Search for proteomic biomarkers related to bovine pre-slaughter stress using liquid isoelectric focusing (OFFGEL) and mass spectrometry

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

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

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

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

Elucidating the Mechanisms of Sodium Benzoate in Alzheimer Disease: Insights from Quantitative Proteomics Analysis of Serum Samples

BACKGROUND

N-methyl-D-aspartate receptors (NMDARs) are crucial components of brain function involved in memory and neurotransmission. Sodium benzoate is a promising NMDAR enhancer and has been proven to be a novel, safe, and efficient therapy for patients with Alzheimer disease (AD). However, in addition to the role of sodium benzoate as an NMDA enhancer, other mechanisms of sodium benzoate in treating AD are still unclear. To elucidate the potential mechanisms of sodium benzoate in Alzheimer disease, this study employed label-free quantitative proteomics to analyze serum samples from AD cohorts with and without sodium benzoate treatment.

METHODS

The serum proteins from each patient were separated into 24 fractions using an immobilized pH gradient, digested with trypsin, and then subjected to nanoLC‒MS/MS to analyze the proteome of all patients. The nanoLC‒MS/MS data were obtained with a label-free quantitative proteomic approach. Proteins with fold changes were analyzed with STRING and Cytoscape to find key protein networks/processes and hub proteins.

RESULTS

Our analysis identified 861 and 927 protein groups in the benzoate treatment cohort and the placebo cohort, respectively. The results demonstrated that sodium benzoate had the most significant effect on the complement and coagulation cascade pathways, amyloidosis disease, immune responses, and lipid metabolic processes. Moreover, Transthyretin, Fibrinogen alpha chain, Haptoglobin, Apolipoprotein B-100, Fibrinogen beta chain, Apolipoprotein E, and Alpha-1-acid glycoprotein 1 were identified as hub proteins in the protein‒protein interaction networks.

CONCLUSIONS

These findings suggest that sodium benzoate may exert its influence on important pathways associated with AD, thus contributing to the improvement in the pathogenesis of the disease.

Role of the endoplasmic reticulum in the search for early biomarkers of meat quality

Defects in meat quality such as dark, firm and dry (DFD) beef have been related to high levels of oxidative stress that produce cellular alterations that may affect to the process of meat quality acquisition. Despite the important role of endoplasmic reticulum (ER) in the cellular response to oxidative stress, its function in the muscle-to-meat conversion process has not yet been studied. In this study, differences in muscular antioxidant defense and the unfolded protein response (UPR) of the ER in CONTROL (normal pH₂₄) and dark, firm, and dry (DFD, pH₂₄ ≥ 6.2) beef at 24 h post-mortem were analyzed to understand the changes in the muscle-to-meat conversion process related to meat quality defects. DFD meat showed poor quality, lower antioxidant activity (P < 0.05) and higher UPR activation (P < 0.05), which indicates higher oxidative stress what could partly explain the occurrence of meat quality defects. Therefore, the biomarkers of these cellular processes (IRE1α, ATF6α, and p-eIF2α) are putative biomarkers of meat quality.

New insights into the search of meat quality biomarkers assisted by Orbitrap Tribrid untargeted metabolite analysis and chemometrics

Metabolite profiles of normal and defective dry, firm and dark (DFD) meat extracts with known ultimate pH (pHu) values were determined by Orbitrap Tribrid ID-X untargeted analysis coupled to chemometrics. An intelligent MS³ AcquireX^TM workflow firstly approached the unambiguous characterization of detected features that were subsequently quantified by a complementary MS¹ study of biological replicates. Chemometric research revealed how threonylphenylalanine (overexpressed in normal meats) together to tetradecadienoyl- and hydroxydodecanoyl-carnitines (both overexpressed in DFD meats) appropriately grouped meat groups assayed. Robustness of such biomarkers was confirmed through a time-delayed study of a blind set of samples (unknown pHu) and evidenced limitations of pHu as an isolated parameter for accurate meat quality differentiation. Other acyl-carnitines also characterized DFD samples, suggesting interferences induced by pre-slaughter stress (PSS) on lipid catabolism that would explain accumulation of such intermediate metabolites. Results achieved can ease understanding of biochemical mechanisms underlying meat quality defects.

Integrating identification and targeted proteomics to discover the potential indicators of postmortem lamb meat quality

The aim of this study was to identify the potential indicators of lamb meat quality by TMT and PRM-based proteomics combined with bioinformatic analysis. Lamb muscles were divided into three different meat quality groups (high, middle and low) according to tenderness (shear force, MFI value), colour (a* value, R630/580), and water-holding capacity (cooking loss, drip loss) at 24 h postmortem. The results showed that the abundance of phosphoglycerate kinase 1 (PGK1), β-enolase (ENO3), myosin-binding protein C (MYBPC1) and myosin regulatory light chain 2 (MYLPF) was significantly different in the three groups and could be used as potential indicators to characterize meat quality. Moreover, the postmortem processes of glycolysis, oxidative phosphorylation, and muscle contraction remarkably changed in different groups, and were the key biological pathways influencing meat quality. Overall, this study depicted the proteomic landscape of meat that furthers our understanding of the molecular mechanism of meat quality and provides a reference for developing non-destructive detection technology for meat quality.

Improving animal welfare status and meat quality through assessment of stress biomarkers: A critical review

Stress induces various physiological and biochemical alterations in the animal body, which are used to assess the stress status of animals. Blood profiles, serum hormones, enzymes, and physiological conditions such as body temperature, heart, and breathing rate of animals are the most commonly used stress biomarkers in the livestock sector. Previous exposure, genetics, stress adaptation, intensity, duration, and rearing practices result in wide intra- and inter-animal variations in the expression of various stress biomarkers. The use of meat proteomics by adequately analyzing the expression of various muscle proteins such as heat shock proteins (HSPs), acute phase proteins (APPs), texture, and tenderness biomarkers help predict meat quality and stress in animals before slaughter. Thus, there is a need to identify non-invasive, rapid, and accurate stress biomarkers that can objectively assess stress in animals. The present manuscript critically reviews various aspects of stress biomarkers in animals and their application in mitigating preslaughter stress in meat production.

Transcriptome profiling reveals stress-responsive gene networks in cattle muscles

In meat-producing animals, preslaughter operations (e.g., transportation, mixing unfamiliar animals, food and water deprivation) may be a source of stress with detrimental effects on meat quality. The objective of this work was to study the effect of emotional and physical stress by comparing the transcriptomes of two muscles (M. longissimus thoracis, LT and M. semitendinosus, ST) in Normand cows exposed to stress (n = 16) vs. cows handled with limited stress (n = 16). Using a microarray, we showed that exposure to stress resulted in differentially expressed genes (DEGs) in both muscles (62 DEGs in LT and 32 DEGs in ST, of which eight were common transcription factors (TFs)). Promoter analysis of the DEGs showed that 25 cis transcriptional modules were overrepresented, of which nine were detected in both muscles. Molecular interaction networks of the DEGs targeted by the most represented cis modules helped identify common regulators and common targets involved in the response to stress. They provided elements showing that the transcriptional response to stress is likely to (i) be controlled by regulators of energy metabolism, factors involved in the response to hypoxia, and inflammatory cytokines; and (ii) initiate metabolic processes, angiogenesis, corticosteroid response, immune system processes, and satellite cell activation/quiescence. The results of this study demonstrate that exposure to stress induced a core response to stress in both muscles, including changes in the expression of TFs. These factors could relay the physiological adaptive response of cattle muscles to cope with emotional and physical stress. The study provides information to further understand the consequences of these molecular processes on meat quality and find strategies to attenuate them.

Proteomic Technologies and their Application for Ensuring Meat Quality, Safety and Authenticity

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Proteomic tools were extensively used to understand the relationship between muscle proteome and conversion of muscle to meat, post-mortem proteolysis, meat texture, and variation in meat color. Developments in proteomic tools have also resulted in their application for addressing the safety and authenticity issues including meat species identification, detection of animal byproducts, non-meat ingredients and tissues in meat products, traceability, identification of genetically modified ingredients, chemical residues and other harmful substances. Proteomic tools are also being used in some of the potential areas like understanding the effect of animal transportation, stunning, slaughter stress, halal authentication and issues related to animal welfare. Emerging advances in proteomic and peptidomic technologies and their application in traceability, meat microbiology, safety and authentication are taking a major stride as an interesting and complementary alternative to DNA-based methods currently in use. Future research in meat science need to be linked to emerging metabolomic, lipidomic and other omic technologies for ensuring integrated meat quality and safety management. In this paper, a comprehensive overview of the use of proteomics for the assessment of quality and safety in the meat value chain and their potential application is discussed.

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

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

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

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

An integrated strategy for holistic quality identification of Chinese patent medicine: Liuwei Dihuang Pills as a case study

INTRODUCTION

Liuwei Dihuang Pills (concentrated pills, simplified as LWDHP), one of the most famous classic Chinese Patent Medicine (CPM), is produced by hundreds of pharmaceutical manufacturers with billions of Chinese yuan (CNY) in annual sales. However, current quality identification of LWDHP mainly relies on a thin-layer chromatography (TLC) method that is complicated and deficient.

OBJECTIVE

The goal of this study is to simplify the identification process and provide a more comprehensive quality assessment method of LWDHP by developing an integrated strategy based on liquid chromatography coupled with mass spectrometry (LC-MS) and multivariate statistical analysis.

METHOD

Ultra-high-performance liquid chromatography coupled with quadrupole-time of flight mass spectrometry (UHPLC/QTOF-MS) was employed to perform qualitative analyses of a home-made LWDHP and to establish a stably characteristic compound library by analysis of batches of its component herbs. Then selective ion monitoring (SIM) of single MS was utilised to develop a rapid identification method based on the UHPLC/QTOF-MS analysis result. Multivariate statistical analysis was subsequently used for the quality assessment of different commercial samples.

RESULTS

Seventy-eight characteristic compounds were characterised, and 68 of them were recorded to establish a stably characteristic compound library. Thirty-one compounds were selected from the library for the establishment of SIM identification method. Good specificity, capability, and feasibility had been respectively verified by the analysis of blank sample, negative control (NC) preparation samples, home-made LWDHP sample, and commercial sample. Multivariate statistical analysis of 20 batches of commercial LWDHP samples revealed the quality consistency of the same vendor's product and quality difference between diverse vendors' products.

CONCLUSION

The SIM identification method by a single analysis could significantly simplify the identification process of LWDHP, and it was performed in a holistic mode for no less than two compounds of each component herb monitored. Moreover, it could also be combined with multivariate statistical analysis to conduct quality assessments of batches of samples. The integrated strategy used in the study of LWDHP could be applied for the identification of other CPM as well.

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

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

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Liquid-Phase Ion Trap for Ion Trapping, Transfer, and Sequential Ejection in Solutions

In this study, a new method/mechanism to manipulate ions in solution was developed, based on which liquid-phase ion trap was built. In this liquid-phase ion trap, ion manipulations conventionally performed in a quadrupole ion trap or in a trapped ion mobility spectrometer placed in a vacuum were achieved in solutions. Through theoretical derivation and numerical simulation, it is found that ions have different motional characteristics than those in vacuum. Instead of a radio frequency quadrupole electric field, tunable DC electric fields together with a constant liquid flow were applied to control ion motions in solution. Different ions could be trapped and focused in a potential well, and ion densities could be increased by over 100-fold. By adjusting the DC electric field of the potential well, trapped ions could be transferred into another trapping region or sequentially released for detection. Ions released from the liquid-phase ion trap were then detected by a mass spectrometer interfaced with an electrospray ionization source. Since the ion manipulation mechanism in solution is different and complementary to that in vacuum, the use of a liquid-phase ion trap could also boost detection sensitivity and the mixture analysis capability of a mass spectrometer.

The first evidence of global meat phosphoproteome changes in response to pre-slaughter stress

BACKGROUND

Pre-slaughter stress (PSS) impairs animal welfare and meat quality. Dark, firm and dry (DFD) are terms used to designate poor quality meats induced by PSS. Protein phosphorylation can be a potentially significant mechanism to explain rapid and multiple physiological and biochemical changes linked to PSS-dependent muscle-to-meat conversion. However, the role of reversible phosphorylation in the response to PSS is still little known. In this study, we report a comparative phosphoproteomic analysis of DFD and normal meats at 24 h post-mortem from the longissimus thoracis (LT) bovine muscle of male calves of the Rubia Gallega breed. For this purpose, two-dimensional gel electrophoresis (2-DE), in-gel multiplex identification of phosphoproteins with PRO-Q Diamond phosphoprotein-specific stain, tandem (MALDI-TOF/TOF) mass spectrometry (MS), novel quantitative phosphoproteomic statistics and bioinformatic tools were used.

RESULTS

Noticeable and statistically significant differences in the extent of protein phosphorylation were detected between sample groups at the qualitative and quantitative levels. Overall phosphorylation rates across significantly changed phosphoproteins were about three times higher in DFD than in normal meat. Significantly changed phosphoproteins involved a variable number of isoforms of 13 myofibrillar and sarcoplasmic nonredundant proteins. However, fast skeletal myosin light chain 2 followed by troponin T, F-actin-capping and small heat shock proteins showed the greatest phosphorylation change, and therefore they were the most important phosphoproteins underlying LT muscle conversion to DFD meat in the Rubia Gallega breed.

CONCLUSIONS

This is the first study reporting global meat phosphoproteome changes in response to PSS. The results show that reversible phosphorylation is a relevant mechanism underlying PSS response and downstream effects on meat quality. This research opens up novel horizons to unravel the complex molecular puzzle underlying muscle-to-meat conversion in response to PSS.