Peptidomic profile of milk of Holstein cows at peak lactation

Optimizing workflow efficiency for analyzing low molecular weight endogenous peptides in colostrum

Bovine milk and colostrum play pivotal roles in the nutritional support of both human and bovine infants. Colostrum, the initial milk secretion, is crucial for neonatal growth, providing essential nutrients, growth factors, immunity, and defense mechanisms through a diverse array of bioactive compounds, including bioactive proteins and peptides. Peptidomics, leveraging the potential health benefits of peptides derived from food and body fluids, has become prominent in contemporary research. Endogenous peptides (EPs) have gained notable scientific and commercial interest due to their potential biofunctional significance in areas such as immune health, antimicrobial, anti-inflammatory, antihypertensive, and antioxidative studies. In this investigation, we aimed to extract and analyze low molecular weight EPs from colostrum using four distinct peptide extraction methods, previously employed for EPs extraction from other bodily fluids. The efficiency of these methods was systematically compared and analysed to identify the most effective extraction technique for maximizing the identification of low molecular weight EPs from colostrum. This study represents a pioneering effort as no prior research has systematically compared different extraction methods for low molecular weight EPs from colostrum. Given the unique physical and chemical composition of colostrum compared to milk and other body fluids, a comprehensive analysis of EPs extraction methods was deemed essential. In the present study, we successfully extracted over 3200 EPs from colostrum using trichloroacetic acid (TCA) and a molecular weight cut off (MWCO) extraction method. The findings of this study revealed the extraction of EPs from colostrum, demonstrating potential inherent bioactivities as predicted by in silico tools.

Peptidome profiling of human, bovine, and donkey colostrum through label-free quantitative analysis reveals proteolysis of milk proteins

Proteins and peptides play vital roles in different biological processes in vivo. As a dynamic hydrolysis system, milk is rich in proteins and proteases and provides a constant supply of endogenous bioactive peptides to newborn mammals. Previous studies have primarily focused on researching bioactive peptides by adding exogenous enzymes to milk samples. However, such an approach overlooks the significance of endogenous peptides and parent proteins that naturally exist in milk. Herein, we analyzed and compared parent proteins and their releasing peptides in human colostrum (HC), bovine colostrum (BC), and donkey colostrum (DC). The predominant proteins and hydrolyzed peptides in the three types of milk were identified. Among them, peptides were found to possess common bioactivities, including ACE inhibitory, antioxidant, antibacterial and immunomodulatory properties in HC, BC, and DC. Furthermore, the biological functions of these parent proteins were clarified using bioinformatics. These insights offer a novel perspective on natural bioactive peptides and the potential utilization of specific parent proteins and peptides to develop infant formulae derived from diverse milk sources.

Revealing the diversity of endogenous peptides and parent proteins in human colostrum and mature milk through peptidomics analysis

Endogenous peptides and their parent proteins are important nutritional components with diverse biological functions. The objective of this study was to analyze and compare endogenous peptides and parent proteins found in human colostrum (HC) and human mature milk (HM) using a 4D label-free technique. In total, 5162 and 940 endogenous peptides derived from 258 parent proteins were identified in human milk by database (DB) search and de novo, respectively. Among these peptides, 2446 differentially expressed endogenous peptides with various bioactivities were identified. The Gene Ontology analysis unveiled the cellular components, biological processes, and molecular functions associated with these parent proteins. Metabolic pathway analysis suggested that neutrophil extracellular trap formation had the greatest significance with 24 parent proteins. These findings will offer a fresh perspective on the development of infant formula powder, highlighting the potential for incorporating these changes to enhance its nutritional composition and benefits.

Comprehensive species- and processing-specific peptide profiling of pasteurized, extended shelf-life and ultra-high temperature milk from cow, goat, sheep, buffalo, and mare

The present study aimed to identify endogenous milk peptides for species differentiation independent of heat exposure. Thus, comprehensive milk peptide profiles from five species and three types of heat treatments were analyzed by micro-flow liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (microLC-IM-QTOF) with subsequent database search leading to ≥ 3000 identified peptides. In the milks, 1154 peptides were unique for cow, 712 for sheep, 466 for goat, 197 for buffalo, and 69 for mare. Most peptides were detected in extended-shelf life (ESL) milk (2010), followed by ultra-high temperature (UHT) processed (1474) and pasteurized milk (1459 peptides), with 693 peptides present in all milk types. A blind test set of 64 samples confirmed eight species-specific, but heat-independent marker peptides in milk from cow, seven from goat, six from sheep, nine from buffalo, and three from mare. The generated peptide profiles can also be used to identify species- and heat-specific markers.

Subclinical Mastitis from Streptococcus agalactiae and Prototheca spp. Induces Changes in Milk Peptidome in Holstein Cattle

Early detection of bovine subclinical mastitis may improve treatment strategies and reduce the use of antibiotics. Herein, individual milk samples from Holstein cows affected by subclinical mastitis induced by S. agalactiae and Prototheca spp. were analyzed by untargeted and targeted mass spectrometry approaches to assess changes in their peptidome profiles and identify new potential biomarkers of the pathological condition. Results showed a higher amount of peptides in milk positive on the bacteriological examination when compared with the negative control. However, the different pathogens seemed not to trigger specific effects on the milk peptidome. The peptides that best distinguish positive from negative samples are mainly derived from the most abundant milk proteins, especially from β- and αs1-casein, but also include the antimicrobial peptide casecidin 17. These results provide new insights into the physiopathology of mastitis. Upon further validation, the panel of potential discriminant peptides could help the development of new diagnostic and therapeutic tools.

Evaluation of the differences in proteomics of high-quality bovine colostrum and low-quality bovine colostrum

BACKGROUND

Although there are studies on colostrum and milk proteomics of different species in the literature, there is no published report about different quality bovine colostrums' proteomics.

OBJECTIVES

The aim of this study was to compare the proteome content of high- and low-quality bovine colostrums for the first time.

METHODS

Colostrum samples were collected from 32 Holstein cows from the same farm that had just calved. Brix% levels of colostrums were measured, and then, those with a Brix% value of ≥27% were classified as high-quality and those with a Brix% value of <22% as low-quality. Three samples from high-quality and low-quality colostrums were selected and proteomic analyses were performed by pooling separately.

RESULTS

Totally 95 proteins were identified in the colostrums, and 19 of them showed significant changes between high- and low-quality colostrums. Expressions in colostrum of glycosylation-dependent cell adhesion molecule-1, cofilin-1, alpha-S2-casein, alpha-lactalbumin, alpha-1B-glycoprotein, actin_cytoplasmic-1, nucleobindin-1, cathelicidin-4, inter-alpha-trypsin inhibitor heavy chain H4, chitinase-3-like protein 1 and monocyte differentiation antigen CD14 were lower, whereas tetranectin, secreted frizzled-related protein-1 (SFRP1), perilipin-2, coatomer subunit epsilon (COPE), butyrophilin subfamily 1 member A1, polyubiquitin-B, lactadherin and albumin levels were higher in high-quality colostrum than low-quality colostrum. Moreover, SFRP1, COPE and cathelicidin-4 proteins were identified for the first time in bovine colostrum. In high-quality colostrum, the most prominently down-regulated proteins were cathelicidin-4 (26.01-fold) and cofilin-1 (17.42-fold), and the most prominently up-regulated proteins were COPE (3.37-fold) and tetranectin (3.07-fold).

CONCLUSIONS

It was detected that the proteome contents of high- and low-quality bovine colostrums were different from each other. As new functions are added to the protein databases regarding these proteins detected in colostrums, the interactions of proteins with each other and with other molecules will be detailed and the effects of high-quality colostrums on passive transfer immunity and calf health will be understood in full detail.

Characterization and biological function analysis of endogenous peptides derived from donkey colostrum proteins

Donkey colostrum, due to its abundance of active ingredients, including lysozyme, proteins, and peptides, is essential for the growth and immune defence of newborns. However, research on endogenous peptides in donkey colostrum is inadequate. This study analysed the profiles of endogenous peptides, their potential bioactivity, and the enzymes that generated these peptides using two different strategies. A total of 6202 endogenous peptides were characterised through a database search, while an additional 2997 peptides were identified de novo. Among the 1142 proteins identified, trypsin and plasmin demonstrated the highest bioactivities. Furthermore, a bioinformatics-based screening identified antioxidant peptides, angiotensin I-converting enzyme inhibitory peptides, and dipeptidyl peptidase IV inhibitory peptides as the three most active peptides. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted. These findings enhance our knowledge of endogenous peptides in donkey colostrum and provide crucial information regarding these peptides as nutritional factors for the future development of functional foods derived from donkey sources.

Identification of Potential Bioactive Peptides in Sheep Milk Kefir through Peptidomic Analysis at Different Fermentation Times

Sheep farming is an important socioeconomic activity in most Mediterranean countries, particularly Spain, where it contributes added value to rural areas. Sheep milk is used in Spain mainly for making cheese, but it can be used also for making other dairy products, such as the lactic-alcoholic fermentation product known as kefir. Dairy products have health benefits because, among other reasons, they contain molecules with biological activity. In this work, we performed a proteomics strategy to identify the peptidome, i.e., the set of peptides contained in sheep milk kefir fermented for four different periods of time, aiming to understand changes in the pattern of digestion of milk proteins, as well as to identify potential bioactive peptides. In total, we identified 1942 peptides coming from 11 different proteins, and found that the unique peptides differed qualitatively among samples and their numbers increased along the fermentation time. These changes were supported by the increase in ethanol, lactic acid, and D-galactose concentrations, as well as proteolytic activity, as the fermentation progressed. By searching in databases, we found that 78 of the identified peptides, all belonging to caseins, had potential biological activity. Of these, 62 were not previously found in any milk kefir from other animal species. This is the first peptidomic study of sheep milk kefir comprising time-course comparison.

The Impact of Low-Temperature Inactivation of Protease AprX from Pseudomonas on Its Proteolytic Capacity and Specificity: A Peptidomic Study

The destabilization of UHT milk during its shelf life can be promoted by the residual proteolytic activity attributed to the protease AprX from Pseudomonas. To better understand the hydrolysis patterns of AprX, and to evaluate the feasibility of using low-temperature inactivation (LTI) for AprX, the release of peptides through AprX activity on milk proteins was examined using an LC-MS/MS-based peptidomic analysis. Milk samples were either directly incubated to be hydrolyzed by AprX, or preheated under LTI conditions (60 °C for 15 min) and then incubated. Peptides and parent proteins (the proteins from which the peptides originated) were identified and quantified. The peptides were mapped and the cleavage frequency of amino acids in the P1/P1′ positions was analyzed, after which the influence of LTI and the potential bitterness of the formed peptides were determined. Our results showed that a total of 2488 peptides were identified from 48 parent proteins, with the most abundant peptides originating from κ-casein and β-casein. AprX may also non-specifically hydrolyze other proteins in milk. Except for decreasing the bitterness potential in skim UHT milk, LTI did not significantly reduce the AprX-induced hydrolysis of milk proteins. Therefore, the inactivation of AprX by LTI may not be feasible in UHT milk production.

Evaluation of potential anti-metastatic and antioxidative abilities of natural peptides derived from Tecoma stans (L.) Juss. ex Kunth in A549 cells

Background

Tecoma stans (L.) Juss. ex Kunth is a well-known medicinal plant found in tropical and subtropical regions. It contains a broad range of bioactive compounds that exhibit many biological effects, including antidiabetic, antibacterial, and antioxidative activities. However, the effect of natural peptides from T. stans against cancer progression and free radical production is unknown. This study aims to evaluate the cytotoxic, anti-metastatic, and antioxidative activities of natural peptides from T. stans on A549 cells.

Methods

The natural peptides were extracted from the flower of T. stans using the pressurized hot water extraction (PHWE) method, followed by size exclusion chromatography and solid-phase extraction-C18. The cytotoxic and anti-metastatic effects of natural peptides were evaluated using MTT and transwell chamber assays, respectively. The free radical scavenging activity of natural peptides was determined using ABTS, DPPH, and FRAP assays. The cells were pretreated with the IC₅₀ dosage of natural peptides and stimulated with LPS before analyzing intracellular reactive oxygen species (ROS) and proteomics.

Results

Natural peptides induced cell toxicity at a concentration of less than 1 ng/ml and markedly reduced cell motility of A549 cells. The cells had a migration rate of less than 10% and lost their invasion ability in the treatment condition. In addition, natural peptides showed free radical scavenging activity similar to standard antioxidants and significantly decreased intracellular ROS in the LPS-induced cells. Proteomic analysis revealed 1,604 differentially expressed proteins. The self-organizing tree algorithm (SOTA) clustered the protein abundances into eleven groups. The volcano plot revealed that the cancer-promoting proteins (NCBP2, AMD, MER34, ENC1, and COA4) were down-regulated, while the secretory glycoprotein (A1BG) and ROS-reducing protein (ASB6) were up-regulated in the treatment group.

Conclusion

The anti-proliferative and anti-metastatic activities of natural peptides may be attributed to the suppression of several cancer-promoting proteins. In contrast, their antioxidative activity may result from the up-regulation of ROS-reducing protein. This finding suggests that natural peptides from T. stans are viable for being the new potential anti-cancer and antioxidative agents.

A novel nanobody as therapeutics target for EGFR-positive colorectal cancer therapy: exploring the effects of the nanobody on SW480 cells using proteomics approach

Background

The epidermal growth factor receptor (EGFR) overexpression is found in metastatic colorectal cancer (mCRC). Targeted molecular therapies such as monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKI) are becoming more precise, targeting specifically for cancer therapeutics. However, there are adverse effects of currently available anti-EGFR drugs, including drug-resistant and side effects. Nanobodies can overcome these limitations. Our previous study has found that cell-penetrable nanobodies targeted at EGFR-tyrosine kinase were significantly reduced EGFR-positive lung cancer cells viability and proliferation. The aim of the present study was to determine the effect of cell-penetrable nanobody (R9VH36) on cell viability and proteomic profile in EGFR-positive human colorectal cancer cell lines.

Methods

The human colorectal carcinoma cell line (SW480) was treated with R9VH36, compared with gefitinib. Cell viability was monitored using the MTT cell viability assay. The proteomic profiling was analyzed by LC–MS/MS .

Results

The half-maximal inhibitory concentration (IC₅₀) values determined for R9VH36 and gefitinib against SW480 were 527 ± 0.03 nM and 13.31 ± 0.02 μM, respectively. Moreover, both the gefitinib-treated group and nanobody-treated group had completely different proteome profiles. A total 6626 differentially expressed proteins were identified. PCA analysis revealed different proteome profiling in R9VH36 experiment. There were 8 proteins in R9VH36 that significantly exhibited opposite expression directions when compared to gefitinib. These proteins are involved in DNA-damage checkpoint processes.

Conclusion

The proteomics explored those 6,626 proteins had different expressions between R9VH36 and gefitinib. There were 8 proteins in R9VH36 exhibited opposite expression direction when comparing to gefitinib. Our findings suggest that R9VH36 has the potential to be an alternative remedy for treating EGFR-positive colon cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12953-022-00190-6.

How can artificial intelligence be used for peptidomics?

INTRODUCTION

Peptidomics is an emerging field of omics sciences using advanced isolation, analysis, and computational techniques that enable qualitative and quantitative analyses of various peptides in biological samples. Peptides can act as useful biomarkers and as therapeutic molecules for diseases.

AREAS COVERED

The use of therapeutic peptides can be predicted quickly and efficiently using data-driven computational methods, particularly artificial intelligence (AI) approach. Various AI approaches are useful for peptide-based drug discovery, such as support vector machine, random forest, extremely randomized trees, and other more recently developed deep learning methods. AI methods are relatively new to the development of peptide-based therapies, but these techniques already become essential tools in protein science by dissecting novel therapeutic peptides and their functions (Figure 1).[Figure: see text].

EXPERT OPINION

Researchers have shown that AI models can facilitate the development of peptidomics and selective peptide therapies in the field of peptide science. Biopeptide prediction is important for the discovery and development of successful peptide-based drugs. Due to their ability to predict therapeutic roles based on sequence details, many AI-dependent prediction tools have been developed (Figure 1).

Heat-Treatments Affect Protease Activities and Peptide Profiles of Ruminants' Milk

Proteases present in milk are heat-sensitive, and their activities increase or decrease depending on the intensity of the thermal treatment applied. The thermal effects on the protease activity are well-known for bovine milk but poorly understood for ovine and caprine milk. This study aimed to determine the non-specific and specific protease activities in casein and whey fractions isolated from raw bovine, ovine, and caprine milk collected in early lactation, and to determine the effects of low-temperature, long-time (63°C for 30 min) and high-temperature, short-time (85°C for 5 min) treatments on protease activities within each milk fraction. The non-specific protease activities in raw and heat-treated milk samples were determined using the substrate azocasein. Plasmin (the main protease in milk) and plasminogen-derived activities were determined using the chromogenic substrate S-2251 (D-Val-Leu-Lys-pNA dihydrochloride). Peptides were characterized using high-resolution liquid chromatography coupled with tandem mass spectrometry. The activity of all native proteases, shown as non-specific proteases, was similar between raw bovine and caprine milk samples, but lower (P < 0.05) than raw ovine milk in the whey fraction. There was no difference (P > 0.05) between the non-specific protease activity of the casein fraction of raw bovine and caprine milk samples; both had higher activity than ovine milk. After 63°C/30 min, the non-specific protease activity decreased (44%; P > 0.05) for the bovine casein fraction only. In contrast, the protease activity of the milk heated at 85°C/5 min changed depending on the species and fraction. For instance, the activity decreased by 49% for ovine whey fraction, but it increased by 68% for ovine casein fraction. Plasmin and plasminogen were in general inactivated (P > 0.05) when all milk fractions were heated at 85°C/5 min. Most of the peptides present in heat-treated milk were derived from β-casein and αS1-casein, and they matched the hydrolysis profile of cathepsin D and plasmin. Identified peptides in ruminant milk samples had purported immunomodulatory and inhibitory functions. These findings indicate that the non-specific protease activity in whey and casein fractions differed between ruminant milk species, and specific thermal treatments could be used to retain better protease activity for all ruminant milk species.

Can cheese mites, maggots and molds enhance bioactivity? Peptidomic investigation of functional peptides in four traditional cheeses

Aside from their amino acid content, dairy proteins are valuable for their ability to carry encrypted bioactive peptides whose activities are latent until released by digestive enzymes or endogenous enzymes within the food. Peptides can possess a wide variety of functionalities, such as antibacterial, antihypertensive, and antioxidative properties, as demonstrated by in vitro and in vivo studies. This phenomenon raises the question as to what impact various traditional cheese-making processes have on the formation of bioactive peptides in the resulting products. In this study, we have profiled the naturally-occurring peptides in two hard and two soft traditional cheeses and have identified their known bioactive sequences. While past studies have typically identified fewer than 100 peptide sequences in a single cheese, we have used modern instrumentation to identify between 2900 and 4700 sequences per cheese, an increase by a factor of about 50. We demonstrated substantial variations in proteolysis and peptide formation between the interior and rind of each cheese, which we ascribed to the differences in microbial composition between these regions. We identified a total of 111 bioactive sequences among the four cheeses, with the greatest number of sequences, 89, originating from Mimolette. The most common bioactivities identified were antimicrobial and inhibition of the angiotensin-converting enzyme. This work revealed that cheese proteolysis and the resulting peptidomes are more complex than originally thought in terms of the number of peptides released, variation in peptidome across sites within a single cheese, and variation in bioactive peptides among cheese-making techniques.

Comprehensive Profiling of the Native and Modified Peptidomes of Raw Bovine Milk and Processed Milk Products

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from α_S- and β-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of β-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from α_S-caseins. The numbers of lactosylated peptides increased with harsher processing.

Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods

Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers 'nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.

Interactions between whey proteins and cranberry juice after thermal or non-thermal processing during in vitro gastrointestinal digestion

This study entails the possible interactions between whey protein and cranberry juice after processing, impacting either the protein digestibility or the bioaccessibility of cranberry antioxidants using an in vitro gastrointestinal digestion model.

Use of Mass Spectrometry to Profile Peptides in Whey Protein Isolate Medium Fermented by Lactobacillus helveticus LH-2 and Lactobacillus acidophilus La-5

Peptides in the 3-kDa ultrafiltrate of fermented whey protein isolate (WPI) medium could be responsible for the antivirulence activity of Lactobacillus helveticus LH-2 and Lactobacillus acidophilus La-5 against Salmonella Typhimurium. Non-fermented and fermented media containing 5.6% WPI were fractionated at a 3 kDa cut-off and the filtrate was analyzed by mass spectrometry. The non-fermented WPI medium contained 109 milk derived peptides, which originated from β-casein (52), αs1-casein (22), αs2-casein (10), κ-casein (8), and β-lactoglobulin (17). Most of these peptides were not found in the fermented media, except for 14 peptides from β-casein and one peptide from αs2-casein. Database searches confirmed that 39 out of the 109 peptides had established physiological functions, including angiotensin-converting-enzyme (ACE) inhibitory, antioxidant, antimicrobial, or immunomodulating activity. A total of 75 peptides were found in the LH-2 cell free spent medium (CFSM): 54 from β-casein, 14 from k-casein, 4 from β-lactoglobulin and 3 from αs2-casein. From these peptides, 19 have previously been associated with several categories of bioactivity. For La-5 CFSM, a total of 15 peptides were sequenced: 8 from β-casein, 5 from αs1-casein, 2 from β-lactoglobulin. Only 5 of these have previously been reported as having bioactivity. Many of the peptides remaining in the fermented medium would contain low-affinity residues for oligopeptide binding proteins and higher resistance to peptidase hydrolysis. These properties of the sequenced peptides could explain their accumulation after fermentation despite the active proteolytic enzymes of LH-2 and La-5 strains. Down-regulated expression of hilA and ssrB genes in S. Typhimurium was observed in the presence of La-5 and LH-2 CFSM. Downregulation was not observed for the Salmonella oppA mutant strain exposed to the same CFSM used to treat the S. Typhimurium DT104 wild-type strain. This result suggests the importance of peptide transport by S. Typhimurium for down regulation of virulence genes in Salmonella.

Identification of peptides reflecting the storage of UHT milk by MALDI-TOF-MS peptide profiling

Proteolysis during the storage of UHT milk is associated with major technological problems, particularly bitter off-flavors and age gelation limiting the shelf life of milk. In this study, untargeted peptide profiling by MALDI-TOF-MS identified peptides that were formed by proteolysis and reflected the storage of UHT milk. Analysis of nine different commercial UHT samples recorded peptide profiles during and at the end of their shelf life. Relative quantification and sequencing of the peptides revealed that the concentrations of 22 peptides increased significantly during the storage of UHT milk due to the activity of endogenous milk proteases and microbial proteases as well as other unidentified proteolytic mechanisms. Based on highly discriminative AUC values from receiver operator characteristic (ROC) curve analysis, we selected ten peptides as marker candidates. Among those, the peptide β-casein_192-206 (m/z 1668.9) was the most suitable marker differentiating expired-UHT from regular-UHT samples with 100% accuracy. Additionally, β-casein_191-206 (m/z 1782.0) showed 100% specificity and β-casein_139-161 (m/z 2696.4) 100% sensitivity. Thus, β-casein_192-206, either by itself or in combination with β-casein_191-206 and β-casein_139-161, presents a reliable marker to monitor the storage of UHT milk based on proteolytic mechanisms. SIGNIFICANCE: Enzymatic hydrolysis is the main reason why processed milk spoils during storage. The present study recorded peptide profiles to monitor the release or degradation of peptides in stored UHT milk. Among the detected peptides, statistical analysis revealed that the relative concentration of β-casein_192-206 reflected those proteolytic processes most precisely. Food authorities can now refer to β-casein_192-206 as a reliable marker to differentiate between freshly processed milk and products at the end of their shelf life. Furthermore, the food industry can use this marker peptide to improve production processes by monitoring the proteolysis during storage. The recorded peptide profile helps to explain the basic mechanisms leading to storage-induced proteolysis.

Profiling of Multiphosphorylated Peptides in Kefir and Their Release During Simulated Gastrointestinal Digestion

Casein phosphopeptides are multiphosphorylated milk peptides, which can have anticariogenic activity and improve mineral absorption by binding bivalent metal ions. The present study investigated phosphopeptides in kefir because fermentation may lead to their enhanced release from milk proteins. After selective enrichment by hydroxyapatite extraction, phosphopeptides and their phosphorylation degree were identified by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) before and after enzymatic dephosphorylation. Peptide structures were determined by ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) revealing 27 phosphopeptides in kefir, including nine peptides containing the motif pSpSpSEE, which binds minerals most efficiently. The majority (18) of phosphopeptides were derived from β-casein, but only three were derived from the most abundant milk protein α_s1-casein. After simulated gastrointestinal digestion, MALDI-TOF-MS analysis detected eight putative phosphopeptides in kefir, four of which were assigned by UHPLC-ESI-MS/MS to α_s2-casein_124-133, α_s2-casein_137-146, β-casein_30-40, and κ-casein_147-161. These results indicate that kefir is a good dietary source of multiphosphorylated peptides.

Proteomic analysis of goat milk kefir: Profiling the fermentation-time dependent protein digestion and identification of potential peptides with biological activity

Kefir is a fermented dairy product, associated to health benefits because of being a probiotic and due to the presence of molecules with biological activity. In this work, we have profiled the peptide composition of goat milk kefir at three different fermentation times using a peptidomics approach, in order to study changes in peptide concentrations and patterns of protein digestion throughout the fermentation time. We identified 2328 unique peptides corresponding to 22 protein annotations, with a maximum of peptides found after 24 h fermentation. We established different digestion patterns according to the nature of the proteins, and quantified the changes in the peptides appearing in all the fermentation times. We also identified 11 peptides that matched exactly to sequences with biological activity in databases, almost all of them belonging to caseins. This is the most comprehensive proteomic analysis of goat milk kefir to date.

Peptidomic and glycomic profiling of commercial dairy products: identification, quantification and potential bioactivities

Peptidomics and glycomics are recently established disciplines enabling researchers to characterize functional characteristics of foods at a molecular level. Milk-derived bioactive peptides and oligosaccharides have garnered both scientific and commercial interest because they possess unique functional properties, such as anti-hypertensive, immunomodulatory and prebiotic activities; therefore, the objective of this work was to employ peptidomic and glycomic tools to identify and measure relative and absolute quantities of peptides and oligosaccharides in widely consumed dairy products. Specifically, we identified up to 2117 unique peptides in 10 commercial dairy products, which together represent the most comprehensive peptidomic profiling of dairy milk in the literature to date. The quantity of peptides, measured by ion-exchange chromatography, varied between 60 and 130 mg/L among the same set of dairy products, which the majority originated from caseins, and the remaining from whey proteins. A recently published bioactive peptide database was used to identify 66 unique bioactive peptides in the dataset. In addition, 24 unique oligosaccharide compositions were identified in all the samples by nano LC Chip QTOF. Neutral oligosaccharides were the most abundant class in all samples (66-91.3%), followed by acidic (8.6-33.7%), and fucosylated oligosaccharides (0-4.6%). Variation of total oligosaccharide concentration ranged from a high of 65.78 to a low of 24.82 mg/L. Importantly, characterizing bioactive peptides and oligosaccharides in a wider number of dairy products may lead to innovations that go beyond the traditional vision of dairy components used for nutritional purposes but that will rather focus on improving human health.

Peptidomic screening of bitter and nonbitter casein hydrolysate fractions for insulinogenic peptides

Sodium caseinate hydrolysates (NaCaH) contain biologically active peptides that can positively influence human health. However, their intense bitterness hinders their inclusion in food products. To our knowledge, no studies have investigated whether a correlation between bitterness and bioactivity exists in NaCaH, so it is not yet known what effect selective removal of bitterness has on NaCaH bioactivity. A deeper understanding of the physicochemical characteristics affecting both bitterness and bioactivity is therefore needed. The aim of this study was to use in silico analysis to elucidate the relationship between bitterness and bioactivity of the insulinogenic NaCaH. The NaCaH fractions were generated by membrane filtration and flash chromatography and were subsequently evaluated for bitterness by a sensory panel. In this present study, peptidomic and bioinformatic processing of these NaCaH fractions allowed for the identification of insulinogenic peptides as well as other literature-identified peptides in each of the fractions. The results showed that the most bitter fraction contained the highest abundance of insulinogenic peptides, whereas another bitter fraction contained the highest abundance of other literature-identified bioactive peptides exhibiting angiotensin-converting enzyme-inhibition activity. Although some bioactive peptides were identified in the least bitter fractions, the abundance of these peptides was very low. These observations show a correlation between bitter taste and bioactivity, highlighting potential complications in removing bitterness while maintaining bioactivity. However, as the most bitter fraction contained the highest abundance of insulinogenic peptides, there is potential for using a lower dose of this enriched bioactive fraction to exert health benefits. The second most bitter fraction contained a very low abundance of insulinogenic peptides and other bioactive peptides. Therefore, removal of this fraction could reduce the NaCaH product's bitterness without significantly altering overall bioactive potential.

Milk Peptidomics to Identify Functional Peptides and for Quality Control of Dairy Products

Human milk and dairy products are important parts of human nutrition. In addition to supplying nutrients, milk proteins contain fragments-peptides-with important biological functions that are released during processing or digestion. Besides their potential functional relevance, peptides released during processing can be used as markers of ripening stage or product deterioration. Hence, identification and quantification of peptides in milk can be used to assay potential health benefits or product quality. This chapter describes how to extract, identify, and analyze peptides within breast milk, dairy products, and dairy digestive samples. We describe how to analyze extracted peptides with liquid chromatography-mass spectrometry, to use software to identify peptides based on database searching, and to extract peak areas for relative quantification of each peptide. We describe methods for data analysis, including predicting which enzymes are responsible for protein cleavage, identifying the site specificity of protein breakdown, mapping identified peptides to known bioactive peptides, and applying models to predict novel functional peptides.

Identification of the Peptide PyroQ-βCasein194-209 as a Highly Specific and Sensitive Marker to Differentiate between Ultrahigh-Temperature Processed (UHT) Milk and Mildly Heated Milk

In this study, a new approach was introduced to identify marker peptides that reflect the thermal treatment of commercial milk samples and differentiate ultrahigh-temperature processed (UHT) milk from mildly heated milk. Peptide profiles of training set samples, pasteurized (n = 20), extended shelf life (n = 29), and UHT (n = 29) milk, were recorded by MALDI-TOF-MS after StageTip microextraction. As marker candidates, 13 peptides were selected, and their cutoff levels were defined. The quality of the cutoff levels was then tested with a blind test set. Thus, the peptide m/z 1701.0, which was identified as pyroQ-βcasein_194-209, could ideally differentiate UHT milk from mildly heated milk with an accuracy of 100%. Due to its high reliability and sensitivity, this peptide may be applied in routine analysis to monitor thermal processing of milk. An additional heating experiment showed that the marker peptide candidates are formed during milk processing by endogenous enzymes and selective thermal cleavage.

Milk Proteins Are Predigested Within the Human Mammary Gland

Previous work demonstrates that proteases present in human milk release hundreds of peptides derived from milk proteins. However, the question of whether human milk protein digestion begins within the mammary gland remains incompletely answered. The primary objective of this study was to determine whether proteolytic degradation of human milk proteins into peptides begins within the mammary gland. The secondary objectives were to determine which milk proteases participate in the proteolysis and to predict which released peptides have bioactivity. Lactating mothers (n = 4) expressed their milk directly into a mixture of antiproteases on ice followed by immediate freezing of the milk to limit post-expression protease activity. Samples were analyzed for their peptide profiles via mass spectrometry and database searching. Peptidomics-based protease prediction and bioactivity prediction were each performed with several different approaches. The findings demonstrate that human milk contains more than 1,100 unique peptides derived from milk protein hydrolysis within the mammary gland. These peptides derived from 42 milk proteins and included 306 potential bioactive peptides. Based on the peptidomics data, plasmin was predicted to be the milk protease most active in the hydrolysis of human milk proteins within the mammary gland. Milk proteases actively cleave milk proteins within the mammary gland, initiating the release of functional peptides. Thus, the directly breastfed infant receives partially pre-digested proteins and numerous bioactive peptides.

Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics

A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30-48 hours post challenge with peak concentrations of APPs at 72-96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection.

Peptidomic analysis reveals proteolytic activity of kefir microorganisms on bovine milk proteins

SCOPE

The microorganisms that make up kefir grains are well known for lactose fermentation, but the extent to which they hydrolyze and consume milk proteins remains poorly understood. Peptidomics technologies were used to examine the proteolytic activity of kefir grains on bovine milk proteins.

METHODS AND RESULTS

Gel electrophoresis revealed substantial digestion of milk proteins by kefir grains, with mass spectrometric analysis showing the release of 609 protein fragments and alteration of the abundance of >1500 peptides that derived from 27 milk proteins. Kefir contained 25 peptides identified from the literature as having biological activity, including those with antihypertensive, antimicrobial, immunomodulatory, opioid and anti-oxidative functions. 16S rRNA and shotgun metagenomic sequencing identified the principle taxa in the culture as Lactobacillus species.

CONCLUSION

The model kefir sample contained thousands of protein fragments released in part by kefir microorganisms and in part by native milk proteases.

Identification of sixteen peptides reflecting heat and/or storage induced processes by profiling of commercial milk samples

Peptide profiles of different drinking milk samples were examined to study how the peptide fingerprint of milk reflects processing conditions. The combination of a simple and fast method for peptide extraction using stage tips and MALDI-TOF-MS enabled the fast and easy generation and relative quantification of peptide fingerprints for high-temperature short-time (HTST), extended shelf life (ESL) and ultra-high temperature (UHT) milk of the same dairies. The relative quantity of 16 peptides changed as a function of increasing heat load. Additional heating experiments showed that among those, the intensity of peptide β-casein 196-209 (m/z 1460.9Da) was most heavily influenced by heat treatment indicating a putative marker peptide for milk processing conditions. Storage experiments with HTST- and UHT milk revealed that the differences between different types of milk samples were not only caused by the heating process. Relevant was also the proteolytic activity of enzymes during storage, which were differently influenced by the heat treatment. These results indicate that the peptide profile may be suitable to monitor processing as well as storage conditions of milk.

SIGNIFICANCE

In the present study, peptide profiling of different types of milk was carried out by MALDI-TOF-MS after stage-tip extraction and relative quantification using an internal reference peptide. Although MALDI-TOF-MS covers only part of the peptidome, the method is easy and quick and is, therefore, suited for routine analysis to address several aspects of food authenticity. Using this method, 16 native peptides were detected in milk that could be modulated by different industrial processes. Subsequent heating and storage experiments with pasteurized and UHT milk confirmed that these peptides are indeed related to the production or storage conditions of the respective products. Furthermore, the heating experiments revealed one peptide, namely the β-casein-derived sequence β-casein 196-209, which underwent particularly sensitive modulation by heat treatment. The present results indicate that the modulated peptides, and especially β-casein 196-209, may be suitable markers to monitor processing parameters for industrial milk production. Furthermore, the model experiments suggest mechanisms leading to the formation or degradation of peptides, which help to evaluate putative marker peptides.

Proteolytic Systems in Milk: Perspectives on the Evolutionary Function within the Mammary Gland and the Infant

Milk contains elements of numerous proteolytic systems (zymogens, active proteases, protease inhibitors and protease activators) produced in part from blood, in part by mammary epithelial cells and in part by immune cell secretion. Researchers have examined milk proteases for decades, as they can cause major defects in milk quality and cheese production. Most previous research has examined these proteases with the aim to eliminate or control their actions. However, our recent peptidomics research demonstrates that these milk proteases produce specific peptides in healthy milk and continue to function within the infant's gastrointestinal tract. These findings suggest that milk proteases have an evolutionary function in aiding the infant's digestion or releasing functional peptides. In other words, the mother provides the infant with not only dietary proteins but also the means to digest them. However, proteolysis in the milk is controlled by a balance of protease inhibitors and protease activators so that only a small portion of milk proteins are digested within the mammary gland. This regulation presents a question: If proteolysis is beneficial to the infant, what benefits are gained by preventing complete proteolysis through the presence of protease inhibitors? In addition to summarizing what is known about milk proteolytic systems, we explore possible evolutionary explanations for this proteolytic balance.

MALDI-TOF-MS Platform for Integrated Proteomic and Peptidomic Profiling of Milk Samples Allows Rapid Detection of Food Adulterations

Adulteration of ovine, caprine, and buffalo milks with more common bovine material occurs for economic reasons and seasonal availability. Frauds are also associated with the use of powdered milk instead of declared, fresh material. In this context, various analytical methods have been adapted to dairy science applications with the aim to evaluate adulteration of milk samples, although time-consuming, suitable only for speciation or thermal treatment analysis, or useful for a specific fraud type. An integrated MALDI-TOF-MS platform for the combined peptidomic and proteomic profiling of milk samples is here presented, which allows rapid detection of illegal adulterations due to the addition of either nondeclared bovine material to water buffalo, goat, and ovine milks or of powdered bovine milk to the fresh counterpart. Peptide and protein markers of each animal milk were identified after direct analysis of a large number of diluted skimmed and/or enriched diluted skimmed filtrate samples. In parallel, markers of thermal treatment were characterized in different types of commercial milks. Principal components scores of ad hoc prepared species- or thermal treatment-associated adulterated milk samples were subjected to partial least-squares regression, permitting a fast accurate estimate of the fraud extents in test samples at either protein and peptide level. With respect to previous reports on MALDI-TOF-MS protein profiling methodologies for milk speciation, this study extends that approach to the analysis of the thermal treatment and introduces an independent, complementary peptide profiling measurement, which integrates protein data with additional information on peptides, validating final results and ultimately broadening the method applicability.

Peptidomic analysis of healthy and subclinically mastitic bovine milk

A variety of proteases release hundreds of endogenous peptide fragments from intact bovine milk proteins. Mass spectrometry-based peptidomics allows for high throughput sequence assignment of a large number of these peptides. Mastitis is known to result in increased protease activity in the mammary gland. Therefore, we hypothesized that subclinically mastitic milks would contain higher concentrations of released peptides. In this work, milks were sampled from three cows and, for each, one healthy and one subclinically mastitic teat were sampled for milk. Peptides were analyzed by nano-liquid chromatography quadrupole time of flight tandem mass spectrometry and identified with database searching. In total, 682 peptides were identified. The total number of released peptides increased 146% from healthy to subclinically mastitic milks (p < 0.05), and the total abundance of released peptides also increased significantly (p < 0.05). Bioinformatic analysis of enzyme cleavage revealed increases in activity of cathepsin D and elastase (p < 0.05) with subclinical mastitis.

Current peptidomics: applications, purification, identification, quantification, and functional analysis

Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.

Endogenous human milk peptide release is greater after preterm birth than term birth

BACKGROUND

Hundreds of naturally occurring milk peptides are present in term human milk. Preterm milk is produced before complete maturation of the mammary gland, which could change milk synthesis and secretion processes within the mammary gland, leading to differences in protein expression and enzymatic activity, thereby resulting in an altered peptide profile.

OBJECTIVE

This study examined differences in peptides present between milk from women delivering at term and women delivering prematurely.

METHODS

Nano-LC tandem mass spectrometry was employed to identify naturally occurring peptides and compare their abundances between term and preterm human milk samples at multiple time points over lactation. Term milk samples were collected from 8 mothers and preterm milk was collected from 14 mothers. The 28 preterm and 32 term human milk samples were divided into 4 groups based on day of collection (<14, 14-28, 29-41, and 42-58 d).

RESULTS

Preterm milk peptide counts, ion abundance, and concentration were significantly higher in preterm milk than term milk. Bioinformatic analysis of the cleavage sites for peptides identified suggested that plasmin was more active in preterm milk than term milk and that cytosol aminopeptidase and carboxypeptidase B2 likely contribute to extensive milk protein breakdown. Many identified milk peptides in both term and preterm milk overlapped with known functional peptides, including antihypertensive, antimicrobial, and immunomodulatory peptides.

CONCLUSION

The high protein degradation by endogenous proteases in preterm milk might attenuate problems because of the preterm infant's immature digestive system. This trial was registered at clinicaltrials.gov as NCT01817127.

Bioactive Functions of Milk Proteins: a Comparative Genomics Approach

The composition of milk includes factors required to provide appropriate nutrition for the growth of the neonate. However, it is now clear that milk has many functions and comprises bioactive molecules that play a central role in regulating developmental processes in the young while providing a protective function for both the suckled young and the mammary gland during the lactation cycle. Identifying these bioactives and their physiological function in eutherians can be difficult and requires extensive screening of milk components that may function to improve well-being and options for prevention and treatment of disease. New animal models with unique reproductive strategies are now becoming increasingly relevant to search for these factors.

Comprehensive peptidomic and glycomic evaluation reveals that sweet whey permeate from colostrum is a source of milk protein-derived peptides and oligosaccharides

Whey permeate is a co-product obtained when cheese whey is passed through an ultrafiltration membrane to concentrate whey proteins. Whey proteins are retained by the membrane, whereas the low-molecular weight compounds such as lactose, salts, oligosaccharides and peptides pass through the membrane yielding whey permeate. Research shows that bovine milk from healthy cows contains hundreds of naturally occurring peptides - many of which are homologous with known antimicrobial and immunomodulatory peptides - and nearly 50 oligosaccharide compositions (not including structural isomers). As these endogenous peptides and oligosaccharides have low-molecular weight and whey permeate is currently an under-utilized product stream of the dairy industry, we hypothesized that whey permeate may serve as an inexpensive source of naturally occurring functional peptides and oligosaccharides. Laboratory fractionation of endogenous peptides and oligosaccharides from bovine colostrum sweet whey was expanded to pilot-scale. The membrane fractionation methodology used was similar to the methods commonly used industrially to produce whey protein concentrate and whey permeate. Pilot-scale fractionation was compared to laboratory-scale fractionation with regard to the identified peptides and oligosaccharide compositions. Results were interpreted on the basis of whether industrial whey permeate could eventually serve as a source of functional peptides and oligosaccharides. The majority (96%) of peptide sequences and the majority (96%) of oligosaccharide compositions found in the laboratory-scale process were mirrored in the pilot-scale process. Moreover, the pilot-scale process recovered an additional 33 peptides and 1 oligosaccharide not identified from the laboratory-scale extraction. Both laboratory- and pilot-scale processes yielded peptides deriving primarily from the protein β-casein. The similarity of the laboratory-and pilot-scale's resulting peptide and oligosaccharide profiles demonstrates that whey permeate can serve as an industrial-scale source of bovine milk peptides and oligosaccharides.

Plasmin activity in UHT milk: relationship between proteolysis, age gelation, and bitterness

Plasmin, the major indigenous protease in milk, is linked to quality defects in dairy products. The specificity of plasmin on caseins has previously been studied using purified caseins and in the indigenous peptide profile of milk. We investigated the specificity and proteolytic pathway of plasmin in directly heated UHT milk (>150 °C for <0.2 s) during 14 weeks of storage at 20 °C in relation to age gelation and bitter peptides. Sixty-six peptides from αS- and β-caseins could be attributed to plasmin activity during the storage period, of which 23 were potentially bitter. Plasmin exhibited the highest affinity for the hydrophilic regions in the caseins that most probably were exposed to the serum phase and the least affinity for hydrophobic or phosphorylated regions. The proteolytic pattern observed suggests that plasmin destabilizes the casein micelle by hydrolyzing casein-casein and casein-calcium phosphate interaction sites, which may subsequently cause age gelation in UHT milk.

A peptidomic analysis of human milk digestion in the infant stomach reveals protein-specific degradation patterns

In vitro digestion of isolated milk proteins results in milk peptides with a variety of actions. However, it remains unclear to what degree protein degradation occurs in vivo in the infant stomach and whether peptides previously annotated for bioactivity are released. This study combined nanospray LC separation with time-of-flight mass spectrometry, comprehensive structural libraries, and informatics to analyze milk from 3 human mothers and the gastric aspirates from their 4- to 12-d-old postpartum infants. Milk from the mothers contained almost 200 distinct peptides, demonstrating enzymatic degradation of milk proteins beginning either during lactation or between milk collection and feeding. In the gastric samples, 649 milk peptides were identified, demonstrating that digestion continues in the infant stomach. Most peptides in both the intact milk and gastric samples were derived from β-casein. The numbers of peptides from β-casein, lactoferrin, α-lactalbumin, lactadherin, κ-casein, serum albumin, bile salt-associated lipase, and xanthine dehydrogenase/oxidase were significantly higher in the gastric samples than in the milk samples (P < 0.05). A total of 603 peptides differed significantly in abundance between milk and gastric samples (P < 0.05). Most of the identified peptides have previously identified biologic activity. Gastric proteolysis occurs in the term infant in the first 2 wk of life, releasing biologically active milk peptides with immunomodulatory and antibacterial properties of clinical relevance to the proximal intestinal tract. Data are available via ProteomeXchange (identifier PXD000688).