Tandem mass tag labeling to characterize muscle-specific proteome changes in beef during early postmortem period

Effects of Nicotinamide Riboside Supplementation on Postmortem Mitochondrial Functionality and Apoptotic Activation

BACKGROUND/OBJECTIVES

Early postmortem mitochondrial function and apoptotic activation affect meat quality development. Nicotinamide riboside (NR) supplementation to pigs prior to harvest can improve pork color stability, but its mechanism remains unclear. This study aimed to evaluate the impact of NR supplementation on early postmortem mitochondrial functionality and apoptosis.

METHODS

Sixteen pigs (N = 16) were individually fed a control or NR-supplemented diet (30 mg·kg body weight-1·d-1) for 10 days prior to harvest. Longissimus dorsi muscle samples were collected at 45 min and 24 h postmortem and analyzed for mitochondrial functionality using high-resolution respirometry and apoptotic protein abundance (apoptosis regulator Bcl-2-associated X (BAX), apoptotic inducing factor (AIF), and caspase 3 (CASP3)) via immunoblotting.

RESULTS

NR-supplemented muscle exhibited lower proton leak-associated respiration at 45 min postmortem (p < 0.05), followed by a slower accumulation of mitochondrial outer membrane permeabilization (MOMP; p < 0.05) and a slower loss of mitochondrial integral function (p < 0.05) from 45 min to 24 h postmortem. NR supplementation decreased BAX abundance at 45 min postmortem but increased mature AIF abundance (62 kDa) at 24 h postmortem (p < 0.05). The abundance of CASP3 fragments (~29 kDa) decreased from 45 min to 24 h postmortem, independent of treatment (p < 0.05).

CONCLUSIONS

NR supplementation demonstrated the potential to protect mitochondrial integral function and alleviate apoptotic activation in early postmortem porcine skeletal muscle, which might contribute to a higher meat color stability in NR-supplemented pork during retail display.

Omics based technology application in poultry meat research

Omics techniques, including genomics, transcriptomics, proteomics, metabolomics, and lipidomics, analyze entire sets of biological molecules to seek comprehensive knowledge on a particular phenotype. These approaches have been extensively utilized to identify both biomarkers and biological mechanisms for various physiological conditions in livestock and poultry. The purpose of this symposium was not only to focus on how recent omics technologies can be used to gather, integrate, and interpret data produced by various methodologies in poultry research, but also to highlight how omics and bioinformatics have increased our understanding of poultry meat quality problems and other complex traits. This Poultry Science Association symposium paper includes 5 sections that cover: 1) functional annotation of cis-regulatory elements in the genome informs genetic control of complex traits in poultry, 2) mass spectrometry for proteomics, metabolomics, and lipidomics, 3) proteomic approaches to investigate meat quality, 4) spatial transcriptomics and metabolomics studies of wooden breast disease, and 5) multiomics analyses on chicken meat quality and spaghetti meat. These topics provide insights into the molecular components that contribute to the structure, function, and dynamics of the underlying mechanisms influencing meat quality traits, including chicken breast myopathies. This information will ultimately contribute to improving the quality and composition of poultry products.

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.

Effects of different electrostatic field intensities assisted controlled freezing point storage on water holding capacity of fresh meat during the early postmortem period

In this study, the effect of different intensity electrostatic fields on the water holding capacity (WHC) of fresh meat during the early postmortem period in controlled freezing point storage (CFPS) were investigated. Significantly lower cooking loss were found in low voltage electrostatic field (LVEF) and high voltage electrostatic field (HVEF) compared to the control group (CK) (p < 0.05). The myofibril fragmentation index and microstructure results suggested that the sample under HVEF treatment remained relatively intact. It has been revealed that the changes in actomyosin properties under electrostatic field treatment groups were due to the combination and dissociation of actomyosin binding into myofilament concentration, which consequently affects the muscle WHC. The study further demonstrated that the electrostatic field, especially HVEF, might increase the WHC of fresh meat by affecting the distribution of water molecules and physiochemical properties of actomyosin during the early postmortem period.

Early postmortem beef muscle proteome and metabolome variations due to supranutritional zinc and ractopamine hydrochloride supplementation

It was hypothesized that the longissimus thoracis (LT) muscle proteome, phosphoproteome, and metabolome could explain postmortem metabolism and tenderness differences in muscle from cattle supplemented zinc (Zn) and/or ractopamine hydrochloride (RH). High percentage Angus steers (N = 20) were fed in a 2 × 2 factorial assigned to Zn and RH treatments: control (CON; n = 10; analyzed 36 mg Zn/kg dry matter [DM]) or supranutritional Zn supplementation (SUPZN; n = 10; control diet + 60 mg Zn/kg DM [from ZnSO4] + 60 mg Zn/kg DM [from Zn-amino acid complex]) for the entire 89-d trial. During the 28 d before harvest, steers were blocked by body weight within Zn treatments to RH treatments of 0 (NO; n = 10) or 300 mg (RAC; n = 10) per steer per day. Steers were harvested at the Iowa State Meat Laboratory, where pH decline (1, 3, 6, and 24 h postmortem) was measured. At 24 h postmortem, LT muscle sections were removed from carcasses, and steaks were analyzed for Warner-Bratzler shear force (WBSF) values at 1, 3, 7, and 14 d postmortem. Muscle samples were taken at 1 h, 1, 3, 7, and 14 d postmortem for the following analysis: troponin-T degradation (1, 3, 7, and 14 d postmortem), myosin heavy chain analysis (1 h postmortem), sarcoplasmic proteome analysis through tandem mass tagging analysis (1 h and 1 d postmortem), metabolome analysis (1 h and 1 d postmortem), and phosphoproteome analysis (1 h postmortem). SUPZN-NO tended to have a lower (P = 0.06) pH at 6 h postmortem and a lower WBSF value (P = 0.06) at 1 d postmortem. CON-RAC had a higher (P = 0.04) pH at 6 h postmortem and WBSF value (P < 0.01) at 1 d postmortem. A lower pH at 6 h postmortem and lower WBSF value at 1 d postmortem in the SUPZN-NO treatment was accompanied by more sorbitol and fructose at 1 d postmortem, and less myosin regulatory light chain 2 at 1 h postmortem, and less adenosine monophosphate deaminase 1 (AMPD1) at 1 d postmortem than all other treatments. A higher pH at 6 h postmortem and higher WBSF value at 1 d postmortem in CON-RAC and SUPZN-RAC was accompanied by more soluble structural proteins (troponin-T and myosin-7) at 1 h postmortem than CON-NO. At 1 h postmortem, CON-RAC had more glyceraldehyde-3-phosphate dehydrogenase than CON-NO or SUPZN-RAC. Differences in energy metabolism enzymes, metabolites, and structural proteins may affect ATP production, rigor development, and lactate buildup which may explain the differences in postmortem metabolism and tenderness development at 1 d postmortem.

Impact of sampling location and aging on the Longissimus thoracis et lumborum muscle proteome of dry-aged beef

This study aimed to explore the differences in the proteome and molecular pathways between two sampling locations (external, internal) of bovine Longissimus thoracis et lumborum (LTL) muscles at 0, 21, and 28 days of dry-aging (i.e. 3, 24, and 31 days post-mortem). It further assessed the impact of post-mortem aging on the meat proteome changes and the biological processes at interplay. Proteins related to defence response to bacterium and regulation of viral entry into host cell were identified to be more abundant on the external location before dry-aging, which may be associated to the oxidative conditions and microbial activity to which post-mortem muscle is exposed during dressing, chilling, and/or quartering of the carcasses. This highlights the relevance of sampling from interior tissues when searching for meat quality biomarkers. As dry-aging progressed, the meat proteome and related biological processes changed differently between sampling locations; proteins related to cell-cell adhesion and ATP metabolic processes pathways were revealed in the external location at 21 and 28 days, respectively. On the other hand, the impact of aging on the proteome of the interior meat samples, evidenced that muscle contraction and structure together with energy metabolism were the major pathways driving dry-aging. Additionally, aging impacted other pathways in the interior tissues, such as regulation of calcium import, neutrophil activation, and regeneration. Overall, the differences in the proteome allowed discriminating the three dry-aging times, regardless of the sampling location. Several proteins were proposed for validation as robust biomarkers to monitor the aging process (tenderization) of dry-aged beef: TTN, GRM4, EEF1A1, LDB3, CILP2, TNNT3, GAPDH, SERPINI1, and OMD.

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.

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.

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.

Proteome alterations in human autopsy tissues in relation to time after death

Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.

Early postmortem muscle proteome and metabolome of beef longissimus thoracis muscle classified by pH at 6 hours postmortem

The objective was to identify metabolome and proteome differences at 1 h and 1 d postmortem between longissimus thoracis (LT) muscle classified based on 6 h pH values. Twenty beef LT rib sections were sorted based on 6 h postmortem pH values into low (LpH; pH < 5.55; n = 9) and high (HpH; pH > 5.84; n = 8) pH classifications. Warner-Bratzler shear force (WBSF), desmin degradation, and calpain-1 autolysis were measured. Two-dimensional difference in gel electrophoresis (3-10, 4-7, and 6-9 pH range) and Tandem mass tagging (TMT) protein analyses were employed to determine how the sarcoplasmic protein profile varied across pH classification. Non-targeted metabolomic analyses were conducted on extracts prepared at 1 h and 1 d postmortem. The LpH classification had a lower WBSF value at 1 d postmortem, which was explained by greater calpain-1 autolysis and desmin degradation at 1 d postmortem. Proteome and metabolome analysis revealed a phenotype that promotes more rapid energy metabolism in the LpH group. Proteome and metabolome analyses identified energy production, apoptotic, calcium homeostasis, and proteasome systems influencing pH classifications that could explain the observed pH, proteolysis, and beef tenderness differences. SIGNIFICANCE: This study is the first to identify proteomic and metabolomic variations early (1 h and 1 day) postmortem that are linked to differences in early (6 h) postmortem pH values and to tenderness differences at 1 day postmortem. This study integrates postmortem biochemical features (protein degradation, proteome, and metabolome variations) to postmortem pH decline and eating quality of beef steaks. Potential biomarkers of more rapid postmortem metabolism linked to earlier tenderization in beef are suggested. Identification of these biochemical features will assist in predicting the eating quality of beef products.

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.

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.

Tandem mass tag labeling to assess proteome differences between intermediate and very tender beef steaks

Tenderness is considered as one of the most important quality attributes dictating consumers' overall satisfaction and future purchasing decisions of fresh beef. However, the ability to predict and manage tenderness has proven very challenging due to the numerous factors that contribute to variation in end-product tenderness. Proteomic profiling allows for global examination of differentially abundant proteins in the meat and can provide new insight into biological mechanisms related to meat tenderness. Hence, the objective of this study was to examine proteomic profiles of beef longissimus lumborum (LL) steaks varying in tenderness, with the intention to identify potential biomarkers related to tenderness. For this purpose, beef LL muscle samples were collected from 99 carcasses at 0 and 384 h postmortem. Based on Warner-Bratzler shear force values at 384 h, 16 samples with the highest (intermediate tender, IT) and lowest (very tender, VT) values were selected to be used for proteomic analysis in this study (n = 8 per category). Using tandem mass tag-based proteomics, a total of 876 proteins were identified, of which 51 proteins were differentially abundant (P < 0.05) between the tenderness categories and aging periods. The differentially identified proteins encompassed a wide array of biological processes related to muscle contraction, calcium signaling, metabolism, extracellular matrix organization, chaperone, and apoptosis. A greater (P < 0.05) relative abundance of proteins associated with carbohydrate metabolism and apoptosis, and a lower (P < 0.05) relative abundance of proteins involved in muscle contraction was observed in the VT steaks after aging compared with the IT steaks, suggesting that more proteolysis occurred in the VT steaks. This may be explained by the greater (P < 0.05) abundance of chaperonin and calcium-binding proteins in the IT steaks, which could have limited the extent of postmortem proteolysis in these steaks. In addition, a greater (P < 0.05) abundance of connective tissue proteins was also observed in the IT steaks, which likely contributed to the difference in tenderness due to added background toughness. The established proteomic database obtained in this study may provide a reference for future research regarding potential protein biomarkers that are associated with meat tenderness.

Housekeeping Proteins in Meat Quality Research: Are They Reliable Markers for Internal Controls in Western Blot? A Mini Review

Advancements in technology and analytical methods enable researchers to explore the biochemical events that cause variation in meat quality. Among those, western blot techniques have been successfully used in identifying and quantifying the key proteins that have critical functions in the development of meat quality. Housekeeping proteins, like β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and tubulins are often used as internal controls in western blots to normalize the abundance of the protein of interest. However, there are increasing concerns about using housekeeping proteins for western blot normalization, as these proteins do not demonstrate any loading differences above the relatively small total protein loading amounts of 10μg. In addition, the interaction between these housekeeping proteins and programmed cell death processes highlights the concerns about using the housekeeping protein as the internal control in meat quality research. Moreover, recent proteomic research has indicated that the abundance of some housekeeping proteins, like β-actin, GAPDH, and tubulin, can be altered by preslaughter stress, dietary supplementation, sex, slaughter method, genotype, breed, aging period, muscle type, and muscle portion. Furthermore, these housekeeping proteins could have differential expression in meat with differing color stability, tenderness, and water holding capacity. Therefore, this review aims to examine the realities of using housekeeping proteins as the loading control in meat quality research and introduce some alternative methods that can be used for western blot normalization.

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

Beef quality is the first deciding factor for consumers to consider before purchasing. The aim of this study was to evaluate the effects of suspension and aging time on beef quality. We compared the differences in pH, drip loss, cooking loss, color, shear force, myofibril fragmentation index (MFI), and electron microscope of three muscle tissues between Achilles tendon (AT) and neck-arm restraint (NR) suspensions during seven aging periods (days 0, 1, 2, 3, 7, 14, and 21) after slaughter using the carcasses of six Xinjiang brown cattle. We found that NR suspension could significantly increase the water loss rate and MFI, as well as reduce the shear force compared to AT suspension. The muscle fiber structure with NR suspension was more severely damaged. The proteomics of longissimus dorsi was checked for the post-mortem days 1, 7, and 14. We detected 50, 26, and 29 differentially expressed proteins between NR and AT suspension at post-mortem days 1, 7, and 14, respectively. These proteins were involved in metabolic and muscle structure associated pathways and contributed to a comprehensive understanding of suspension-dependent meat quality regulation by proteins in beef cattle. To conclude, NR suspension can accelerate the aging time of beef carcasses, which will reduce the cost of carcass suspension and bring more benefits in the beef industry.

Tandem Mass Tag Labeling-Based Analysis to Characterize Muscle-Specific Proteome Changes during Postmortem Aging of Bison Longissimus Lumborum and Psoas Major Muscles

The objective of the study was to examine the variations in sarcoplasmic proteomes of bison longissimus lumborum (LL) and psoas major (PM) muscles during postmortem aging utilizing tandem mass tag (TMT) isobaric labeling coupled with liquid chromatography mass-spectrometry (LC-MS/MS) for the categorization of muscles with muscle-specific inherent color stability. A total of 576 proteins were identified (P < 0.05) in both bison LL and PM muscles, where 97 proteins were identified as differentially abundant (fold change > 1.5, P < 0.05) from the three comparisons between muscles during postmortem aging periods (PM vs LL at 2 d, 7 d and 14 d). Among those proteins, the most important protein groups based on functions are related to electron transport chain (ETC) or oxidative phosphorylation, tricarboxylic acid cycle (TCA), ATP transport, carbohydrate metabolism, fatty acid oxidation, chaperones, oxygen transport, muscle contraction, calcium signaling, and protein synthesis. In PM, most of the proteins from ETC, TCA cycle, fatty acid oxidation, ATP and oxygen transport, and muscle contraction were more abundant or exhibited increased expression during aging compared to LL. On the other hand, the proteins involved in carbohydrate metabolism, chaperone function and protein synthesis mostly exhibited decreased expression in PM muscle relative to LL. These results clearly demonstrate that the proteins associated with oxidative metabolism showed increased expression in PM muscles. This indicates that oxidative damage or subsequent color deterioration resulted in bison PM muscles being attacked by the reactive oxygen species produced during those metabolic process. In contrast, proteins involved in glycolysis and chaperone activity exhibited a decrease in expression in bison PM muscles, resulting decline in color stability compared with LL. Because glycolytic enzymes and chaperones maintain oxidative and/or color stability by producing reducing equivalents in glycolytic pathway and with the protein folding ability of chaperones, respectively in LL muscles.

Quantitative proteomic analysis of beef tenderness of Piemontese young bulls by SWATH-MS

Quantitative proteomic approach is a suitable way to tackle the beef tenderness. Ten aged-beef samples from Longissimus thoracis of Piemontese breed classified as tender (n = 5) and tough (n = 5) meat were evaluated using SWATH-MS and bioinformatic tools for the identification of the proteins and pathways most influencing tenderness variability. Between the two textural groups, proteomic changes were mainly caused by 43 differentially abundant proteins (DAPs) arranged in reference patterns as displayed by the heat map analysis. Most of these DAPs were associated with energy metabolism. From the functional proteomic analysis, two clusters of proteins, including ACO2, MDH1, MDH2 and CS in one cluster and FBP2, PFKL, LDHA, TPI1 and GAPDH/S in the other cluster, suggest gluconeogenesis, glycolysis and citrate cycle as key pathways for Piemontese breed beef tenderness. These findings contribute to a deeper insight into molecular pathways related to beef tenderness.

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.

Molecular signatures of beef tenderness: Underlying mechanisms based on integromics of protein biomarkers from multi-platform proteomics studies

Over the last two decades, proteomics have been employed to decipher the underlying factors contributing to variation in the quality of muscle foods, including beef tenderness. One such approach is the application of high-throughput protein analytical platforms in the identification of meat quality biomarkers. To broaden our understanding about the biological mechanisms underpinning meat tenderization across a large number of studies, an integromics study was performed to review the current status of protein biomarker discovery targeting beef tenderness. This meta-analysis is the first to gather and propose a comprehensive list of 124 putative protein biomarkers derived from 28 independent proteomics-based experiments, from which 33 robust candidates were identified worthy of evaluation using targeted or untargeted data-independent acquisition proteomic methods. We further provide an overview of the interconnectedness of the main biological pathways impacting tenderness determination after multistep analyses including Gene Ontology annotations, pathway and process enrichment and literature mining, and specifically discuss the major proteins and pathways most often reported in proteomics research.

Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem period

Bovine longissimus lumborum (LL) and psoas major (PM) muscles biopsy samples were collected from four carcasses (n = 4) at 45 min, 12 h, and 36 h postmortem from a commercial beef processing facility. Proteins present in the early postmortem LL and PM proteomes were identified and quantified using tandem mass tag (TMT) labelled, fractionated peptides coupled to liquid chromatography tandem mass spectrometry (LC-MS/MS). The data are supplied in this article and are related to "Tandem mass tag labeling to characterize muscle-specific proteome changes in beef during early postmortem period" by Zhai et al. [1].