Proteomic Advances in Milk and Dairy Products.

Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.

Proteomic Advances in Cereal and Vegetable Crops.

The importance of vegetables in human nutrition, such as cereals, which in many cases represent the main source of daily energy for humans, added to the impact that the incessant increase in demographic pressure has on the demand for these plant foods, entails the search for new technologies that can alleviate this pressure on markets while reducing the carbon footprint of related activities. Plant proteomics arises as a response to these problems, and through research and the application of new technologies, it attempts to enhance areas of food science that are fundamental for the optimization of processes. This review aims to present the different approaches and tools of proteomics in the investigation of new methods for the development of vegetable crops. In the last two decades, different studies in the control of the quality of crops have reported very interesting results that can help us to verify parameters as important as food safety, the authenticity of the products, or the increase in the yield by early detection of diseases. A strategic plan that encourages the incorporation of these new methods into the industry will be essential to promote the use of proteomics and all the advantages it offers in the optimization of processes and the solution of problems.

Evaluation of linseed oil oleogels to partially replace pork backfat in fermented sausages.

BACKGROUND: Nowadays, fat replacement in meat products is a matter of concern in the meat industry. The objective of this study was to evaluate the replacement of pork backfat with two oleogels of linseed in dry-cured sausages. RESULTS: Five batches of dry-cured sausages were prepared with two oleogels, a mixture of γ-oryzanol and ß-sitosterol (SO) and beeswax (B), at two levels of replacement (20% and 40%) (SO-20, SO-40, B-20, and B-40, respectively) and a control batch. The fatty acid profile improved in terms of nutrition: the polyunsaturated fatty acid / saturated fatty acid (PUFA/SFA) and n-6/n-3 ratio was about 1.41 and 0.93 for the higher levels of replacement, SO-40 and B-40, respectively. Quality parameters such as pH and color also changed with the inclusion of oleogels, resulting in changes in the sensory quality. CONCLUSION: Oleogels based on linseed enabled the replacement of pork backfat in fermented sausages. Depending on the level of fat substitution, such oleogels could replace fat in dry-cured sausages at the industrial level. © 2019 Society of Chemical Industry.

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.

The Major Storage Protein in Potato Tuber Is Mobilized by a Mechanism Dependent on Its Phosphorylation Status.

The role of the protein phosphorylation mechanism in the mobilization of vegetative storage proteins (VSPs) is totally unknown. Patatin is the major VSP of the potato (Solanum tuberosum L.) tuber that encompasses multiple differentially phosphorylated isoforms. In this study, temporal changes in the phosphorylation status of patatin isoforms and their involvement in patatin mobilization are investigated using phosphoproteomic methods based on targeted two-dimensional electrophoresis (2-DE). High-resolution 2-DE profiles of patatin isoforms were obtained in four sequential tuber life cycle stages of Kennebec cultivar: endodormancy, bud break, sprouting and plant growth. In-gel multiplex identification of phosphorylated isoforms with Pro-Q Diamond phosphoprotein-specific stain revealed an increase in the number of phosphorylated isoforms after the tuber endodormancy stage. In addition, we found that the phosphorylation status of patatin isoforms significantly changed throughout the tuber life cycle (P < 0.05) using the chemical method of protein dephosphorylation with hydrogen fluoride-pyridine (HF-P) coupled to 2-DE. More specifically, patatin phosphorylation increased by 32% from endodormancy to the tuber sprouting stage and subsequently decreased together with patatin degradation. Patatin isoforms were not randomly mobilized because highly phosphorylated Kuras-isoforms were preferably degraded in comparison to less phosphorylated non-Kuras isoforms. These results lead us to conclude that patatin is mobilized by a mechanism dependent on the phosphorylation status of specific isoforms.

Advances in the Biology of Seed and Vegetative Storage Proteins Based on Two-Dimensional Electrophoresis Coupled to Mass Spectrometry.

Seed storage proteins play a fundamental role in plant reproduction and human nutrition. They accumulate during seed development as reserve material for germination and seedling growth and are a major source of dietary protein for human consumption. Storage proteins encompass multiple isoforms encoded by multi-gene families that undergo abundant glycosylations and phosphorylations. Two-dimensional electrophoresis (2-DE) is a proteomic tool especially suitable for the characterization of storage proteins because of their peculiar characteristics. In particular, storage proteins are soluble multimeric proteins highly represented in the seed proteome that contain polypeptides of molecular mass between 10 and 130 kDa. In addition, high-resolution profiles can be achieved by applying targeted 2-DE protocols. 2-DE coupled with mass spectrometry (MS) has traditionally been the methodology of choice in numerous studies on the biology of storage proteins in a wide diversity of plants. 2-DE-based reference maps have decisively contributed to the current state of our knowledge about storage proteins in multiple key aspects, including identification of isoforms and quantification of their relative abundance, identification of phosphorylated isoforms and assessment of their phosphorylation status, and dynamic changes of isoforms during seed development and germination both qualitatively and quantitatively. These advances have translated into relevant information about meaningful traits in seed breeding such as protein quality, longevity, gluten and allergen content, stress response and antifungal, antibacterial, and insect susceptibility. This review addresses progress on the biology of storage proteins and application areas in seed breeding using 2-DE-based maps.

Evidence for phosphorylation of the major seed storage protein of the common bean and its phosphorylation-dependent degradation during germination.

Phaseolin is the major seed storage protein of common bean, Phaseolus vulgaris L., accounting for up to 50 % of the total seed proteome. The regulatory mechanisms responsible for the synthesis, accumulation and degradation of phaseolin in the common bean seed are not yet sufficiently known. Here, we report on a systematic study in dormant and 4-day germinating bean seeds from cultivars Sanilac (S) and Tendergreen (T) to explore the presence and dynamics of phosphorylated phaseolin isoforms. High-resolution two-dimensional electrophoresis in combination with the phosphoprotein-specific Pro-Q Diamond phosphoprotein fluorescent stain and chemical dephosphorylation by hydrogen fluoride-pyridine enabled us to identify differentially phosphorylated phaseolin polypeptides in dormant and germinating seeds from cultivars S and T. Phosphorylated forms of the two subunits of type α and ß that compose the phaseolin were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and MALDI-TOF/TOF tandem MS. In addition, we found that the levels of phosphorylation of the phaseolin changed remarkably in the seed transition from dormancy to early germination stage. Temporal changes in the extent of phosphorylation in response to physiological and metabolic variations suggest that phosphorylated phaseolin isoforms have functional significance. In particular, this prospective study supports the hypothesis that mobilization of the phaseolin in germinating seeds occurs through the degradation of highly phosphorylated isoforms. Taken together, our results indicate that post-translational phaseolin modifications through phosphorylations need to be taken into consideration for a better understanding of the molecular mechanisms underlying its regulation.

A review on bioactive peptides derived from meat and by-products: Extraction methods, biological activities, applications and limitations.

Meat and its by-products offer a rich source of bioactive compounds which have potential applications in both the food and pharmaceutical industries. In this review, we present several extraction methods and report the identification and properties of bioactive peptides. We also examine the challenges and limitations associated with their use in food applications. Enzymatic hydrolysis and fermentation using starts cultures are common methods for generating bioactive peptides from meat proteins. Additionally, natural gastrointestinal digestion can also produce bioactive peptides. However, emerging technologies like high hydrostatic pressure, subcritical extraction and pulsed electric fields can improve hydrolysis and increase the yield of bioactive peptides. Online bioinformatics applications have emerged as an established method for identifying potentially bioactive peptides. These tools reduce the cost and time required for traditional methods of research. Finally, incorporating bioactive peptides into diets for specific purposes such as supporting vulnerable populations like children and the elderly ensures safety and efficacy.

A proteomic approach to identify biomarkers of foal meat quality: A focus on tenderness, color and intramuscular fat traits.

Foal meat is considered a healthy alternative to other meat sources and more environmentally sustainable. However, its quality is highly variable and there is lack of knowledge about the molecular mechanisms underlying its determination. Genotype and diet play a relevant role as the main factors that can allow a control of the final quality and the use of high-throughput analytical methods such as proteomics is a way to achieve this lofty goal. This research aimed to study-two breeds (Burguete and Jaca Navarra) supplemented with two different finishing diets: conventional concentrate and straw (C) vs silage and organic feed (S). The proteomic approach built a library of 294 proteins that were subjected to several statistical and bioinformatic analyses. Burguete breed finished with concentrate produced higher meat quality in terms of tenderness, intramuscular fat and color lightness mainly due to the high abundance of energy metabolic proteins. Tenderness was correlated to myofibrillar proteins (ACTA1, MYBPH, MYL1 and TNNC1) and energy metabolic proteins (ALDOA, CKM, TPI1 and PGMA2). Regarding color, the main pathways were energy metabolism, involving several glycolytic enzymes (ALDOA, PKM, PFKM and CKM). Oxidative stress and response to stress proteins (HSPA1A, SOD2 and PRDX2) were further involved in color variation. Moreover, we revealed that several proteins were related to the intramuscular fat accordingly to the breed. This study proposed several candidate protein biomarkers for foal meat quality that are worthy to evaluate in the future.

Advanced Proteomic and Bioinformatic Tools for Predictive Analysis of Allergens in Novel Foods.

In recent years, novel food is becoming an emerging trend increasingly more demanding in developed countries. Food proteins from vegetables (pulses, legumes, cereals), fungi, bacteria and insects are being researched to introduce them in meat alternatives, beverages, baked products and others. One of the most complex challenges for introducing novel foods on the market is to ensure food safety. New alimentary scenarios drive the detection of novel allergens that need to be identified and quantified with the aim of appropriate labelling. Allergenic reactions are mostly caused by proteins of great abundance in foods, most frequently of small molecular mass, glycosylated, water-soluble and with high stability to proteolysis. The most relevant plant and animal food allergens, such as lipid transfer proteins, profilins, seed storage proteins, lactoglobulins, caseins, tropomyosins and parvalbumins from fruits, vegetables, nuts, milk, eggs, shellfish and fish, have been investigated. New methods for massive screening in search of potential allergens must be developed, particularly concerning protein databases and other online tools. Moreover, several bioinformatic tools based on sequence alignment, motif identification or 3-D structure predictions should be implemented as well. Finally, targeted proteomics will become a powerful technology for the quantification of these hazardous proteins. The ultimate objective is to build an effective and resilient surveillance network with this cutting-edge technology.

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.

Valorisation of pork by-products to obtain antioxidant and antihypertensive peptides.

The porcine liver could be used for the extraction of zinc-protoporphyrin (ZnPP) as a natural red meat pigment. During the autolysis process, porcine liver homogenates was incubated at pH 4.8 and 45 °C under anaerobic conditions to obtain insoluble ZnPP. After incubation, the homogenates were readjusted at pH 4.8, and at pH 7.5 before being centrifuged at 5500 × g for 20 min at 4 °C and the resulting supernatant were compared with the obtained at pH 4.8 at the beginning of the incubation. The molecular weight distributions of the porcine liver fractions at both pHs were very similar, however, eight essential amino acids were more abundant in fractions obtained at pH 4.8. Regarding the ORAC assay, porcine liver protein fraction at pH 4.8 showed the highest antioxidant capacity but antihypertensive inhibition was similar for both pHs. Peptides with strong bioactivity potential from aldehyde dehydrogenase, lactoylglutathione lyase, SEC14-like protein 3 and others were identified. The findings have demonstrated the potential of the porcine liver to extract natural pigments and bioactive peptides.

Advances in Natural Antioxidants for Food Improvement.

In the food industry, antioxidants are natural and synthetic compounds added to neutralize free radicals that deteriorate fats, proteins and cellular DNA, causing rancidity of fats and accelerating the ageing process, which lead to undesirable smells and tastes [...].

Finding Biomarkers in Antioxidant Molecular Mechanisms for Ensuring Food Safety of Bivalves Threatened by Marine Pollution.

Aquaculture production as an important source of protein for our diet is sure to continue in the coming years. However, marine pollution will also likely give rise to serious problems for the food safety of molluscs. Seafood is widely recognized for its high nutritional value in our diet, leading to major health benefits. However, the threat of marine pollution including heavy metals, persistent organic pollutants and other emerging pollutants is of ever-growing importance and seafood safety may not be guaranteed. New approaches for the search of biomarkers would help us to monitor pollutants and move towards a more global point of view; protocols for the aquaculture industry would also be improved. Rapid and accurate detection of food safety problems in bivalves could be carried out easily by protein biomarkers. Hence, proteomic technologies could be considered as a useful tool for the discovery of protein biomarkers as a first step to improve the protocols of seafood safety. It has been demonstrated that marine pollutants are altering the bivalve proteome, affecting many biological processes and molecular functions. The main response mechanism of bivalves in a polluted marine environment is based on the antioxidant defense system against oxidative stress. All these proteomic data provided from the literature suggest that alterations in oxidative stress due to marine pollution are closely linked to robust and confident biomarkers for seafood safety.

Role of Food Hydrocolloids as Antioxidants along with Modern Processing Techniques on the Surimi Protein Gel Textural Properties, Developments, Limitation and Future Perspectives.

Texture is an important parameter in determining the quality characteristics and consumer acceptability of seafood and fish protein-based products. The addition of food-based additives as antioxidants (monosaccharides, oilgosaccharides, polysaccharides and protein hydrolysates) in surimi and other seafood products has become a promising trend at an industrial scale. Improvement in gelling, textural and structural attributes of surimi gel could be attained by inhibiting the oxidative changes, protein denaturation and aggregation with these additives along with new emerging processing techniques. Moreover, the intermolecular crosslinking of surimi gel can be improved with the addition of different food hydrocolloid-based antioxidants in combination with modern processing techniques. The high-pressure processing (HPP) technique with polysaccharides can develop surimi gel with better physicochemical, antioxidative, textural attributes and increase the gel matrix than conventional processing methods. The increase in protein oxidation, denaturation, decline in water holding capacity, gel strength and viscoelastic properties of surimi gel can be substantially improved by microwave (MW) processing. The MW, ultrasonication and ultraviolet (UV) treatments can significantly increase the textural properties (hardness, gumminess and cohesiveness) and improve the antioxidative properties of surimi gel produced by different additives. This study will review potential opportunities and primary areas of future exploration for high-quality surimi gel products. Moreover, it also focuses on the influence of different antioxidants as additives and some new production strategies, such as HPP, ultrasonication, UV and MW and ohmic processing. The effects of additives in combination with different modern processing technologies on surimi gel texture are also compared.

A proteomic approach for in-depth characterization and understanding the impact of immunocastration on dry-cured ham of male and female pigs.

Dry-cured ham is a high-quality product elaborated through a long and complex process. To ensure the success of the process, it is necessary to select the most suitable pork leg and one of the major factors is pig castration. Due to animal welfare, pig castration is becoming a paramount issue in recent years. The proteomic differences of dry-cured ham from immunecastrated pigs against entire females, as well as, between immunecastrated pigs and surgically castrated males were analysed. The identification and quantification of proteins were carried out by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 249 proteins were identified across the samples of dry-cured ham, resulting in 17 and 37 differentially abundant proteins in the case of males and females, respectively. In the case of males, a high abundance of structural proteins in dry-cured ham from surgically castrated animals as well as a high abundance of trypsinogen and proteosome subunit C9-like protein with protease activity in samples from immunocastrated males suggests that immunocastration impact on myofibrils of dry-cured ham. Regarding females, the immunocastration provoked an increase of abundance in several structural proteins of the myosin heavy chain (MYH7, MYH7B and MYH4) and a decrease in others (ACTN2, TNNT3, MYL3 and TCAP) concerning entire. Overall, MYH4 and ACT were found to a greater degree in immunocastrated males and females indicating a potential for biomarkers.

In Search of Antioxidant Peptides from Porcine Liver Hydrolysates Using Analytical and Peptidomic Approach.

The search for antioxidant peptides as health-promoting agents is of great scientific interest for their biotechnological applications. Thus, the main goal of this study was to identify antioxidant peptides from pork liver using alcalase, bromelain, flavourzyme, and papain enzymes. All liver hydrolysates proved to be of adequate quality regarding the ratio EAA/NEAA, particularly flavourzyme hydrolysates. The peptidomic profiles were significantly different for each enzyme and their characterizations were performed, resulting in forty-four differentially abundant peptides among the four treatments. Porcine liver hydrolysates from alcalase and bromelain are demonstrated to have the most antioxidant capacity. On the other hand, hydrophobic amino acid residues (serine, threonine, histidine and aspartic acid) might be reducing the hydrolysates antioxidant capacity. Seventeen peptides from collagen, albumin, globin domain-containing protein, cytochrome ß, fructose-bisphosphate aldolase, dihydropyrimidinase, argininosuccinate synthase, and ATP synthase seem to be antioxidant. Further studies are necessary to isolate these peptides and test them in in vivo experiments.

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.

Peptidomic analysis of antioxidant peptides from porcine liver hydrolysates using SWATH-MS.

There is a growing interest in the production and identification of bioactive peptides as health-promoting agents. A relevant method to produce biopeptides is enzymatic hydrolysis from protein-rich meat by-products. Pork liver proved to be a good source of protein (18.54%) with a low-fat content (3.38%). After hydrolysis at different times (4,6,8 and 10 h) with Alcalase, relevant amino acids such as hydrophobic (leucine, valine and isoleucine) and aromatic (tyrosine and phenylalanine) involved in antioxidant capacity were strongly increased. For the peptidomic analysis, a novel technique called sequential window acquisition of all theoretical mass spectra (SWATH-MS) was used. Regarding the effect of hydrolysis time, PCA demonstrated a great differentiation among the peptidomic pattern. Fifty-one peptides were correlated with antioxidant activity measured by DPPH, ABTS, FRAP and ORAC assays. SWATH-MS allowed the identification and quantification of six peptides from trypsinogen, ferritin, keratin, carboxylic ester hydrolase and globin domain-containing protein as potential antioxidant compounds. SIGNIFICANCE: The pork liver tissue contains a substantial amount of proteins whose enzymatic hydrolysis might generate antioxidant peptides. The bioactive peptides from pork liver would contribute to harnessing by-products of the swine industry as well as added-value products will be produced. The antioxidant activity of the mixtures revealed potential antioxidant peptides which could be used in the development of nutraceutical and functional food 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.