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.

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.

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.

Histone derived antimicrobial peptides identified from Mytilus coruscus serum by peptidomics

Histones and their N-terminal or C-terminal derived peptides have been studied in vertebrates and presented as potential antimicrobial agents playing important roles in the innate immune defenses. Although histones and their derived peptides had been reported as components of innate immunity in invertebrates, the knowledge about the histone derived antimicrobial peptides (HDAPs) in invertebrates are still limited. Using a peptidomic technique, a set of peptide fragments derived from the histones was identified in this study from the serum of microbes challenged Mytilus coruscus. Among the 85 identified histone-derived-peptides with high confidence, 5 HDAPs were chemically synthesized and the antimicrobial activities were verified, showing strong growth inhibition against Gram-positive bacteria, Gram-negative bacteria, and fungus. The gene expression level of the precursor histones matched by representative HDAPs were further tested using q-PCR, and the results showed a significant upregulation of the histone gene expression levels in hemocytes, gill, and mantle of the mussel after immune stress. In addition, three identified HDAPs were selected for preparation of specific antibodies, and the corresponding histones and their derived C-terminal fragments were detected by Western blotting in the blood cell and serum of immune challenged mussel, respectively, indicating the existence of HDAPs in M. coruscus. Our findings revealed the immune function of histones in Mytilus, and confirmed the existence of HDAPs in the mussel. The identified Mytilus HDAPs represent a new source of immune effector with antimicrobial function in the innate immune system, and thus provide promising candidates for the treatment of microbial infections in aquaculture and medicine.

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.

Preparation, identification, and molecular docking of novel angiotensin-converting enzyme inhibitory peptides derived from rice-based distillers' spent cakes

BACKGROUND

Rice-based distillers' spent cake (RDSC), a by-product of the Chinese liquor (Baijiu) industry, is a potential source of ACE inhibitory peptide. Since angiotensin-converting enzyme (ACE) plays a crucial role in controlling hypertension, inhibition of ACE has been widely emphasized. The ACE inhibitory active peptide derived from by-products of food has been recognized as safer and cheaper inhibitors.

RESULTS

Aimed to discover ACE-inhibiting active peptides in RDSC. Hydrolysis of RDSC by alcalase for 4 h followed by ultrafiltration yielded low-molecular-weight (< 3 kDa) fractions. Subsequently, a comprehensive method that using a combination of LC-Q-TOF-MS and LC-Q Exactive-MS to identify the novel short- (3-5 amino acids residues; n = 7) and medium-sized peptides (more than 6 amino acids residues; n = 6). In vitro activity assay showed that the peptides KPFFPGL, GFPRPLL, GPPGVF, and VGK exhibited the highest activity with IC50 of 11.63, 12.34, 19.55, and 33.54 μM. Molecular docking reveal that the active and inactive sites (Glu123, Asp121, Arg522, and Lys118) play important roles in enhancing the ACE inhibitory activity of peptides.

CONCLUSION

Here we report a comprehensive method that effectively extracted and identified the bioactive peptides from RDSC. Four highly active novel peptides may be the most promising candidates for functional foods to against hypertension, provide significant information for enhancing value of rice-based distilled by-products. This article is protected by copyright. All rights reserved.

Effect of peptide formation during rapeseed fermentation on meat analogue structure and sensory properties at different pH conditions

This study aimed to modify the sensory properties of rapeseed protein concentrate using a combination of fermentation and high-moisture extrusion processing for producing meat analogues. The fermentation was carried out with Lactiplantibacillus plantarum and Weissella confusa strains, known for their flavour and structure-enhancing properties. Contrary to expectations, the sensory evaluation revealed that the fermentation induced bitterness and disrupted the fibrous structure formation ability due to the generation of short peptides. On the other hand, fermentation removed the intensive off-odour and flavour notes present in the native raw material. Several control treatments were produced to understand the reasons behind the hindered fibrous structure formation and induced bitterness. The results obtained from peptidomics, free amino ends, and solubility analyses strongly indicated that the proteins were hydrolysed by endoproteases activated during the fermentation process. Furthermore, it was suspected that the proteins and/or peptides formed complexes with other components, such as hydrolysis products of glucosinolates and polysaccharides.

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.

Gestational Age-Related Urinary Peptidome Changes in Preterm and Term Born Infants

INTRODUCTION

Preterm infants are at risk for a variety of somatic and neurological disorders. In recent years, biofluid proteomics has emerged as a potential diagnostic tool for biomarker analysis. The aim of this study was to determine gestational age (GA)-related patterns of the urinary peptidome in preterm infants for researching potential novel prognostic biomarkers.

METHODS

We performed urinary peptidomics in longitudinal samples of 24 preterm (mean GA weeks 28 + 1 [24+1-31 + 6]) and 27 term born controls (mean GA weeks 39 + 2 [37+0-41 + 1]) using capillary electrophoresis combined with mass spectrometry (CE-MS). Peptides were sequenced using CE-MS/MS or LC-MS/MS analysis and were deposited, matched, and annotated in a Microsoft SQL database for statistical analysis. We compared their abundance in urine of preterm and term born infants and performed a validation analysis as well as correlations to GA and clinical risk scores.

RESULTS

Our results confirmed significant differences in the abundance of peptides and the hypothesis of age-dependent urinary peptidome changes in preterm and term infants. In preterm infants, SLC38A10 (solute carrier family 38 member 10) is one of the most abundant peptides. Combined urinary peptides correlated with clinical risk scores (p < 0.05).

CONCLUSION

This is the first study reporting GA-related urinary peptidome changes of preterm infants detected by CE-MS and a modulation of the peptidome with GA. Further research is required to locate peptidome clusters correlated with specific clinical complications and long-term outcome. This may identify preterm infants at higher risk for adverse outcome who would benefit from early intervention.

In vitro protein digestibility of RuBisCO from alfalfa obtained from different processing histories: Insights from free N-terminal and mass spectrometry study

Ribulose-1,5-bisphosphate-carboxylase/oxygenase (RuBisCO) from alfalfa is a potentially climate-friendly alternative protein with a promising amino acid composition. The balance between yield and purity is a challenge for alternative plant proteins, partly due to the naturally occurring antinutrients. Therefore, measuring the in vitro protein digestibility (IVPD) of RuBisCO with various purity levels is of interest. It was hypothesized that the digestibility of RuBisCO from alfalfa might vary with different processing histories and levels of refinement. To test this hypothesis, RuBisCO from alfalfa with 4 different processing histories were subjected to the INFOGEST IVPD protocol and measurement of free N-terminals and peptidomics. The result showed that the digestibility of RuBisCO was high regardless of the processing history and purity, as demonstrated by 77-99% sequence coverage in the gastric phase. In intestinal phase, increase of free N-terminals and lower sequence coverage (< 10%) indicated that the proteins were hydrolyzed to smaller peptides.

Identification and prediction of milk-derived bitter taste peptides based on peptidomics technology and machine learning method

Bitter taste peptides (BPs) are vital for drug and nutrition research, but large-scale screening of them is still time-consuming and costly. This study developed a complete workflow for screening BPs based on peptidomics technology and machine learning method. Using an expanded dataset and a new combination of BPs' characteristic factors, a novel classification prediction model (CPM-BP) based on the Light Gradient Boosting Machine algorithm was constructed with an accuracy of 90.3 % for predicting BPs. Among 724 significantly different peptides between spoiled and fresh UHT milk, 180 potential BPs were predicted using CPM-BP and eleven of them were previously reported. One known BP (FALPQYLK) and three predicted potential BPs (FALPQYL, FFVAPFPEVFGKE, EMPFPKYP) were verified by determination of calcium mobilization of HEK293T cells expressing human bitter taste receptor T2R4 (hT2R4). Three potential BPs could activate the hT2R4 and are demonstrated to be BPs, which proved the effectiveness of CPM-BP.

Effect of fat concentration on protein digestibility of Chinese sausage

Chinese sausage is a popular traditional Chinese meat product, but its high-fat content makes consumers hesitant. The purpose of this study is to compare the nutritional differences of Chinese sausages with different fermentation times (0, 10, 20, 30 d) and fat content (the initial content was 11.59% and 20.14%) during digestion. The comparison of digestion degree, protein structure, and peptide composition between different sausages were studied through in vitro simulated digestion. Chinese sausages with high-fat content had higher α-helix, β-turn, and random coil, making them easier to digest. The fermentation process made this phenomenon more pronounced. The high-fat sausage fermented for 10 d showed the highest release of primary amino acids (about 9.5%), which was about 3.5% higher than the low-fat sausage under the same conditions. The results of peptidomics confirmed the relevant conclusions. After gastric digestion, the types of peptides in the digestive fluid of high-fat sausages were generally more than those in low-fat sausages, while after intestinal digestion, the opposite results were observed. The type of peptide reached its peak after fermentation for 20 d. These findings are of obvious significance for selecting the appropriate fermentation time and fat content of Chinese sausages.

Comparative analysis of hippocampal extracellular space uncovers widely altered peptidome upon epileptic seizure in urethane-anaesthetized rats

BACKGROUND

The brain extracellular fluid (ECF), composed of secreted neurotransmitters, metabolites, peptides, and proteins, may reflect brain processes. Analysis of brain ECF may provide new potential markers for synaptic activity or brain damage and reveal additional information on pathological alterations. Epileptic seizure induction is an acute and harsh intervention in brain functions, and it can activate extra- and intracellular proteases, which implies an altered brain secretome. Thus, we applied a 4-aminopyridine (4-AP) epilepsy model to study the hippocampal ECF peptidome alterations upon treatment in rats.

METHODS

We performed in vivo microdialysis in the hippocampus for 3-3 h of control and 4-AP treatment phase in parallel with electrophysiology measurement. Then, we analyzed the microdialysate peptidome of control and treated samples from the same subject by liquid chromatography-coupled tandem mass spectrometry. We analyzed electrophysiological and peptidomic alterations upon epileptic seizure induction by two-tailed, paired t-test.

RESULTS

We detected 2540 peptides in microdialysate samples by mass spectrometry analysis; and 866 peptides-derived from 229 proteins-were found in more than half of the samples. In addition, the abundance of 322 peptides significantly altered upon epileptic seizure induction. Several proteins of significantly altered peptides are neuropeptides (Chgb) or have synapse- or brain-related functions such as the regulation of synaptic vesicle cycle (Atp6v1a, Napa), astrocyte morphology (Vim), and glutamate homeostasis (Slc3a2).

CONCLUSIONS

We have detected several consequences of epileptic seizures at the peptidomic level, as altered peptide abundances of proteins that regulate epilepsy-related cellular processes. Thus, our results indicate that analyzing brain ECF by in vivo microdialysis and omics techniques is useful for monitoring brain processes, and it can be an alternative method in the discovery and analysis of CNS disease markers besides peripheral fluid analysis.

Peptidomics of Zebrafish Brain in a 6-OHDA-Induced Neurodegeneration Model

Bioactive peptides such as neuropeptides and peptide hormones are largely understood in their involvement in a variety of physiologic systems. In addition to the neuropeptides produced and processed by the classic secretory pathway, intracellular peptides (InPeps) have shown biological activity in studies involving different organisms. A model that has become attractive in many research fields is the zebrafish (Danio rerio), which has allowed correlating behavioral responses or physiological processes with underlying molecular pathways or signaling cascades, improving the understanding of homeostasis mechanisms of the central nervous system, as well as pathological processes such as neurodegenerative diseases. Here, we provide a detailed description of the protocol of treatment with 6-OHDA, which mimics some features of Parkinson's Disease, as well as the validation of the treatment by evaluation of the locomotor activity and the protocol of peptide extraction followed by isotopic labeling to peptide relative quantitation by mass spectrometry.

Albumen and Yolk Plasma Peptidomics for the Identification and Quantitation of Bioactive Molecules and the Quality Control of Hen Egg Products

Hen eggs and the corresponding food products are essential components of human diet. In addition to supplying basic nutrients, they contain functional peptides that are released in vivo within the intact raw material following physiological proteolytic events affecting specific proteins or derive from technological processing of albumen and yolk fractions as a result of the dedicated use of proteases from plant and microbial sources. Besides their potential importance for functional applications, peptides released under physiological conditions in intact egg can be used as markers of product storage and deterioration. Therefore, characterization and quantitation of peptides in egg and egg-derived products can be used to implement evaluation of potential bioactivities as well as to assess food product qualitative characteristics. Here, we provide dedicated information on extraction, identification, and quantitative analysis of peptides from albumen and yolk plasma; nano-liquid chromatography-mass spectrometry combined with bioinformatic analysis of resulting raw data by different software tools allowed to assign molecules based on database searching and to evaluate their relative quantity in different samples.

Intracellular and Extracellular Peptidomes of the Model Plant, Physcomitrium patens

Here, we report our approach to peptidomic analysis of the plant model Physcomitrium patens. Intracellular and extracellular peptides were extracted under conditions preventing proteolytic digestion by endogenous proteases. The extracts were fractionated on size exclusion columns to isolate intracellular peptides and on reversed-phase cartridges to isolate extracellular peptides, with the isolated peptides subjected to LC-MS/MS analysis. Mass spectrometry data were analyzed for the presence of peptides derived from the known proteins or microproteins encoded by small open reading frames (<100 aa, smORFs) predicted in the moss genome. Experimental details are provided for each step.

Current Challenges and Future Directions in Peptidomics

The field of peptidomics has been under development since its start more than 20 years ago. In this chapter we provide a personal outlook for future directions in this field. The applications of peptidomics technologies are spreading more and more from classical research of peptide hormones and neuropeptides towards commercial applications in plant and food-science. Many clinical applications have been developed to analyze the complexity of biofluids, which are being addressed with new instrumentation, automization, and data processing. Additionally, the newly developed field of immunopeptidomics is showing promise for cancer therapies. In conclusion, peptidomics will continue delivering important information in classical fields like neuropeptides and peptide hormones, benefiting from improvements in state-of-the-art technologies. Moreover, new directions of research such as immunopeptidomics will further complement classical omics technologies and may become routine clinical procedures. Taken together, discoveries of new substances, networks, and applications of peptides can be expected in different disciplines.

Identification of Peptides in Spider Venom Using Mass Spectrometry

Spider venoms are composed of hundreds of proteins and peptides. Several of these venom toxins are cysteine-rich peptides in the mass range of 3-9 kDa. Small peptides (<3 kDa) can be fully characterized by mass spectrometry analysis, while proteins are generally identified by the bottom-up approach in which proteins are first digested with trypsin to generate shorter peptides for MS/MS characterization. In general, it is sufficient for protein identification to sequence two or more peptides, but for venom peptidomics it is desirable to completely elucidate peptide sequences and the number of disulfide bonds in the molecules. In this chapter, we describe a methodology to completely sequence and determine the number of disulfide bonds of spider venom peptides in the mass range of 3-9 kDa by multiple enzyme digestion, mass spectrometry of native and digested peptides, de novo analysis, and sequence overlap alignment.

Integrating a Multi-label Deep Learning Approach with Protein Information to Compare Bioactive Peptides in Brain and Plasma

Peptide therapeutics is gaining momentum. Advances in the field of peptidomics have enabled researchers to harvest vital information from various organisms and tissue types concerning peptide existence, expression and function. The development of mass spectrometry techniques for high-throughput peptide quantitation has paved the way for the identification and discovery of numerous known and novel peptides. Though much has been achieved, scientists are still facing difficulties when it comes to reducing the search space of the large mass spectrometry-generated peptidomics datasets and focusing on the subset of functionally relevant peptides. Moreover, there is currently no straightforward way to analytically compare the distributions of bioactive peptides in distinct biological samples, which may reveal much useful information when seeking to characterize tissue- or fluid-specific peptidomes. In this chapter, we demonstrate how to identify, rank, and compare predicted bioactive peptides and bioactivity distributions from extensive peptidomics datasets. To aid this task, we utilize MultiPep, a multi-label deep learning approach designed for classifying peptide bioactivities, to identify bioactive peptides. The predicted bioactivities are synergistically combined with protein information from the UniProt database, which assist in navigating through the jungle of putative therapeutic peptides and relevant peptide leads.

Untargeted Analysis of Short-Chain Peptides in Urine Samples Short Peptides Analysis

Short-chain peptides have attracted increasing attention in different research fields, including biomarker discovery, but also a well-known analytical challenge in complex matrices due to their low abundance compared to other molecules, which can cause extensive ion suppression during mass spectrometric acquisition. Moreover, there is a lack of analytical workflows for their comprehensive characterization since ordinary peptidomics strategies cannot identify them. In this context, an enrichment strategy was introduced and developed to isolate and clean up short-chain peptides by graphitized carbon black solid phase extraction. For better coverage of peptide polarity, urine samples were analyzed by ultrahigh performance liquid chromatography by reversed-phase and hydrophilic interaction liquid chromatography. High-resolution mass spectrometry allowed the detection of the eluting peptides by data-dependent mode using a suspect screening strategy with an inclusion list; peptides were identified by a semiautomated workflow implemented on Compound Discoverer. The complementarity of the orthogonal separation strategy was confirmed by peptide identification, resulting in 101 peptides identified from the RP runs, and 111 peptides from the HILIC runs, with 60 common identifications.

Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry

The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. The nervous system, with its 302 neurons, is probably the best-known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display numerous similarities with those observed in other metazoans. Here, we describe two label-free approaches for neuropeptidomics in C. elegans: one for discovery purposes, and another for targeted quantification and comparisons of neuropeptide levels between different samples. Starting from a detailed peptide extraction procedure, we here outline the liquid chromatography tandem mass spectrometry (LC-MS/MS) setup and describe subsequent data analysis approaches.

Data-Independent Acquisition Peptidomics

In recent years, data-independent acquisition (DIA) has emerged as a powerful analysis method in biological mass spectrometry (MS). Compared to the previously predominant data-dependent acquisition (DDA), it offers a way to achieve greater reproducibility, sensitivity, and dynamic range in MS measurements. To make DIA accessible to non-expert users, a multifunctional, automated high-throughput pipeline DIAproteomics was implemented in the computational workflow framework "Nextflow" ( https://nextflow.io ). This allows high-throughput processing of proteomics and peptidomics DIA datasets on diverse computing infrastructures. This chapter provides a short summary and usage protocol guide for the most important modes of operation of this pipeline regarding the analysis of peptidomics datasets using the command line. In brief, DIAproteomics is a wrapper around the OpenSwathWorkflow and relies on either existing or ad-hoc generated spectral libraries from matching DDA runs. The OpenSwathWorkflow extracts chromatograms from the DIA runs and performs chromatographic peak-picking. Further downstream of the pipeline, these peaks are scored, aligned, and statistically evaluated for qualitative and quantitative differences across conditions depending on the user's interest. DIAproteomics is open-source and available under a permissive license. We encourage the scientific community to use or modify the pipeline to meet their specific requirements.

Extraction of Apoplastic Peptides for the Structural Elucidation of Mature Peptide Hormones in Arabidopsis

Various secreted peptides, including peptide hormones, are present in the apoplast, but their biochemical characterization remains a challenge due to their low abundance, difficulty in extraction, and interference from numerous secondary metabolites. Here, we describe a simple and straightforward protocol for the extraction of apoplastic peptides with a high purity. This protocol takes advantage of the fact that apoplastic peptides diffuse and accumulate in the culture medium when Arabidopsis seedlings are subjected to whole-plant submerged culture. The peptides in the culture medium are efficiently recovered by o-chlorophenol extraction followed by acetone precipitation. The recovered peptides can be subjected to nano-liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) without any additional clean-up. This procedure enables the structural elucidation of mature peptide hormones in the apoplast with the use of Arabidopsis plants that overexpress peptide hormone genes.

Construction of hypoallergenic microgel by soy major allergen β-conglycinin through enzymatic hydrolysis and lactic acid bacteria fermentation

Soy allergenicity is a public concern, and the combination of multiple processing methods may be a promising strategy for reducing soy allergenicity. In this study, a novel two-step enzymatic hydrolysis followed by lactic acid bacteria fermentation was proposed for the construction of hypoallergenic soybean protein microgel. β-Conglycinin was used as the main soy allergen. The effects of different enzymatic hydrolysis (Alcalase, Neutrase, and Protamex) and LAB fermentation on β-conglycinin microgel formation and its immunoreactivity were investigated. Results showed that the use of different enzymes and the attainment of different degrees of hydrolysis affected the particle distribution and zeta potential in the microgels and leads to differences in microstructure and immunoreactivity. All hydrolysates compared with intact protein accelerated the formation of gel during LAB fermentation. Among the three assayed enzymes, fermented Protamex hydrolysates at 60 min (PF-60) demonstrated a microgel with an overall reduced average particle size (741.20±7.18 nm), lower absolute values of zeta potential (10.43±0.65 mV), and regular gel network. The antigenicity and IgE-binding capacity decreased to the lowest value of 0.30 % and 6.93 %, respectively. Peptidomics and immunoinformatic analysis suggested that PF-60 disrupted 17/30, 16/44, and 23/75 epitopes in the α, α', and β subunits, respectively. Unlike the LAB-fermented unhydrolyzed β-conglycinin disrupted epitopes mostly located at the loop domain, PF-60 primarily promoted the exposure and disruption of allergen epitopes with β-sheet structure located at the core barrel domain. These findings can provide new perspectives on the preparation of hypoallergenic soybean-gel products on edible particulate systems.

Peptidomics Strategies to Evaluate Cancer Diagnosis, Prognosis, and Treatment

Peptides have potential bioactive functions, and the peptidomics landscape has been broadly investigated for various diseases, including cancer. In this chapter, we reviewed the past four years of literature available and selected 16 peer-reviewed publications exploring peptidomics in diagnosis, prognosis, and treatment in cancer research. We highlighted their main aims, mass spectrometry-based peptidomics, multi-omics, data-driven and in silico strategies, functional assays, and clinical applications. Moreover, we underscored several levels of difficulties in translating the peptidomics findings to clinical practice, aiming to learn with the accumulated knowledge and guide upcoming studies. Finally, this review reinforces the peptidomics robustness in discovering potential candidates for monitoring the several stages of cancer disease and therapeutic treatment, leveraging the management of cancer patients in the future.

Label-Free Quantitation of Endogenous Peptides

Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.

Anti-inflammatory effect of two novel peptides derived from Binglangjiang buffalo whey protein in lipopolysaccharide-stimulated RAW264.7 macrophages

Whey protein hydrolysate from Binglangjiang buffalo, a unique genetic resource, has anti-inflammatory activity, but its anti-inflammatory composition and effects are unknown. The aim of this study was to investigate the anti-inflammatory peptides from Binglangjiang buffalo whey protein hydrolysate. A total of 1483 peptides were identified using LC-MS/MS, and 12 peptides were chosen for chemical synthesis using peptidomics, and then two novel anti-inflammatory peptides (DQPFFHYN (DN8) and YSPFSSFPR (YR9)) were screened out using LPS-stimulated RAW264.7 cells. The molecular weights of DN8 and YR9 with β-turn conformations were 1067.458 Da and 1087.52 Da, respectively, and showed a high in-vitro safety profile and thermal stability, but were intolerant to pepsin. Furthermore, ELISA and Western blot analysis indicated that peptides DN8 and YR9 significantly suppressed the secretion of pro-inflammatory cytokines NO, TNF-α, and IL-6 and the expression of mediators iNOS, TNF-α, and IL-6 in LPS-stimulated RAW264.7 cells. The study provides insights into the development of novel food-based anti-inflammatory nutritional supplements.

Generation of kokumi γ-glutamyl short peptides in Spanish dry-cured ham during its processing

The typical dry-cured ham flavor is rich in umami and brothy perceptions, for which short peptides may contribute. Particularly, γ-glutamyl peptides could be the responsible of these previously reported attributes, as they exert a synergistic interaction with other basic tastes and modify the intensity of salty, sweet, and umami tastes. The content of peptides has been reported to evolve along the processing, but no kokumi γ-glutamyl peptides have been identified in Spanish dry-cured hams yet. In this research, nine γ-glutamyl dipeptides (γ-EA, γ-EC, γ-EE, γ-EF, γ-EL, γ-EM, γ-EV, γ-EW, and γ-EY) and two γ-glutamyl tripeptides (GSH and γ-EVG) have been quantitated at 6, 12, 18 and 24 months of traditional processing of Spanish dry-cured ham by performing a Q Exactive Orbitrap-based tandem mass spectrometry. The results show an increase of γ-EA, γ-EE, γ-EF, γ-EL, γ-EM and γ-EVG, obtaining maximums at 24 months of curing ranging from 0.14 (γ-EVG) to 18.86 (γ-EL) μg/g dry-cured ham. Otherwise, γ-EV, γ-EW and γ-EY accumulated until the 18th month of storage to 15.10, 0.54 and 3.17 μg/g dry-cured ham, respectively; whereas γ-EC and GSH amounts decreased starting from 0.0676 and 4.41 μg/g dry-cured ham, respectively at earlier stages. The concentration dynamics of these compounds may be linked with proteolytic and oxidative reactions during processing. In addition, due to their synergistic effect on kokumi activity, this could constitute insights of the brothy perceptions of dry-cured ham, and these peptides probably contribute to the sensory differences existing in long processed Spanish dry-cured hams.

Application of serum peptidomics for Parkinson's disease in SNCA-A30P mice

Intraneuronal inclusions of alpha-synuclein (α-synuclein, α-syn) are commonly found in the brain of patients with Parkinson's disease (PD). The pathogenesis of the abundant α-syn protein in the blood has been extensively studied to understand its properties better. In recent years, peptidome analysis has received increasing attention. In this study, we identified and analyzed serum peptides from wild-type (WT) and the (Thy-1)-h[A30P] alpha-synuclein transgenic mice (SNCA-A30P mice) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). One thousand eight hundred fifty-six peptides from 771 proteins were analyzed. Among them, 151 peptides from 107 proteins were significantly differentially expressed. The glycoprotein VI platelet pathway (GP6) was the pathway's most significant differentially expressed signaling pathway. Cleavage sites of the differentially expressed peptides may reflect protease distribution and activity. We selected the most significantly differentially expressed peptide, VGGDPI, and found that it contained cathepsin K (Ctsk) and trypsin-1 cleavage sites, suggesting that Ctsk and trypsin-1 may be key peptidases in PD. α-syn is a protein associated with the pathogenesis of PD. mutations in several genes, including SNCA, which encodes α-syn, are associated with the development of PD. Bioinformatics analysis of the physiological pathways related to SNCA genes and apoptosis genes found the five most markedly up-regulated proteins: formin homology 2 domain-containing 1 (FHOD1), insulin receptor substrate 1(IRS1), TRPM8 channel-associated factor 1 (TCAF1), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and interleukin-16 (IL-16). Therefore, the differentially expressed peptides in the five precursor protein domains may be potential bioactive peptides associated with α-syn and apoptosis. This study provides a validated peptidomics profile of SNCA-A30P mice and identifies potentially bioactive peptides linked to α-syn and apoptosis.

Exploring novel ANGICon-EIPs through ameliorated peptidomics techniques: Can deep learning strategies as a core breakthrough in peptide structure and function prediction?

Dairy-derived angiotensin-I-converting enzyme inhibitory peptides (ANGICon-EIPs) have been regarded as a relatively safe supplementary diet-therapy strategy for individuals with hypertension, and short-chain peptides may have more relevant antihypertensive benefits due to their direct intestinal absorption. Our previous explorations have confirmed that endogenous goat milk short-chain peptides are also an essential source of ANGICon-EIPs. Nonetheless, there are limited explorations on endogenous ANGICon-EIPs owing to the limitations of the extraction and enrichment of endogenous peptides, currently. This review outlined ameliorated pre-treatment strategies, data acquisition methods, and tools for the prediction of peptide structure and function, aiming to provide creative ideas for discovering novel ANGICon-EIPs. Currently, deep learning-based peptide structure and function prediction algorithms have achieved significant advancements. The convolutional neural network (CNN) and peptide sequence-based multi-label deep learning approach for determining the multi-functionalities of bioactive peptides (MLBP) can predict multiple peptide functions with absolute true value and accuracy of 0.699 and 0.708, respectively. Utilizing peptide sequence input, torsion angles, and inter-residue distance to train neural networks, APPTEST predicted the average backbone root mean square deviation (RMSD) value of peptide (5-40 aa) structures as low as 1.96 Å. Overall, with the exploration of more neural network architectures, deep learning could be considered a critical research tool to reduce the cost and improve the efficiency of identifying novel endogenous ANGICon-EIPs.

Unveiling the peptidome diversity of Lachesismuta snake venom: Discovery of novel fragments of metalloproteinase, l-amino acid oxidase, and bradykinin potentiating peptides

Snake venoms are known to be major sources of peptides with different pharmacological properties. In this study, we comprehensively explored the venom peptidomes of three specimens of Lachesismuta, the largest venomous snake in South America, using mass spectrometry techniques. The analysis revealed 19 main chromatographic peaks common to all specimens. A total of 151 peptides were identified, including 69 from a metalloproteinase, 58 from the BPP-CNP precursor, and 24 from a l-amino acid oxidase. To our knowledge, 126 of these peptides were reported for the first time in this work, including a new SVMP-derived peptide fragment, Lm-10a. Our findings highlight the dynamic nature of toxin maturation in snake venoms, driven by proteolytic processing, post-translational modifications, and cryptide formation.

Effect of pH treatment on egg white protein digestion and the peptidomics of their in vitro digests

The pH treatment significantly enhanced the functional properties of egg white protein (EWP), but little is known about the relationship between pH treatment and in vitro digestion of EWP. In this paper, we explored the effect of pH treatment (pH 2, pH 2-7, pH 12 and pH 12-7) on the digestibility of egg white protein and peptide profiling using the digestion kinetics and peptidomics methods, separately. The results implied that all pH treatment reduced the protein digestibility in gastric phase, while alkaline pH (pH 12 and pH 12-7) showed greater digestion level and more gastric peptides, and more importantly, produced a greater amount of potentially bioactive peptides than acid treated samples. Besides, the least number of potentially bioactive peptides was obtained at pH 2, but this could be improved by adjusting pH 2 back to 7. Notably, the unique bioactive peptides induced by pH were mainly relevant to DPP IV inhibitor. These differences of digestibility and peptide profiling might be attributed to the change of protein structure and the formation of molten sphere, altering cleavage sites of digestive enzymes. This work would give an enlightening insight into the digestive and nutritional characteristics of the pH-induced EWP to expand their application in the field of food and healthcare.

Identification of novel α-glucosidase and ACE inhibitory peptides from Douchi using peptidomics approach and molecular docking

In this study, the effect of Douchi extract (DWE) on α-glucosidase and angiotensin-converting enzymes (ACE) were investigated, and several novel peptides with inhibitory activity against α-glucosidase and ACE were identified using peptidomics approach based on UPLC-MS/MS. The average inhibition rates of DWE on α-glucosidase and ACE were 73.75-78.10% and 4.56-27.07%, respectively. In the DWE, a total of 710 peptides were detected. Two novel peptides with potential inhibitory activity against α-glucosidase were identified using the correlation analysis, database alignment and molecular docking methods. They were DVFRAIPSEVL and DRPSINGLAGAN, with the IC50 values of 0.121 and 0.128 mg/mL, respectively. Also, four novel peptides with potential inhibitory activity against ACE were identified: PSSPFTDLWD, EEQDERQFPF, PVPVPVQQAFPF and PSSPFTDL, with IC50 values of 1.388, 0.041, 0.761 and 0.097 mg/mL, respectively. These results indicated that combining peptidomics and molecular docking is an effective alternative strategy for rapidly screening numbers of novel bioactive peptides from foods.

Raw to charred: Changes of protein oxidation and in vitro digestion characteristics of grilled lamb

This study aimed to evaluate protein oxidation and in vitro digestion characteristics of lamb that was grilled from raw to charred (0-30 min). Results showed that protein oxidation was aggravated with the time of grilling, indicated by a significant linear increase in carbonyl groups and a linear decrease in sulfhydryl groups. Proteins had the highest simulated gastric and gastrointestinal digestibility at 10-15 min of grilling. Newly formed specific peptides were continuously released during the grilling process. The identified peptides were mainly derived from creatine kinase, phosphoglycerate kinase, actin and myosin light chain. Protein oxidation was closely related to digestive characteristics, and grilling for >15 min would aggravate protein oxidation and reduce its digestibility. Therefore, at 220 °C lamb should not be grilled for longer than 15 min.

Anti-inflammatory therapeutic biomarkers identified of human bone marrow mesenchymal stem cell therapy on aging mice by serum proteomics and peptidomics study

Aging is accompanied by deterioration in physical condition, and creates high risks of diseases. Stem cell therapy exhibited promising potential in delaying aging. However, the unelucidated therapeutic mechanism limits future clinical application. Herein, to systematically understand the response to stem cell transfusion at the molecular level, we performed quantitative serum proteomic and peptidomics analyses in the 24-month-old aging mice model with or without mesenchymal stem cell (MSC) treatment. As a result, a total of 560 proteins and 2131 endogenous peptides were identified, among which, 6 proteins and 9 endogenous peptides derived from 6 precursor proteins were finally identified as therapeutic biomarkers after MSC transfusion on aging mice both by untargeted label-free quantification and targeted parallel reaction monitoring (PRM) quantification. Amazingly, the biological function of these differential proteins was mainly related to inflammation, which is not only the important hallmark of aging, but also the main cause of inducing aging. The reduction of these inflammatory protein content after MSC treatment further suggests the anti-inflammatory effect of MSC therapy reported elsewhere. Therefore, our study provides new evidence for the anti-inflammatory effect of MSC therapy for anti-aging and offers abundant data to support deeper investigations of the therapeutic mechanism of MSC in delaying aging.

Urinary peptides provide information about the risk of mortality across a spectrum of diseases and scenarios

BACKGROUND

There is evidence of pre-established vulnerability in individuals that increases the risk of their progression to severe disease or death, although the mechanisms causing this are still not fully understood. Previous research has demonstrated that a urinary peptide classifier (COV50) predicts disease progression and death from SARS-CoV-2 at an early stage, indicating that the outcome prediction may be partly due to vulnerabilities that are already present. The aim of this study is to examine the ability of COV50 to predict future non-COVID-19-related mortality, and evaluate whether the pre-established vulnerability can be generic and explained on a molecular level by urinary peptides.

METHODS

Urinary proteomic data from 9193 patients (1719 patients sampled at intensive care unit (ICU) admission and 7474 patients with other diseases (non-ICU)) were extracted from the Human Urinary Proteome Database. The previously developed COV50 classifier, a urinary proteomics biomarker panel consisting of 50 peptides, was applied to all datasets. The association of COV50 scoring with mortality was evaluated.

RESULTS

In the ICU group, an increase in the COV50 score of one unit resulted in a 20% higher relative risk of death [adjusted HR 1.2 (95% CI 1.17-1.24)]. The same increase in COV50 in non-ICU patients resulted in a higher relative risk of 61% [adjusted HR 1.61 (95% CI 1.47-1.76)], consistent with adjusted meta-analytic HR estimate of 1.55 [95% CI 1.39-1.73]. The most notable and significant changes associated with future fatal events were reductions of specific collagen fragments, most of collagen alpha I (I).

CONCLUSION

The COV50 classifier is predictive of death in the absence of SARS-CoV-2 infection, suggesting that it detects pre-existing vulnerability. This prediction is mainly based on collagen fragments, possibly reflecting disturbances in the integrity of the extracellular matrix. These data may serve as a basis for proteomics-guided intervention aiming towards manipulating/ improving collagen turnover, thereby reducing the risk of death.

CCK and GLP-1 response on enteroendocrine cells of semi-dynamic digests of hydrolyzed and intact casein

A semi-dynamic gastrointestinal device was employed to explore the link between protein structure and metabolic response upon digestion for two different substrates, a casein hydrolysate and the precursor micellar casein. As expected, casein formed a firm coagulum that remained until the end of the gastric phase while the hydrolysate did not develop any visible aggregate. Each gastric emptying point was subjected to a static intestinal phase where the peptide and amino acid composition changed drastically from that found during the gastric phase. Gastrointestinal digests from the hydrolysate were characterized by a high abundancy of resistant peptides and free amino acids. Although all gastric and intestinal digests from both substrates induced the secretion of cholecystokinin (CCK) and glucagon-like peptide-1 (GLP-1) in STC-1 cells, GLP-1 levels were maximum in response to gastrointestinal digests from the hydrolysate. The enrichment of protein ingredients with gastric-resistant peptides by enzymatic hydrolysis is proposed as strategy to deliver protein stimuli to the distal gastrointestinal tract to control food intake or type 2 diabetes.

Bioactive milk peptides: an updated comprehensive overview and database

Partial digestion of milk proteins leads to the formation of numerous bioactive peptides. Previously, our research team thoroughly examined the decades of existing literature on milk bioactive peptides across species to construct the milk bioactive peptide database (MBPDB). Herein, we provide a comprehensive update to the data within the MBPDB and a review of the current state of research for each functional category from in vitro to animal and clinical studies, including angiotensin-converting enzyme (ACE)-inhibitory, antimicrobial, antioxidant, dipeptidyl peptidase (DPP)-IV inhibitory, opioid, anti-inflammatory, immunomodulatory, calcium absorption and bone health and anticancer activity. This information will help drive future research on the bioactivities of milk peptides.

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.

A multi-centre peptidomics investigation of food digesta: current state of the art in mass spectrometry analysis and data visualisation

Mass spectrometry has become the technique of choice for the assessment of a high variety of molecules in complex food matrices. It is best suited for monitoring the evolution of digestive processes in vivo and in vitro. However, considering the variety of equipment available in different laboratories and the diversity of sample preparation methods, instrumental settings for data acquisition, statistical evaluations, and interpretations of results, it is difficult to predict a priori the ideal parameters for optimal results. The present work addressed this uncertainty by executing an inter-laboratory study with samples collected during in vitro digestion and presenting an overview of the state-of-the-art mass spectrometry applications and analytical capabilities available for studying food digestion. Three representative high-protein foods - skim milk powder (SMP), cooked chicken breast and tofu - were digested according to the static INFOGEST protocol with sample collection at five different time points during gastric and intestinal digestion. Ten laboratories analysed all digesta with their in-house equipment and applying theirconventional workflow. The compiled results demonstrate in general, that soy proteins had a slower gastric digestion and the presence of longer peptide sequences in the intestinal phase compared to SMP or chicken proteins, suggesting a higher resistance to the digestion of soy proteins. Differences in results among the various laboratories were attributed more to the peptide selection criteria than to the individual analytical platforms. Overall, the combination of mass spectrometry techniques with suitable methodological and statistical approaches is adequate for contributing to the characterisation of the recently defined digestome.

The use of urine peptidomics to define dietary gluten peptides from patients with celiac disease and the clinical relevance

INTRODUCTION

Determination of urinary gluten immunogenic peptides (GIP) has emerged as one of the most attractive test to monitor the adherence to the gluten-free diet (GFD) of patients with celiac disease (CD), being a simple, noninvasive and direct method to detect gluten contamination of the GFD.

AREAS COVERED

We conducted a scoping review in Medline (PubMed) of articles published up to April 2023 that analyzed any aspect of the clinical relevance of the use of urinary GIP measurement in patients with CD. A total of 17 articles reporting the clinical use of urinary peptidomics for the follow-up of CD patients were finally included.

EXPERT OPINION

Available data suggest that a negative urinary GIP result is a reliable noninvasive predictor of intestinal mucosa healing in CD patients treated with the GFD, especially if testing three urine samples on different days including the weekend. Due to conflicting results about the sensitivity and the specificity of the urinary GIP determination, additional in-depth information is needed, particularly related to (1) the relationship between the amount of ingested gluten and the quantity of urinary GIP excreted in treated CD patients, (2) the GIP kinetics and best timing for sample collection.

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.

Insights into the in vitro digestibility of pork myofibrillar protein with different ionic polysaccharides from the perspective of gel characteristics

In this work, the simulated gastrointestinal digestion of myofibrillar protein gels (MPGs) with anionic xanthan (XMP) and sodium alginate (SMP)/cationic chitosan (CSMP)/neutral curdlan (CMP) and konjac (KMP) was investigated to develop muscle-gelled foods with good qualities before and after eating. The results indicated that the neutral CMP and KMP groups had higher gel strength and protein digestibility than the CSMP group. Xanthan and sodium alginate facilitated myosin degradation in gastrointestinal digestion because of the weak wraps between protein and anionic polysaccharides, gaining plentiful peptides (1790 and 1692 respectively) with molecular weights below 2000 Da. Chitosan and neutral curdlan could improve the strength of MP gel but inhibited proteolysis and resulted in low contents of released amino acids via the strong cross-linked network blocking trypsin contact. This work provides a theoretical basis for developing low-fat meat products with good qualities and digestion behaviors by simply controlling the ionic types of polysaccharides.

Peptidomic Analysis Reveals that Novel Peptide LDP2 Protects Against Hepatic Ischemia/Reperfusion Injury

BACKGROUND AND AIMS

Hepatic ischemia/reperfusion (I/R) injury has become an inevitable issue during liver transplantation, with no effective treatments available. However, peptide drugs provide promising regimens for the treatment of this injury and peptidomics has gradually attracted increasing attention. This study was designed to analyze the spectrum of peptides in injured livers and explore the potential beneficial peptides involved in I/R injury.

METHODS

C57BL/6 mice were used to establish a liver I/R injury animal model. Changes in peptide profiles in I/R-injured livers were analyzed by mass spectrometry, and the functions of the identified peptides were predicted by bioinformatics. AML12 cells were used to simulate hepatic I/R injury in vitro. After treatment with candidate liver-derived peptides (LDPs) 1-10, the cells were collected at various reperfusion times for further study.

RESULTS

Our preliminary study demonstrated that 6 h of reperfusion caused the most liver I/R injury. Peptidomic results suggested that 10 down-regulated peptides were most likely to alleviate I/R injury by supporting mitochondrial function. Most importantly, a novel peptide, LDP2, was identified that alleviated I/R injury of AML12 cells. It increased cell viability and reduced the expression of inflammation- and apoptosis-related proteins. In addition, LDP2 inhibited the expression of proteins related to autophagy.

CONCLUSIONS

Investigation of changes in the profiles of peptides in I/R-injured livers led to identification of a novel peptide, LDP2 with potential function in liver protection by inhibiting inflammation, apoptosis, and autophagy.

A fast stop-flow two-dimensional liquid chromatography tandem mass spectrometry and its application in food-derived protein hydrolysates

Food-derived bioactive peptides have many outstanding features like high safety, easy absorption, etc. However, explorations of the peptides are suffering from the limited knowledge of sample composition and low efficiency of separation techniques. In this work, a fast stop-flow two-dimensional liquid chromatography tandem mass spectrometry (2DLC-MS) was designed and constructed in-house. For chromatographic system optimization, the effects of column pairs and fraction transfer volumes on separation performance were studied. The pair of Protein BEH SEC and HSS T3 columns was found of high orthogonality. The peak capacity detected by the optimized 2DLC reached 1165 (for corn protein hydrolysates), indicating high resolving power. Moreover, the number of peptides identified from corn, soybean and casein protein hydrolysates reached as high as 8330, 8925 and 7215, respectively, demonstrating the high potential of the system. This would help reveal the peptide composition and facilitate the research on exploring bioactive peptides from food-derived protein hydrolysates.

Neurobiochemical, Peptidomic, and Bioinformatic Approaches to Characterize Tauopathy Peptidome Biomarker Candidates in Experimental Mouse Model of Traumatic Brain Injury

Traumatic brain injury (TBI) is a multidimensional damage, and currently, no FDA-approved medicine is available. Multiple pathways in the cell are triggered through a head injury (e.g., calpain and caspase activation), which truncate tau and generate variable fragment sizes (MW 400-45,000 K). In this study, we used an open-head TBI mouse model generated by controlled cortical impact (CCI) and collected ipsilateral (IC) and contralateral (CC) mice htau brain cortices at one (D1) three (D3), and seven (D7) days post-injury. We implemented immunological (antibody-based detection) and peptidomic approaches (nano-reversed-phase liquid chromatography/tandem mass spectrometry) to investigate proteolytic tau peptidome (low molecular weight (LMW) < 10 K)) and pathological phosphorylation sites (high-molecular-weight (HMW); > 10 K) derived from CCI-TBI animal models. Our immunoblotting analysis verified tau hyperphosphorylation, HMW, and HMW breakdown products (HMW-BDP) formation of tau (e.g., pSer₂₀₂, pThr₁₈₁, pThr₂₃₁, pSer₃₉₆, and pSer₄₀₄), following CCI-TBI. Peptidomic data revealed unique sequences of injury-dependent proteolytic peptides generated from human tau protein. Among the N-terminal tau peptides, EIPEGTTAEEAGIGDTPSLEDEAAGHVTQA (a.a. 96-125) and AQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQARM (a.a. 91-127). Examples of tau C-terminal peptides identified include NVSSTGSIDMVDSPQLATLADEVSASLAKQGL (a.a. 410-441) and QLATLADEVSASLAKQGL (a.a. 424-441). Our peptidomic bioinformatic tools showed the association of proteases, such as CAPN1, CAPN2, and CTSL; CASP1, MMP7, and MMP9; and ELANE, GZMA, and MEP1A, in CCI-TBI tau peptidome. In clinical trials for novel TBI treatments, it might be useful to monitor a subset of tau peptidome as targets for biomarker utility and use them for a "theranostic" approach.

Peptidomic Analysis and Antimicrobial Activity of Serum Peptide from Hevea brasiliensis clone BPM24

BACKGROUND

Hevea brasiliensis is severely affected by the fungal disease caused by Phytophthora spp. Significant loss of rubber yield is widespread and extensive use of chemical fungicides has resulted in health and environmental problems.

OBJECTIVE

This work aims to extract and identify the latex serum peptides from a disease tolerant clone of Hevea brasiliensis, and study the inhibitory efficacy against pathogenic bacteria and fungi.

METHODS

Serum peptides were extracted from H. brasiliensis BPM 24 using mixed lysis solution. Low molecular weight peptides were screened and fractionated by solid-phase extraction and then identified by tandem mass spectrometry. Total and fractionated serum peptides were assayed for bacterial and fungal inhibition using broth microdilution and poisoned food methods. An inhibitory control study in the greenhouse was also performed using susceptible clones for pre- and post-infection with Phytophthora spp.

RESULTS

Forty-three serum peptide sequences were successfully identified. Thirty-four peptides matched with the proteins associated with plant defense response signaling, host resistance, and adverse environmental factors. The inhibitory study of total serum peptides demonstrated anti-bacterial and anti-fungal properties. The greenhouse study exhibited disease inhibitory efficacy of 60% for the treatment of Phytophthora spp. in post-infected plants and 80% for pre-treated samples.

CONCLUSION

Latex serum peptides from disease tolerant H. brasiliensis revealed several proteins and peptides associated with plant defense and disease resistance. The peptides play a vital role for defense against bacteria and fungi pathogens, including Phytophthora spp. Enhanced disease protection can be obtained when the extracted peptides were applied to the susceptible plants before exposure to the fungi. These findings provided an insight and may pave the way for the development of biocontrol peptides from natural resources.

Peptidomics: LC-MS operational parameters do matter

The sensitive and specific detection of peptides at low levels in biofluids is critical to increase the lab-to-human translation of peptidomic research. An interesting group of peptides with increasing evidence for involvement in human diseases are quorum sensing peptides. To obtain more reliable conclusions on peptide measurands in biofluids, a selection of often neglected parts of the analytical process using LC-MS were investigated, with novel approaches recommended for each part. Quorum sensing peptides were used as the main model-peptides. The peptidomic parts investigated and discussed here are: Our work addresses aQbD-approached solutions to these challenges, encompassing sample stabilization measures, a suitable peptide anti-adsorption tool, judicious choice of injection solvent versus gradient system and optimal duty cycle parameters. Our recommendations will improve the peptidomics bio-analytics of not only quorum sensing peptides, but can also be of value for other measurands at low concentrations.

Peptidomics analysis of Jiang-Flavor Daqu from high-temperature fermentation to mature and in different preparation season

Jiang-Flavor Daqu (JFDQ) is a grain-type fermented starter for brewing Chinese liquor. Peptides, the metabolites of proteins in JFDQ, are important for the quality and flavor of JFDQ or even the liquor. The peptide variations in the progress of JFDQ preparation were investigated using RPLC-MS/MS. The JFDQ after high-temperature fermenting (HTF_SU) and after ripening (M_SU), as well as the mature JFDQ prepared in spring (M_SP) and in summer (M_SU), were compared respectively. These two groups were investigated from peptides, precursor proteins, abundance, interactions, and potential antimicrobial peptides (pAMPs). A total of 177, 158, and 262 peptides from HTF_SU, M_SP, and M_SU were identified, respectively. Significant differences (P < 0.01) in the abundance of shared peptides were found in different fermentation stage group (HTF_M), and stronger positive correlations were observed in different preparation season group (MSP_MSU). The interactions of the shared peptides in HTF_M and in MSP_MSU were investigated respectively. In addition, 8 pAMPs in HTF_SU, 5 in M_SP, and 22 in M_SU were predicted using CAMPR3, and their core functional regions were analyzed. This systematic study demonstrated the influences of fermentation stage and preparation season on the peptide profiles in JFDQ, which would provide theoretical guidance and be helpful for JFDQ production. SIGNIFICANCE: Peptidomics analysis showed that the peptide profiles of JFDQ varied in different fermentation stages and different preparation seasons, which mainly resulted from the peptides with high abundance, high interaction degrees, and potential antimicrobial activity, as well as the important precursor proteins such as glutens. This systematic study would benefit for the insufficiency of peptide research of JFDQ till now, and provide theoretical guidance for JFDQ production.

Peptidomic analysis of the angiotensin-converting-enzyme inhibitory peptides in milk fermented with Lactobacillus delbrueckii QS306 after ultrahigh pressure treatment

In this study, we assessed the effect of ultrahigh pressure (UHP) treatment on the concentration of peptides and angiotensin-converting enzyme (ACE) inhibitory activity in milk fermented with Lactobacillus delbrueckii QS306. The peptides were identified using peptidomic analysis, and 313 unique peptides were identified. These peptides were derived from 53 precursor proteins. Before and after UHP treatment, 361 (22.2%) peptide sequences exhibited difference, and 53 peptide segments were significantly different. Among them, small peptides (amino acid residues ≤6) isoelectric were point at pH 5-6, and the net charge was mainly positive or neutral. With hydrophobicity and ACE inhibitory activity as screening indicators, 214 small peptides with potential ACE inhibitory activity were identified, and 130 new peptides had potential ACE inhibitory activity. A novel ACE inhibitory peptide VAPFP was synthesized, whose in vitro inhibition rate was 10.56 μmol\/L. Therefore, using peptidomics, the changes in peptide sequences and enhancement in ACE inhibitory activity before and after UHP treatment could be effectively identified in milk fermented with Lactobacillus delbrueckii QS306. This study provided a convenient method for the discovery and identification of new ACE inhibitory peptides.