbial changes postmortem and during beef aging

The purpose of this review is to provide an overview of the current knowledge about proteomic and metabolic changes in beef, the microbiological alteration postmortem and during aging, and observe the influence on beef quality parameters, such as tenderness, taste and flavor. This review will also focus on the different aging types (wet- and dry-aging), the aging or postmortem time of beef and their effect on the proteome and metabolome of beef. The Ca2+ homeostasis and adenosine 5'-triphosphate breakdown are the main reactions in the pre-rigor phase. After rigor mortis, the enzymatic degradation of connective tissues and breakdown of energy metabolism dominate molecular changes in beef. Important metabolic processes leading to the formation of saccharides, nucleotides, organic acids (e.g. lactic acid), creatine and fatty acids are considered in this context as possible flavor precursors or formers of beef flavor and taste. Flavor precursors are substrates for lipid oxidation, Strecker degradation and Maillard reaction during cooking or roasting. The findings presented should serve as a basis for a better understanding of beef aging and its molecular effects and are intended to contribute to meeting the challenges of improving beef quality.

Alteration of Mitochondrial Lipidome and Its Potential Effect on Apoptosis, Mitochondrial Reactive Oxygen Species Production, and Muscle Oxidation in Beef during Early Postmortem

Lipid molecules are important participants in mitochondria-mediated apoptosis. This study explored the effect of mitochondrial lipids on mitochondria-mediated apoptosis, mitochondrial reactive oxygen species (ROS) production, and muscle oxidation of beef longissimus lumborum (LL, n = 6) and psoas major (PM, n = 6) during 24 h postmortem. A total of 432 lipid species matched with 21 lipid classes were identified. Remarkably, at 12 h postmortem, the levels of cardiolipin and phosphatidylserine in PM and ceramide, cardiolipin, phosphatidylserine, and sphingosine in LL increased significantly compared with 1 h postmortem, indicating that mitochondria-mediated apoptosis in beef muscle was accelerated during early postmortem. Moreover, PM had higher levels of cardiolipin and phosphatidylserine than LL, also suggesting a higher degree of apoptosis in PM during postmortem. Lipid molecules may assist the production of mitochondrial ROS and decrease the mitochondrial membrane potential (MMP) during postmortem apoptosis, resulting in muscle oxidation and the damage of antioxidant system. Notably, compared with LL, PM had higher abundance of apoptosis-related lipid molecules, a higher amount of ROS, faster diminishment in MMP, and then a higher degree of apoptosis. These findings provided new insights into the apoptosis and muscle biochemistry in beef during early postmortem.

Color attributes and myoglobin chemistry exhibit relationships with tenderness and calpain-1 abundance in postmortem Longissimus lumborum muscles from Holstein heifers

The objective of this study was to determine the extent that myoglobin and beef color are associated with calpain-1 relative abundance relative and tenderness. Longissimus lumborum (LL) samples from the left side of Holstein beef carcasses (n = 31) were collected immediately post-evisceration for 0 h analyses. At 48 h postmortem six steaks were removed from the right side of each carcass for analyses at 48 and 336 h postmortem. Myoglobin concentrations resulted in negative correlations (P < 0.05) to Warner-Bratzler shear force (WBSF) values at 336 h postmortem. L*, a*, and b* values at 48 h resulted in positive correlations (P < 0.05) with WBSF values at 48 and 336 h. Values for b* at 336 h had positive correlations with calpain-1 concentration at 0 and 336 h. Data from this study indicate a potential relationship between myoglobin concentration and meat color with tenderness aspects and calpain-1 relative abundance.

The Investigation of Protein Profile and Meat Quality in Bovine Longissimus thoracic Frozen under Different Temperatures by Data-Independent Acquisition (DIA) Strategy

The influence of freezing on the protein profile and quality traits in bovine Longissimus thoracic (LT) muscle was investigated by the data-independent acquisition (DIA) technique. Compared to fresh meat, a total of 262 proteins were identified as differential abundance proteins (DAPs) in four frozen groups (−12 °C, −18 °C, −38 °C, and −80 °C). According to the bioinformatics analysis, most of the DAPs in the significant Go terms and the KEGG pathway were structure proteins and enzymes. Proteome changes in the frozen bovine muscle at −12 °C and −18 °C were more significant than those at −38 °C and −80 °C. The result was consistent with the deterioration trend of the meat quality. The correlation analysis revealed that 17 proteins were correlated closely with the color, shear force, thawing loss, and cooking loss of the frozen meat, which could be used as putative biomarkers for frozen meat quality. MYO18A and ME3 are newly discovered proteins that are associated with frozen beef quality. In addition, CTTN and SERPINB6 were identified in frozen groups, which exhibited a significant inverse correlation with thawing loss (p < 0.01). These findings reveal the quality changes induced by freezing at the protein molecular level and provide new insights into the control of quality deterioration.

Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle

We aimed to investigate the effects of the maternal plane of nutrition during gestation on the proteome profile of the skeletal muscle of the newborn. Pregnant goats were assigned to the following experimental treatments: restriction maintenance (RM) where pregnant dams were fed at 50% of their maintenance requirements from 8−84 days of gestation, and then feed of 100% of the maintenance requirements was supplied from 85—parturition (n = 6); maintenance restriction (MR) where pregnant dams were fed at 100% of their maintenance requirements from 8−84 days of gestation, and then experienced feed restriction of 50% of the maintenance requirements from 85—parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis. The network analyses were performed to identify the biological processes and KEGG pathways of the proteins identified as differentially abundant protein and were deemed significant when the adjusted p-value (FDR) < 0.05. Our results suggest that treatment RM affects the energy metabolism of newborns’ skeletal muscle by changing the energy-investment phase of glycolysis, in addition to utilizing glycogen as a carbon source. Moreover, the RM plane of nutrition may contribute to fatty acid oxidation and increases in the cytosolic α-KG and mitochondrial NADH levels in the skeletal muscle of the newborn. On the other hand, treatment MR likely affects the energy-generation phase of glycolysis, contributing to the accumulation of mitochondrial α-KG and the biosynthesis of glutamine.

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.

DIA-based quantitative proteomic analysis on the meat quality of porcine Longissimus thoracis et lumborum cooked by different procedures

A DIA-based quantitative proteomic strategy was used to investigate the effects of different cooking procedures (steaming and boiling) on pork meat quality. Results showed that steamed meats had higher redness, cohesion, springiness, but lower lightness, yellowness, shear force, hardness, chewiness and cooking loss than boiled meats. In total of 1608 proteins were identified and 103 proteins exhibited significant difference (fold change > 1.5, P < 0.05). These DAPs mainly involved in protein structure, metabolic enzyme, protein turnover and oxidation stress. ALDOC, PVALB, PPP1R14C, AMPD1, CRYAB and SOD1 were validated as potential indicators of color variations in cooked meat. CFL1, COL1A1, COL3A1, RTN4, NRAP, NT5C3A, and SOD1 might be potential biomarker for texture changes of cooked meats. Moreover, these validated proteins exhibited significant (P < 0.05) correlation with cooking loss and could be serve as candidate predictors for cooking loss changes of meats in different cooking procedures.

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.

Proteomic Changes in Sarcoplasmic and Myofibrillar Proteins Associated with Color Stability of Ovine Muscle during Post-Mortem Storage

The objective of this study was to investigate the proteomic characteristics for the sarcoplasmic and myofibrillar proteomes of M. longissimus lumborum (LL) and M. psoasmajor (PM) from Small-tailed Han Sheep. During post-mortem storage periods (1, 3, and 5 days), proteome analysis was applied to elucidate sarcoplasmic and myofibrillar protein changes in skeletal muscles with different color stability. Proteomic results revealed that the identified differentially abundant proteins were glycolytic enzymes, energy metabolism enzymes, chaperone proteins, and structural proteins. Through Pearson’s correlation analysis, a few of those identified proteins (Pyruvate kinase, Adenylate kinase isoenzyme 1, Creatine kinase M-type, and Carbonic anhydrase 3) were closely correlated to representative meat color parameters. Besides, bioinformatics analysis of differentially abundant proteins revealed that the proteins mainly participated in glycolysis and energy metabolism pathways. Some of these proteins may have the potential probability to be predictors of meat discoloration during post-mortem storage. Within the insight of proteomics, these results accumulated some basic theoretical understanding of the molecular mechanisms of meat discoloration.

Green Coating Polymers in Meat Preservation

Edible coatings, including green polymers are used frequently in the food industry to improve and preserve the quality of foods. Green polymers are defined as biodegradable polymers from biomass resources or synthetic routes and microbial origin that are formed by mono- or multilayer structures. They are used to improve the technological properties without compromising the food quality, even with the purpose of inhibiting lipid oxidation or reducing metmyoglobin formation in fresh meat, thereby contributing to the final sensory attributes of the food and meat products. Green polymers can also serve as nutrient-delivery carriers in meat and meat products. This review focuses on various types of bio-based biodegradable polymers and their preparation techniques and applications in meat preservation as a part of active and smart packaging. It also outlines the impact of biodegradable polymer films or coatings reinforced with fillers, either natural or synthesized, via the green route in enhancing the physicochemical, mechanical, antimicrobial, and antioxidant properties for extending shelf-life. The interaction of the package with meat contact surfaces and the advanced polymer composite sensors for meat toxicity detection are further considered and discussed. In addition, this review addresses the research gaps and challenges of the current packaging systems, including coatings where green polymers are used. Coatings from renewable resources are seen as an emerging technology that is worthy of further investigation toward sustainable packaging of food and meat products.

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.

A comprehensive review on molecular mechanism of defective dry-cured ham with excessive pastiness, adhesiveness, and bitterness by proteomics insights

Excessive bitterness, pastiness, and adhesiveness are the main organoleptic and textural defects of dry-cured ham, which often cause a lot of financial losses to manufacturers and seriously damage the quality of the product. These sensory and textural defects are related to the protein degradation of dry-cured ham. Proteomics shows great potential to improve our understanding of the molecular mechanism of sensory and textural defects and identify biomarkers for monitoring their quality traits. This review presents some of the major achievements and considerations in organoleptic and textural defects of dry-cured ham by proteomics analysis in the recent decades and gives an overview about how to correct sensory and textural defects of dry-cured ham. Proteomics reveals that muscle proteins derived from myofibril and cytoskeleton and involved in metabolic enzymes and oxygen transport have been identified as potential biomarkers in defective dry-cured ham. Relatively high residual activities of cathepsin B and L are responsible for the excessive degradation of these protein biomarkers in defective dry-cured ham. Ultrasound-assisted mild thermal or high-pressure treatment shows a good correction for the organoleptic and textural defects of dry-cured ham by changing microstructure and conformation of muscle proteins by accelerating degradation of proteins and polypeptides into free amino acids.

A Proteomic Study for the Discovery of Beef Tenderness Biomarkers and Prediction of Warner-Bratzler Shear Force Measured on Longissimus thoracis Muscles of Young Limousin-Sired Bulls

Beef tenderness is of central importance in determining consumers’ overall liking. To better understand the underlying mechanisms of tenderness and be able to predict it, this study aimed to apply a proteomics approach on the Longissimus thoracis (LT) muscle of young Limousin-sired bulls to identify candidate protein biomarkers. A total of 34 proteins showed differential abundance between the tender and tough groups. These proteins belong to biological pathways related to muscle structure, energy metabolism, heat shock proteins, response to oxidative stress, and apoptosis. Twenty-three putative protein biomarkers or their isoforms had previously been identified as beef tenderness biomarkers, while eleven were novel. Using regression analysis to predict shear force values, MYOZ3 (Myozenin 3), BIN1 (Bridging Integrator-1), and OGN (Mimecan) were the major proteins retained in the regression model, together explaining 79% of the variability. The results of this study confirmed the existing knowledge but also offered new insights enriching the previous biomarkers of tenderness proposed for Longissimus muscle.

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.

Understanding the Determination of Meat Quality Using Biochemical Characteristics of the Muscle: Stress at Slaughter and Other Missing Keys

Despite increasingly detailed knowledge of the biochemical processes involved in the determination of meat quality traits, robust models, using biochemical characteristics of the muscle to predict future meat quality, lack. The neglecting of various aspects of the model paradigm may explain this. First, preslaughter stress has a major impact on meat quality and varies according to slaughter context and individuals. Yet, it is rarely taken into account in meat quality models. Second, phenotypic similarity does not imply similarity in the underlying biological causes, and several models may be needed to explain a given phenotype. Finally, the implications of the complexity of biological systems are discussed: a homeostatic equilibrium can be reached in countless ways, involving thousands of interacting processes and molecules at different levels of the organism, changing over time and differing between animals. Consequently, even a robust model may explain a significant part, but not all of the variability between individuals.

Insights on meat quality from combining traditional studies and proteomics

Following a century of major discoveries on the mechanisms determining meat colour and tenderness using traditional scientific methods, further research into complex and interactive factors contributing to variations in meat quality is increasingly being based on data-driven "omics" approaches such as proteomics. Using two recent meta-analyses of proteomics studies on beef colour and tenderness, this review examines how knowledge of the mechanisms and factors underlying variations in these meat qualities can be both confirmed and extended by data-driven approaches. While proteomics seems to overlook some sources of variations in beef toughness, it highlights the role of post-mortem energy metabolism in setting the conditions for development of meat colour and tenderness, and also points to the complex interplay of energy metabolism, calcium regulation and mitochondrial metabolism. In using proteomics as a future tool for explaining variations in meat quality, the need for confirmation by further hypothesis-driven experimental studies of post-hoc explanations of why certain proteins are biomarkers of beef quality in data-driven studies is emphasised.

Application of Proteomic Technologies to Assess the Quality of Raw Pork and Pork Products: An Overview from Farm-To-Fork

The quality assurance of pork meat and products includes the study of factors prior to slaughter such as handling practices, diet and castration, and others during the post-mortem period such as aging, storage, and cooking. The development over the last two decades of high-throughput techniques such as proteomics offer great opportunities to examine the molecular mechanisms and study a priori the proteins in the living pigs and main post-mortem changes and post-translational modifications during the conversion of the muscle into the meat. When the most traditional crossbreeding and rearing strategies to improve pork quality were assessed, the main findings indicate that metabolic pathways early post-mortem were affected. Among the factors, it is well documented that pre-slaughter stress provokes substantial changes in the pork proteome that led to defective meat, and consequently, novel protein biomarkers should be identified and validated. Additionally, modifications in pork proteins had a strong effect on the sensory attributes due to the impact of processing, either physical or chemical. Maillard compounds and protein oxidation should be monitored in order to control proteolysis and volatile compounds. Beyond this, the search of bioactive peptides is becoming a paramount goal of the food and nutraceutical industry. In this regard, peptidomics is a major tool to identify and quantify these peptides with beneficial effects for human health.