Peptidomics: new trends in food science

Milk serum peptidomics revealed the age gelation of direct UHT milk

Age gelation is undesirable for direct UHT (dUHT) milk, which is closely related to protein hydrolysis. However, little information is available for the role of serum peptides during the age gelation. In this study, the composition and protein morphology of serum phase were characterized by RP-HPLC, ICP-MS and TEM. The results showed significant increases in soluble proteins, free amino acids, calcium, and phosphorus from casein micelles, indicating protein hydrolysis and peptide release into the serum phase. 23,466 peptides derived from caseins and other proteins were identified in serum phase by peptidomics. The serum peptide profiles of age gelation milk changed dramatically. Peptide fingerprinting revealed that plasmin and cathepsin contributed to the protein hydrolysis during age gelation, with a significant increase in their activity observed. 23 characteristic peptides were ultimately selected as potential indicators for age gelation. These findings provide new insights into the age gelation of UHT milk.

In-depth discovery and taste presentation mechanism studies on umami peptides derived from fermented sea bass based on peptidomics and machine learning

Umami peptides originating from fermented sea bass impart a distinctive flavor to food. Nevertheless, large-scale and rapid screening for umami peptides using conventional techniques is challenging because of problems such as prolonged duration and complicated operation. Therefore, we aimed to screen fermented sea bass using peptidomics and machine learning approaches. The taste presentation mechanism of umami peptides was assessed by molecular docking of T1R1/T1R3. Seventy umami peptides identified in fermented sea bass predominantly originated from 28 precursor proteins, including troponin, myosin, motor protein, and creatine kinase. Six umami peptides with the lowest energies formed stable complexes by binding to T1R3. SER170, SER147, GLN389, and HIS145 are critical binding sites for T1R1/T1R3. Four dominant interacting surface forces were identified: aromatic interactions, hydrogen bonding, hydrophilic bonds, and solvent-accessible surfaces. Our study unveils a method to screen umami peptides efficiently, providing a basis for further exploration of their flavor in fermented sea bass.

Comparative peptidomics analysis in the discovery of umami peptides from Chinese Douchi

Douchi is a kind of traditional Chinese fermented soybean product with outstanding umami taste. Besides the umami amino acids in Douchi, peptides were also considered as an important contributor for the umami taste of Douchi. Peptides with molecular weight below 0.66 kDa accounted for more than 50 % in all samples except for TongChuan Douchi, and a total of 421 peptides were identified from the ten kinds of Douchi samples by using LC-MS/MS. Combined with sensory evaluation results, 19 peptides containing Glu, Asp or known umami peptide sequences were chosen as potential umami peptides via PLS-DA and RDA analysis. Among them, 17 soluble peptides exhibited obvious umami taste and the threshold of 7 peptides were lower than MSG solution. Especially, the VD was detected with a minimum umami taste threshold at 0.16 mg/mL. The results indicated that the umami peptides might be the important components affecting the umami taste of Douchi.

Identification and characterization of a calcium-binding peptide from salmon bone for the targeted inhibition of α-amylase in digestion

α-Amylase, essential for carbohydrate digestion, relies on calcium (Ca) for its structural integrity and enzymatic activity. This study explored the inhibitory effect of salmon bone peptides on α-amylase activity through their interaction with the enzyme's Ca-binding sites. Among the various salmon bone hydrolysates, salmon bone trypsin hydrolysate (SBTH) exhibited the highest α-amylase inhibition. The peptide IEELEEELEAER (PIE), with a sequence of Ile-Glu-Glu-Leu-Glu-Glu-Glu-Glu-Leu-Glu-Ala-Glu-Arg from SBTH, was found to specifically target the Ca-binding sites in α-amylase, interacting with key residues such as Asp206, Trp203, His201, etc. Additionally, cellular experiments using 3 T3-L1 preadipocytes indicated PIE's capability to suppress adipocyte differentiation, and decreases in intracellular triglycerides, total cholesterol, and lipid accumulation. In vivo studies also showed a significant reduction in weight gain in the group treated with PIE(6.61%)compared with the control group (33.65%). These findings suggest PIE is an effective α-amylase inhibitor, showing promise for obesity treatment.

PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides

Short peptides have become the focus of recent research due to their variable bioactivities, good digestibility and wide existences in food-derived protein hydrolysates. However, due to the high complexity of the samples, identifying short peptides still remains a challenge. In this work, a tool, named PeposX-Exhaust, was developed for short peptide identification. Through validation with known peptides, PeposX-Exhaust identified all the submitted spectra and the accuracy rate reached 75.36%, and the adjusted accuracy rate further reached 98.55% when with top 5 candidates considered. Compared with other tools, the accuracy rate by PeposX-Exhaust was at least 70% higher than two database-search tools and 15% higher than the other two de novo-sequencing tools, respectively. For further application, the numbers of short peptides identified from soybean, walnut, collagen and bonito protein hydrolysates reached 1145, 628, 746 and 681, respectively. This fully demonstrated the superiority of the tool in short peptide identification.

Insights into characteristic metabolites and potential bioactive peptides profiles of fresh cheese fermented with three novel probiotics based metabolomics and peptidomics

The metabolite and peptide profiles of fresh cheese fermented by three novel probiotics, Lacticaseibacillus rhamnosus B6, Limosylactobacillus fermentum B44 and Lacticaseibacillus rhamnosus KF7, were investigated using LC-MS/MS-based metabolomics and peptidomics. The multivariate analysis revealed significant differences in metabolite composition between the probiotic fresh cheese and the control sample. The differential metabolites were primarily lipids and lipid-like molecules and organic oxygen compounds, which were associated with fatty acid and carbohydrate-related pathways. Among three probiotics, L. rhamnosus KF7 showed the highest effectiveness in sucrose decomposition. 147 potential bioactive peptides, mainly derived from casein, were identified in probiotic fresh cheese. Furthermore, 112 bioactive peptides were significantly up-regulated in probiotic fresh cheese. Molecular docking analysis indicated that two short peptides (LVYPFPGPIP and YPQRDMPIQ) in the B44 and KF7 groups exhibited low estimated binding energy values (-9.9 and -6.9 kcal/mol) with ACE. These findings provide a theoretical basis for developing novel probiotic-enriched fresh cheese.

Identification, structural characterization, and molecular dynamic simulation of ACE inhibitory peptides in whey hydrolysates from Chinese Rushan cheese by-product

To realize the high-value utilization of Rushan cheese by-product, Rushan cheese whey was used as a raw material to prepare angiotensin-Ⅰ-converting enzyme inhibitory peptides (ACEIPs). After enzymatic hydrolysisn and ultrafiltration, the sequences of peptides were identified by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Two novel ACE inhibitory peptides Phe-Asp-Arg-Pro-Phe-Leu (FDRPFL) and Lys-Trp-Glu-Lys-Pro-Phe (KWEKPF) were identified. Additionally, both of the peptides exhibited good water-solubility and no toxicity according to in-silico prediction. Fourier transform infrared spectroscopy results show that both FDRPFL and KWEKPF were enriched in β-turn and β-sheet structures. Lineweaver-Burk plots revealed that FDRPFL and KWEKPF exhibited non-competitive and mixed inhibition patterns, respectively. Molecular docking and MD simulation showed that hydrogen bonds and ionic bonds forces allowed FDRPFL and KWEKPF to form stable and compact complexes with ACE. In conclusion, enzymatic hydrolysis of Rushan cheese by-products yields bioactive peptides, increases the added value of whey and reduces environmental pollution.

Comprehensive workflow encompassing discovery, verification, and quantification of indicator peptide in snail mucin using LC-quadrupole Orbitrap high-resolution tandem mass spectrometry

Peptidomics analysis was conducted using high-resolution tandem mass spectrometry (MS2) to determine the peptide profile of snail-derived mucin extract (SM). The study was also aimed to identify an indicator peptide and validate a quantification method for this peptide. The peptide profiling and identification were conducted using discovery-based peptidomics analysis employing data-dependent acquisition, whereas the selected peptides were verified and quantified using parallel reaction monitoring acquisition. Among the 16 identified peptides, the selected octapeptide (TEAPLNPK) was quantified via precursor ion ionization (m/z 435.2400), followed by quantification of the corresponding quantifier ion fragment (m/z 639.3824) using MS2. The quantification method was optimized and validated in terms of specificity, linearity, accuracy, precision, and limit of detection/quantification. The validated method accurately quantified the TEAPLNPK content in the SM as 7.5 ± 0.2 μg/g. Our study not only identifies an indicator peptide from SM but also introduces a novel validation method, involving precursor ion ionization and quantification of specific fragments. Our findings may serve as a comprehensive workflow for the monitoring, selection, and quantification of indicator peptides from diverse food resources.

Proteomics and Peptidomics As a Tool to Compare the Proteins and Endogenous Peptides in Human, Cow, and Donkey Milk

Cow's milk is the most widely used ingredient in infant formulas. However, its specific protein composition can cause allergic reactions. Finding alternatives to replace cow's milk and fill the nutritional gap with human milk is essential for the health of infants. Proteomic and peptidomic techniques have supported the elucidation of milk's nutritional ingredients. Recently, omics approaches have attracted increasing interest in the investigation of milk because of their high throughput, precision, sensitivity, and reproducibility. This review offers a significant overview of recent developments in proteomics and peptidomics used to study the differences in human, cow, and donkey milk. All three types of milks were identified to have critical biological functions in human health, particularly in infants. Donkey milk proteins were closer in composition to human milk, were less likely to cause allergic reactions, and may be developed as novel raw materials for formula milk powders.

Study on the effects and mechanisms of ultrasound on the peptide profile and taste of unsmoked bacon using peptidomics and bioinformatics

The ultrasound-induced impacts on the peptide characteristics and taste of unsmoked bacon have been evaluated through the use of peptidomics and bioinformatics approaches. Furthermore, the effect of such ultrasound-induced changes on the main endogenous proteases responsible for peptide generation was also investigated. In fact, the activity of main endogenous proteases was significantly increased after ultrasonic treatment during the processing of unsmoked bacon, and contributed to an increased number and an enhanced LFQ intensity of peptides. Besides, such increased amount of peptides and LFQ intensity with up to 500 W ultrasonic treatment were beneficial for the taste improvement of the final products as shown by taste prediction analysis. Nevertheless, an excessive ultrasonic power like 750 W hindered protein hydrolysis and further exerted a negative effect on peptide generation. Therefore, ultrasound under controlled conditions could be considered as a promising way to improve the taste of unsmoked bacon.

Effect of Fermentation with Streptococcus thermophilus Strains on In Vitro Gastro-Intestinal Digestion of Whey Protein Concentrates

Three Streptococcus thermophilus strains, namely RBC6, RBC20, and RBN16, were proven to release bioactive peptides during whey protein concentrate (WPC) fermentation, resulting in WPC hydrolysates with biological activities. However, these bioactive peptides can break down during gastro-intestinal digestion (GID), hindering the health-promoting effect of fermented WPC hydrolysates in vivo. In this work, the effect of simulated GID on three WPC hydrolysates fermented with S. thermophilus strains, as well as on unfermented WPC was studied in terms of protein hydrolysis, biological activities, and peptidomics profiles, respectively. In general, WPC fermentation enhanced protein hydrolysis compared to unfermented WPC. After in vitro GID, WPC fermented with S. thermophilus RBC20 showed the highest antioxidant activity, whereas WPC fermented with strain RBC06 displayed the highest angiotensin-converting enzyme (ACE)- and dipeptidyl peptidase IV (DPP-IV)-inhibitory activities. Peptidomics analysis revealed that all digested WPC samples were highly similar to each other in peptide profiles, and 85% of the 46 identified bioactive peptides were shared among fermented and unfermented samples. However, semi-quantitative analysis linked the observed differences in biological activities among the samples to differences in the amount of bioactive peptides. The anti-hypertensive peptides VPP and IPP, as well as the DPP-IV-inhibitory peptide APFPE, were quantified. In conclusion, WPC fermentation with S. thermophilus positively impacted protein hydrolysis and bioactive peptide release during GID.

Integrated metabolomics and peptidomics to delineate characteristic metabolites in milk fermented with novel Lactiplantibacillus plantarum L3

A novel wild-type Lactiplantibacillus plantarum (L. plantarum) L3 with good fermentation characteristics and protein degradation capacity was isolated from raw milk samples. In this study, the metabolites in milk fermented with L. plantarum L3 were investigated by metabolomic and peptidomics analyses. The metabolomics results revealed that the metabolites in milk fermented with L. plantarum L3 were Thr-Pro, Val-Lys, l-creatine, pyridoxine, and muramic acid, which improved the taste and nutritional qualities of the milk. Moreover, the water-soluble peptides derived from L3 fermented milk exhibited high antioxidant properties and angiotensin I-converting enzyme inhibitory (ACEI) activities. Additionally, 152 peptides were found using liquid chromatography-mass spectrometry (LC-MS/MS). Furthermore, endogenous enzymes secreted by L. plantarum L3 cleaved β- and α-casein to release six ACEI peptides (ACEIPs), nineteen antioxidant peptides (AOPs), and five antimicrobial peptides (AMPS). Overall, these findings could be valuable in improving the quality of fermented milk.

Peptide profiles and allergy-reactivity of extensive hydrolysates of milk protein

Milk protein concentrate (MPC) is one of the major allergens in food. This study aimed to analyze the peptide profiles and potential allergenicity of the extensive hydrolysates of MPC (EMPHs) using the peptidomics approach. Results demonstrated that when the hydrolysis time was 4 h, the degree of hydrolysis of the four EMPHs (AX, Alcalase-Protamex), (AD, Alcalase-Protease A 2SD), (AE, Alcalase-Flavourzyme) and (AH, Alcalase-ProteAXH) were 12.45 %, 18.48 %, 18.87 % and 16.77 %, respectively. The results of size exclusion chromatography showed no significant difference, when the hydrolysis time exceeded 3 h. A total of 16 allergic peptides were identified in the EMPHs by LC-MS/MS. The peptide profiles and the coverage of master protein of the four EMPHs were different. The results of the enzyme-linked immunoassay and KU812 cell model showed that the allergenicity of the EMPHs samples was significantly reduced. This study provided strong support for the application of EMPHs in hypoallergenic formula foods.

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

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

Improving Effects of Laccase-Mediated Pectin–Ferulic Acid Conjugate and Transglutaminase on Active Peptide Production in Bovine Lactoferrin Digests

Bovine lactoferrin (bLf) is a multifunctional glycoprotein and a good candidate for producing diverse bioactive peptides, which are easily lost during over-digestion. Accordingly, the effects of laccase-mediated pectin–ferulic acid conjugate (PF) and transglutaminase (TG) on improving the production of bLf active peptides by in vitro gastrointestinal digestion were investigated. Using ultra-high-performance liquid chromatography tandem mass spectroscopy (UPLC-MS-MS), the digests of bLf alone, PF-encapsulated bLf complex (LfPF), and TG-treated LfPF complex (LfPFTG) produced by conditioned in vitro gastric digestion (2000 U/mL pepsin, pH 3.0, 37 °C, 2 h) were identified with seven groups of active peptide-related fragments, including three common peptides (VFEAGRDPYKLRPVAAE, FENLPEKADRDQYEL, and VLRPTEGYL) and four differential peptides (GILRPYLSWTE, ARSVDGKEDLIWKL, YLGSRYLT, and FKSETKNLL). The gastric digest of LfPF contained more diverse and abundant detectable peptides of longer lengths than those of bLf and LfPFTG. After further in vitro intestinal digestion, two active peptide-related fragments (FEAGRDPYK and FENLPEKADRDQYE) remained in the final digest of LfPFTG; one (EAGRDPYKLRPVA) remained in that of bLf alone, but none remained in that of LfPF. Conclusively, PF encapsulation enhanced the production of bLf active peptide fragments under the in vitro gastric digestion applied. TG treatment facilitated active peptide FENLPEKADRDQYE being kept in the final gastrointestinal digest.

Novel insight into the transformation of peptides and potential benefits in brown fermented goat milk by mesoporous magnetic dispersive solid phase extraction-based peptidomics

Brown fermented goat milk as an excellent source of bioactive peptides has only been partially elucidated. Meticulously synthesized MOF@MG as magnetic sorbent for enriching endogenous peptides owned higher reproducibility and uniform distribution of peptides PI compared with ultrafiltration. Combined with UHPLC-Q-Orbitrap, fermentation for 12 h in brown goat milk with the highest overall acceptable degree through sensory evaluation was utilized to explore the transformation of peptides and health benefits, with trypsin or plasmin hydrolyzing proteins and aminopeptidase or carboxypeptidase hydrolyzing peptides to small peptides or amino acids. A total of 1317 peptides were identified by database matching (1259) and de novo sequencing (58), among 18 peptides could originate from gene-independent enzymatic formation and top 25 characteristic peptides were quantified with concentration ranging from 0.12 to 6.40 mg L^-1. Bioinformatic analysis results indicated that brown fermented goat milk possesses higher health benefits because of more than 50 peptides with potential bioactivity.

Peptidomics as a useful tool in the follow-up of food bioactive peptides

There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.

Analysis of the relationship between microorganisms and flavour development in dry-cured grass carp by high-throughput sequencing, volatile flavour analysis and metabolomics

Complex microbial community plays an important role for flavor formation in traditional dry-cured grass carp. To investigate the correlation between microorganisms and flavour development, the bacterial diversity and flavour quality of dry-cured fish at different stages of fermentation were analysed using high-throughput sequencing, volatile flavour analysis and metabolomics. Cobetia, Staphylococcus and Ralstonia were the dominant genera in dry-cured fish, with relative abundances of 37.78%, 34.46% and 3.2%, respectively. The flavour of dry-cured fish samples varied as the abundance of aldehydes, alcohols, small peptides, FAAs and carboxylic acids showed a great increase during fermentation. Moreover, there were significant correlations (P < 0.05) between specific microorganisms and volatile indicators, as well as flavour metabolites. Staphylococcus, as the dominant bacterial genus, is involved in the mechanism of flavour formation in dry-cured fish during fermentation. This information is useful for elucidating the mechanism of flavour formation in dry-cured fish.

Peptidomic analysis characterising proteolysis in thaw-aging of beef short plate

Recent studies have suggested that thaw-aging can improve sensory attributes of freeze-thawed meat. Acceleration of proteolysis is expected to promote tenderisation and improve taste; however, the details of protein degradation, including substrate proteins and cleavage sites, remain unclear. Here, we report a time course overview of the peptidome of beef short plates during thaw-aging. The accelerated degradation of key proteins for meat tenderisation, such as troponin T and desmin, was confirmed. Additionally, 11 cleavage sites in troponin T related to taste-active peptide generation were identified. Terminome analysis showed that the contribution of each protease varies depending on the substrate proteins and the thaw-aging period. Based on our results; proteases, not only calpains, but also others contributed to the degradation of myofibrillar proteins. The techniques employed indicate that meat proteolysis during thaw-aging is not constant but dynamic.

Application of a Combined Peptidomics and In Silico Approach for the Identification of Novel Dipeptidyl Peptidase-IV-Inhibitory Peptides in In Vitro Digested Pinto Bean Protein Extract

The conventional approach in bioactive peptides discovery, which includes extensive bioassay-guided fractionation and purification processes, is tedious, time-consuming and not always successful. The recently developed bioinformatics-driven in silico approach is rapid and cost-effective; however, it lacks an actual physiological significance. In this study a new integrated peptidomics and in silico method, which combines the advantages of the conventional and in silico approaches by using the pool of peptides identified in a food hydrolysate as the starting point for subsequent application of selected bioinformatics tools, has been developed. Pinto bean protein extract was in vitro digested and peptides were identified by peptidomics. The pool of obtained peptides was screened by in silico analysis and structure–activity relationship modelling. Three peptides (SIPR, SAPI and FVPH) were selected as potential inhibitors of the dipeptidyl-peptidase-IV (DPP-IV) enzyme by this integrated approach. In vitro bioactivity assay showed that all three peptides were able to inhibit DPP-IV with the tetra-peptide SAPI showing the highest activity (IC50 = 57.7 μmol/L). Indeed, a new possible characteristic of peptides (i.e., the presence of an S residue at the N-terminus) able to inhibit DPP-IV was proposed.

Antioxidant and Angiotensin I-Converting Enzyme (ACE) Inhibitory Peptides Obtained from Alcalase Protein Hydrolysate Fractions of Hemp (Cannabis sativa L.) Bran

Proteins from hemp bran (HPB), a byproduct of the hemp seed food-processing chain, were chemically extracted, hydrolyzed by Alcalase, and separated by membrane ultrafiltration into four fractions (MW <1, 1-3, 3-5, and >5 kDa). The antioxidant and antihypertensive properties of the initial extract and the fractions were evaluated by in vitro assays for their ability to scavenge radical species, bind with metal ions, reduce ferric ions, and inhibit angiotensin-converting enzyme (ACE) activity. Bioactive peptides were identified by high-resolution mass spectrometry and sequence comparison with BIOPEP and BioPep DB databases. The hydrolysate was strongly antioxidant and ACE-inhibiting; the most bioactive peptides were further concentrated by ultrafiltration. Of the 239 peptides identified, 47 (12 antioxidant and 35 ACE-inhibitory) exhibited structural features correlated with the specific bioactivity. These results highlight the promise of hydrolysate and size-based HPB fractions as natural functional ingredients for the food or pharmaceutical industry.