Umami peptides play important roles in the flavor of fermented broad bean paste(FBBP),and proteases produced by microorganisms contributed to the production of umami peptides.In order to reveal the formation of umami ...Umami peptides play important roles in the flavor of fermented broad bean paste(FBBP),and proteases produced by microorganisms contributed to the production of umami peptides.In order to reveal the formation of umami peptides and their relationships with protease-producing microorganisms during the natural fermentation of FBBP,peptidomics and virtual screening were used to identify and screen umami peptides.Meanwhile,macrogenomics was used to analyze the abundance of microbial-derived protease genes during FBBP fermentation.Then,based on the Pearson correlation coefficient,the correlation network diagram of each protease-producing microorganism with umami peptides was constructed.The results showed that a total of two exopeptidases and four endopeptidases were annotated from FBBP.Staphylococcus,Lactobacillus,Aspergillus,and Weissella can produce most proteases.The species Lactobacillus curvatus,Dyella jiangningensis,Erythrobacter sp.,and unclassified_g_Pantoea had strong correlation with umami peptides,and they may contribute to the process of protein hydrolysis to produce umami peptides.This study is expected to reveal the formation mechanism of umami peptides in FBBP,and the results of this study provided a better understanding of the relationship between proteases,microbiota,and core umami peptides in FBBP,which could help to improve the umami taste of Pixian Douban paste during fermentation.展开更多
Pheretima,also called“earthworms”,is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines(CPMs)in Chinese Pharmacopoeia(2020 edition).However,its zool...Pheretima,also called“earthworms”,is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines(CPMs)in Chinese Pharmacopoeia(2020 edition).However,its zoological origin is unclear,both in the herbal market and CPMs.In this study,a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms(restricted search,open search,and de novo)was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima,including Pheretima aspergillum(PA),Pheretima vulgaris(PV),and Metaphire magna(MM).We identified 10,477 natural peptides in the PA,7,451 in PV,and 5,896 in MM samples.Five specific signature peptides were screened and then validated using synthetic peptides;these demonstrated robust specificity for the authentication of PA,PV,and MM.Finally,all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills,revealing the inconsistent Pheretima species used in these CPMs.In conclusion,our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines,especially non-model species with poorly annotated protein databases.展开更多
Plant viruses are the most infectious agents in commercially important crops worldwide. Plant viral diseases are important because both decreased yielding and quality of fruits, flowers or vegetables lead to million-d...Plant viruses are the most infectious agents in commercially important crops worldwide. Plant viral diseases are important because both decreased yielding and quality of fruits, flowers or vegetables lead to million-dollar losses in production. At present there are no reports which suggest a direct control of plant virus. A new strategy for plant virus control has been raised since 13 years ago—the use of peptides. Peptides could offer a direct interaction by affinity selection against viral proteins involved in infection cycle, like capsid or movement protein (e.g.) and affect viral replication. Peptidomics, as a new tool to study peptides, led us screening and selecting the best peptide with antiviral activity, and re-designing it to enhance the biological effect as well as the potential of bioactivity of those peptides secreted by microbes present in soil. In this paper we review current aspects in the use of peptides and peptidomics as a strategy to study new methods that lead a direct control against plant viral diseases.展开更多
Taste peptides are crucial food flavor compounds,but how the extraction method affects their characteristics remains unclear.Here,the taste profiles and sequence composition of Huangjiu peptides obtained by different ...Taste peptides are crucial food flavor compounds,but how the extraction method affects their characteristics remains unclear.Here,the taste profiles and sequence composition of Huangjiu peptides obtained by different extraction methods were studied by sensory evaluation,label-free peptidomics and computational peptidology.The target peptide fractions were prepared by four methods.Cationic resin extraction(CX)was superior to ul-trafiltration(UF)alone,with the highest peptide yield(65.44%),purity(82.04%)and umami,followed by ethanol precipitation(ETP).Macroporous resin extraction(MR)exhibited the highest bitterness(score 7.3).A total of 3131 peptides were identified from the CX,UF,ETP,and MR extracted fractions,80.18%of the peptides were 2-4 amino acid in length,and umami peptides accounted for 24.24%.Further analysis revealed that the intensity,hydrophobicity,isoelectric point values,and amino acid types of peptides affected the taste of the four extract peptide fractions.Moreover,molecular simulation revealed that the taste mechanism of the identified umami and bitter peptides are related to interaction with T1R1-T1R3 and TAS2R receptors through hydrogen bonding and hydrophobic forces.Overall,this study provides a reference for the extraction of taste peptides.展开更多
Rice-derived peptides are a sustainable protein source with emerging lipid regulation functions.In this study,peptides with novel pancreatic lipase(PL)and cholesterol esterase(CE)inhibition from rice protein hydrolysa...Rice-derived peptides are a sustainable protein source with emerging lipid regulation functions.In this study,peptides with novel pancreatic lipase(PL)and cholesterol esterase(CE)inhibition from rice protein hydrolysates(RPHs)were identified by peptidomics.Then their alleviating effects and mechanisms on lipid accumulation in cells were investigated.55 peptides were identified,showing significant enrichment of Phe,Pro,Arg,and Leu,with hydrophobic/polar amino acids at terminal positions.Among them,five peptides(WQ7,FR6,GF6,GA7,and GY7)exhibited potent inhibitory activity against PL and CE,with IC_(50)values of 0.19-0.70μg/mL and 0.22-0.25μg/mL,respectively.Molecular docking studies revealed that five peptides bind stably to the active sites of PL(Phe77,Tyr114,Phe215,and His263)and CE(Ser194 and His435)through hydrogen bonding,PIalkyl,and PI-PI interactions.Dynamic simulations demonstrated that three peptides(WQ7,FR6,and GF6)form stable complexes with both CE and PL,exhibiting strong binding affinity.In vitro study confirmed that these peptides reduced levels of TC,TG,and LDL-c while increasing HDL-c content,with WQ7 showing superior efficacy.Western blot and qPCR results indicated WQ7 regulated lipid metabolism by suppressing the PPARγpathway and downregulating the protein expression of related factors,such as ACS,FASN,and SREBP-1c.This study showed that the WQ7,a multifunctional bioactive peptide,demonstrates direct enzyme-inhibitory activity and regulates core transcriptional pathways,providing theoretical support for utilizing rice protein in the development of lipid-lowering functional food.展开更多
The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large data sets of ...The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large data sets of proteins or peptides involved in various biologic and disease progression processes generating testable hypothesis for complex biologic questions. This review provides an introduction to relevant topics in proteomics and peptidomics including biologic material selection, sample preparation, separation techniques, peptide fragmentation, post-translational modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature, remaining challenges, and emerging technologies for proteomics and peptidomics are presented.展开更多
Neuropeptides are crucial in regulation of a rich variety of developmental,physiological,and behavioral functions throughout the life cycle of insects.Using an integrated approach of multiomics,we identified neuropept...Neuropeptides are crucial in regulation of a rich variety of developmental,physiological,and behavioral functions throughout the life cycle of insects.Using an integrated approach of multiomics,we identified neuropeptide precursors in the greater wax moth Galleria mellonella,which is a harmful pest of honeybee hives with a worldwide distribution.Here,a total of 63 and 67 neuropeptide precursors were predicted and annotated in the G.mellonella genome and transcriptome,in which 40 neuropeptide precursors were confirmed in the G.mellonella peptidome.Interestingly,we identified 12 neuropeptide precursor genes present in G.mellonella but absent in honeybees,which may be potential novel pesticide target sites.Honeybee hives were contaminated with heavy metals such as lead,enabling its bioaccumulation in G.mellonella bodies through the food chain,we performed transcriptome sequencing to analyze the effects of Pb stress on the mRNA expression level of G.mellonella neuropeptide precursors.After treatment by Pb,the expression of neuropeptide F1 was found to be significantly downregulated,implying that this neuropeptide might be associated with responding to the heavy metal stress in G.mellonella.This study comprehensively identified neuropeptide precursors in G.mellonella,and discussed the effects of heavy metals on insect neuropeptides,with the example of G.mellonella.The results are valuable for future elucidation of how neuropeptides regulate physiological functions in G.mellonella and contribute to our understanding of the insect's environmental plasticity and identify potential new biomarkers to assess heavy metal toxicity in insects.展开更多
Food components possessing zinc ligands can be used to inhibit zinc-dependent enzymes.In this study,zinc-binding peptides were derived from whey protein hydrolysates,and their ultrafiltration(>1 and<1 kDa)fracti...Food components possessing zinc ligands can be used to inhibit zinc-dependent enzymes.In this study,zinc-binding peptides were derived from whey protein hydrolysates,and their ultrafiltration(>1 and<1 kDa)fractions,produced with Esperase(WPH-Esp),Everlase and Savinase.Immobilized metal affinity chromatography(IMAC-Zn^(2+))increased the zinc-binding capacity of the peptide fraction(83%)when compared to WPH-Esp(23%)and its<1 kDa fraction(40%).The increased zinc-binding capacity of the sample increased the inhibitory activity against the zinc-dependent“a disintegrin and metalloproteinase 17”.LC-MS/MS analysis using a shotgun peptidomics approach resulted in the identification of 24 peptides originating from bovineβ-lactoglobulin,α-lactalbumin,serum albumin,β-casein,κ-casein,osteopontin-k,and folate receptor-αin the fraction.The identified peptides contained different combinations of the strong zinc-binding group of residues,His+Cys,Asp+Glu and Phe+Tyr,although Cys residues were absent in the sequences.In silico predictions showed that the IMAC-Zn^(2+)peptides were non-toxins.However,the peptides possessed poor drug-like and pharmacokinetic properties;this was possibly due to their long chain lengths(5–19 residues).Taken together,this work provided an array of food peptide-based zinc ligands for further investigation of structure-function relationships and development of nutraceuticals against inflammatory and other zinc-related diseases.展开更多
As a subset of the proteome, peptidomics is the best tool to analyze peptides in different food matrices. Milk peptides are produced by protease hydrolysis in the mammary gland, which plays an important role in the gr...As a subset of the proteome, peptidomics is the best tool to analyze peptides in different food matrices. Milk peptides are produced by protease hydrolysis in the mammary gland, which plays an important role in the growth and development of infants. However, methods of probing endogenous peptides are limited because the concentration of peptides is low, the peptides are easily lost during extraction/enrichment, and database searches are complicated. Based on the peptidomics analysis process, this paper reviews the research progress and applications of endogenous peptides with a focus on extraction, fractionation, identification, and bioinformatics analysis. Additionally, in-depth analysis of endogenous peptides in milk and milk-related products using joint strategies (a combined analysis of proteome/peptidomics/metabolomic approaches) was also introduced. New methodologies are provided to study peptides through bioinformatics and tracking the release of bioactive peptides from various milk sources by in vitro digestion models, which can better track the utilization of endogenous peptides in vivo. Challenges and future perspectives are also discussed, with a goal of exploring more bioactive peptides in milk and dairy products as well as simulating human milk in formula milk powder in the future.展开更多
Target peptides containing branched-chain amino acids(BCAAs)possess various proven physiologic functions,yet there has been a limited focus on the manufacturing processes associated with these peptides.Herein,target B...Target peptides containing branched-chain amino acids(BCAAs)possess various proven physiologic functions,yet there has been a limited focus on the manufacturing processes associated with these peptides.Herein,target BCAA-containing oligopeptides were purposefully produced from biomacromolecules via the site-complementary perspective based on the combination of peptidomics and chemometrics strategies employing Antarctic krill rich in BCAAs as the material.Based on peptidomics profile and principal component analysis,a portfolio of 566 peptides,with the number and abundance percentage of target oligopeptides being 80.74%and 86.50%respectively,was identified from protein hydrolysate by papain,establishing papain as the most suitable cutting tool under single-enzymatic hydrolysis.Terminal amino acid frequency and chemometric analysis further revealed that alcalase,when employed in conjunction with papain,complemented the hydrolysis of papain and significantly enhanced the content of BCAAs from 13.27%to 15.00%within the target peptides.Another portfolio of 411 peptides was identified,accounting for 90.75%in number and 90.36%in abundance percentage for target oligopeptides,demonstrating strong radical scavenging capacities.This investigation provided a comprehensive understanding of the intricate relationship between enzymatic conversion and the molecular composition of target peptides at a molecular scale,which not only contributed valuable insights into the manufacturing processes but also proposed a promising strategy for the rational combination of proteases in the production of target peptides.展开更多
Imaging mass spectrometry (IMS) methodology for biological tissue component distribution map using MALDI-TOF MS and MALDI-TOF/TOF MS was established.Peak density distribution was probed to be quite useful for MS image...Imaging mass spectrometry (IMS) methodology for biological tissue component distribution map using MALDI-TOF MS and MALDI-TOF/TOF MS was established.Peak density distribution was probed to be quite useful for MS image classification.More than 40 000 spectra from 200 tissue sections were acquired and reproducibility between various of species groups was great than 80%.Tens of differentiately expressed components were detected by t-test (P<0.01).Classification modeling was created based on the differentiate components,blind species were analyzed for model validation,accuracy was above 90%.展开更多
A protocol for serum peptidomics using peptide electrophoresis combining with mass spectrometry was reported in this paper.Results showed that the improved peptide electrophoresis and MALDI-TOF MS could evaluate the e...A protocol for serum peptidomics using peptide electrophoresis combining with mass spectrometry was reported in this paper.Results showed that the improved peptide electrophoresis and MALDI-TOF MS could evaluate the efficiency of serum peptide processing methods.Our protocol was verified with a high reproducibility.展开更多
Enzymatic hydrolysis of proteins is a breakdown process of peptide bond in proteins,releasing some peptides with potential biological functions.Previous studies on enzymatic hydrolysis of whey proteins have not identi...Enzymatic hydrolysis of proteins is a breakdown process of peptide bond in proteins,releasing some peptides with potential biological functions.Previous studies on enzymatic hydrolysis of whey proteins have not identified the complete peptide profiles after hydrolysis.In this study,we reconstructed a profile of peptides from whey hydrolysates with two enzymes and different processing conditions.We also developed an ensemble machine learning predictor to classify peptides obtained from whey hydrolysis.A total of 2572 peptides were identified over three process conditions with two enzymes in duplicate.499 peptides were classified and chosen as potential antioxidant peptides from whey proteins.The peptides classified as antioxidants in the hydrolysates had a proportion of 13.1%-24.5%regarding all peptides identified.These results facilitate the selection of promising peptides involved in the antioxidant properties during the enzymatic hydrolysis of whey proteins,aiding the discovery of novel antioxidant peptides.展开更多
Animal venom research is a specialized investigation field, in which a number of different methods are used and this array is constantly expanding. Thus, recently emerged omics and nanotechnologies have already been s...Animal venom research is a specialized investigation field, in which a number of different methods are used and this array is constantly expanding. Thus, recently emerged omics and nanotechnologies have already been successfully applied to venom research. Animal venoms have been studied for quite a long time. The traditional reductionist approach has been to isolate individual toxins and then study their structure and function. Unfortunately, the characterization of the venom as a whole system and its multiple effects on an entire organism were not possible until recent times. The development of new methods in mass spectrometry and sequencing have allowed such characterizations of venom, encompassing the identification of new toxins present in venoms at extremely low concentrations to changes in metabolism of prey organisms after envenomation. In particular, this type of comprehensive research has become possible due to the development of the various omics technologies: Proteomics, peptidomics, transcriptomics, genomics and metabolomics. As in other research fields, these omics technologies ushered in a revolution for venom studies, which is now entering the era of big data. Nanotechnology is a very new branch of technology and developing at an extremely rapid pace. It has found application in many spheres and has not bypassed the venom studies. Nanomaterials are quite promising in medicine, and most studies combining venoms and nanomaterials are dedicated to medical applications. Conjugates of nanoparticles with venom components have been proposed for use as drugs or diagnostics. For example, nanoparticles conjugated with chlorotoxin- a toxin in scorpion venom, which has been shown to bind specifically to glioma cells- are considered as potential glioma-targeted drugs, and conjugates of neurotoxins with fluorescent semiconductor nanoparticles or quantum dots may be used to detect endogenous targets expressed in live cells. The data on application of omics and nanotechnologies in venom research are systematized concisely in this paper.展开更多
Biomarkers can be used for the screening and clinical diagnosis of cancer,and peptidomics approach has been proven successful in the research of biomarkers.To develop better peptidomic technologies for fast,accurate,a...Biomarkers can be used for the screening and clinical diagnosis of cancer,and peptidomics approach has been proven successful in the research of biomarkers.To develop better peptidomic technologies for fast,accurate,and reliable detection of peptides biomarkers for lung cancer,we have improved the procedures of blood collection to minimize the degradation of the blood proteins and optimize the extraction of peptidome peptides from plasma samples based on acetonitrile precipitation associated with size exclusion chromatography（SEC）.Studies show that squamous cell carcinomas are found to express CAGEl,SPAT9 and TEX28 genes at significantly higher rates,and the results suggest that as tumors progress,the level of CAGEl,SPAT9 and TEX28 genes are likely to increase and lead to immunization.This suggests a potentially important therapeutic method for cancer testis-based cancer vaccines.展开更多
AIM： To investigate the relationship between urinary peptide changes and Helicobacter pylori （H. pylorl） infection using urinary peptidome profiling. METHODS： The study was performed in volunteers （n = 137） who ...AIM： To investigate the relationship between urinary peptide changes and Helicobacter pylori （H. pylorl） infection using urinary peptidome profiling. METHODS： The study was performed in volunteers （n = 137） who gave informed consent. Urinary peptides were enriched by magnetic beads based weak cation exchange chromatography＇and spectrums acquired by matrix-assisted laser desorption/ionization time-of-flight （MALDI-TOF） mass spectrometry （MS）. ClinProTools bioinformatics software was used for statistical analysis and the recognition of peptide patterns. The marker peptides were identified by LTQ Obitrap XL tandem MS. RESULTS： Approximately 50 proteins or peptides which loaded onto the magnetic beads were detected by MAL-DI-TOF MS. By optimizing the parameters of the model, the Genetic Algorithm model had good recognition capability （97%） and positive predictive value （94%）. Based on the model, 2 markers with molecular masses of 6788 and 1912 Da were found that differentiated between H. pylori positive and negative volunteers. The m/z 1912 sequence was parsed as SKQFTSSTSYN- RGDSTF. The peptide was identified as isoform 1 of the fibrinogen a chain precursor, whose concentration in urine was markedly higher in H. pylori infected volunteers than in H. pylori non-infected ones. CONCLUSION： The appearance of urinary fibrinogen degradation products is caused by an active H. pyloriinduced process.展开更多
Enzymatic hydrolysis has been widely used to produce bioactive hydrolysates from sea cucumber body wall.Here,inspired by the clarification of Apostichopus japonicus genome,we investigated the enzymatic hydrolysis of s...Enzymatic hydrolysis has been widely used to produce bioactive hydrolysates from sea cucumber body wall.Here,inspired by the clarification of Apostichopus japonicus genome,we investigated the enzymatic hydrolysis of sea cucumber body wall by using the omics strategy.Shared proteins,including major yolk proteins,collagens,extracellular matrix glycoproteins and muscle proteins,were released from the body wall by different hydrolysis condition.A portfolio of 216 shared peptides were detected in the peptidome by papain with different hydrolysis time,while 32 shared peptides were detected in the peptidome by differing proteases.Unshared peptides and the relative abundance distribution profiles of shared peptides changed depending on hydrolysis approaches,indicating dynamic changes of peptidome during hydrolysis.Moreover,release of sulfated fucan and fucosylated chondroitin sulfate changed with the hydrolysis condition.The monitoring of dynamic enzymatic hydrolysis process at a molecular scale would contribute to production and quality control of sea cucumber hydrolysates.展开更多
As the most common pathological type of nephrotic syndrome,membranous nephropathy(MN)presents diversity in progression trends,facing severe complications.The precise discrimination of MN from healthy people,other type...As the most common pathological type of nephrotic syndrome,membranous nephropathy(MN)presents diversity in progression trends,facing severe complications.The precise discrimination of MN from healthy people,other types of nephrotic syndrome or those with therapeutic remission has always been huge challenge in clinics,not to mention comprehensive individualized monitoring relied on minimally invasive molecular detection means.Herein,we construct a functionalized pore architecture to couple with machine learning to aid all-round peptidome enrichment and data profiling from hundreds of human serum samples,and finally establish a set of defined peptide panel consisting of 12 specific feature signals.In addition to the realization of above-mentioned precise discrimination with more than 97%of sensitivity,88%of accuracy and f1 score,the simultaneously comprehensive individualized monitoring for MN can also be achieved,including conventionally screening diagnosis,congeneric distinction and prognostic evaluation.This work greatly advances the development of peptidome data-driven individualized monitoring means for complex diseases and undoubtedly inspire more devotion into molecular detection field.展开更多
Peptides in shrimp hemolymph play an important role in the innate immune response.Analysis of hemolymph will help to detect and identify potential novel biomarkers of microbial infection.We used magnetic bead-based pu...Peptides in shrimp hemolymph play an important role in the innate immune response.Analysis of hemolymph will help to detect and identify potential novel biomarkers of microbial infection.We used magnetic bead-based purification(ClinProt system) and matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF MS) to characterize shrimp hemolymph peptides.Shrimp serum and plasma were used as the source of samples for comparative analysis,and it was found that serum was more suitable for shrimp hemolymph peptidomic analysis.To screen potential specific biomarkers in serum of immune-challenged shrimps,we applied magnetic bead-based MALDI-TOF MS to serum samples from 10 immune-challenged and 10 healthy shrimps.The spectra were analyzed using FlexAnalysis 3.0 and ClinProTools 2.1 software.Thirteen peptide peaks significantly different between the two groups were selected as candidate biomarkers of lipopolysaccharide(LPS)-infection.The diagnostic model established by genetic algorithm using five of these peaks was able to discriminate LPS-challenged shrimps from healthy control shrimps with a sensitivity of 90% and a specificity of 100%.Our approach in MALDITOF MS-based peptidomics is a powerful tool for screening bioactive peptides or biomarkers derived from hemolymph,and will help to enable a better understanding of the innate immune response of shrimps.展开更多
基金supported by the Science and Technology Department of Sichuan Province,China(2020YFN0151,23ZDYF3100)Chongqing Science and Technology Commission(cstc2021jscx-cylhX0014).
文摘Umami peptides play important roles in the flavor of fermented broad bean paste(FBBP),and proteases produced by microorganisms contributed to the production of umami peptides.In order to reveal the formation of umami peptides and their relationships with protease-producing microorganisms during the natural fermentation of FBBP,peptidomics and virtual screening were used to identify and screen umami peptides.Meanwhile,macrogenomics was used to analyze the abundance of microbial-derived protease genes during FBBP fermentation.Then,based on the Pearson correlation coefficient,the correlation network diagram of each protease-producing microorganism with umami peptides was constructed.The results showed that a total of two exopeptidases and four endopeptidases were annotated from FBBP.Staphylococcus,Lactobacillus,Aspergillus,and Weissella can produce most proteases.The species Lactobacillus curvatus,Dyella jiangningensis,Erythrobacter sp.,and unclassified_g_Pantoea had strong correlation with umami peptides,and they may contribute to the process of protein hydrolysis to produce umami peptides.This study is expected to reveal the formation mechanism of umami peptides in FBBP,and the results of this study provided a better understanding of the relationship between proteases,microbiota,and core umami peptides in FBBP,which could help to improve the umami taste of Pixian Douban paste during fermentation.
基金supported by the Key Program of the National Natural Science Foundation of China(Grant No.:82130111)the National Natural Science Foundation of China(Grant No.:81803716)+1 种基金the Qi-Huang Chief Scientist Project of the National Administration of Traditional Chinese Medicine,China(2020)the SIMM-SHUTCM Traditional Chinese Medicine Innovation Joint Research Program,China(Grant No.:E2G809H).
文摘Pheretima,also called“earthworms”,is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines(CPMs)in Chinese Pharmacopoeia(2020 edition).However,its zoological origin is unclear,both in the herbal market and CPMs.In this study,a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms(restricted search,open search,and de novo)was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima,including Pheretima aspergillum(PA),Pheretima vulgaris(PV),and Metaphire magna(MM).We identified 10,477 natural peptides in the PA,7,451 in PV,and 5,896 in MM samples.Five specific signature peptides were screened and then validated using synthetic peptides;these demonstrated robust specificity for the authentication of PA,PV,and MM.Finally,all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills,revealing the inconsistent Pheretima species used in these CPMs.In conclusion,our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines,especially non-model species with poorly annotated protein databases.
文摘Plant viruses are the most infectious agents in commercially important crops worldwide. Plant viral diseases are important because both decreased yielding and quality of fruits, flowers or vegetables lead to million-dollar losses in production. At present there are no reports which suggest a direct control of plant virus. A new strategy for plant virus control has been raised since 13 years ago—the use of peptides. Peptides could offer a direct interaction by affinity selection against viral proteins involved in infection cycle, like capsid or movement protein (e.g.) and affect viral replication. Peptidomics, as a new tool to study peptides, led us screening and selecting the best peptide with antiviral activity, and re-designing it to enhance the biological effect as well as the potential of bioactivity of those peptides secreted by microbes present in soil. In this paper we review current aspects in the use of peptides and peptidomics as a strategy to study new methods that lead a direct control against plant viral diseases.
基金funded by National Natural Science Foundation of China(22138004)National Key Research and Development Pro-gram of China(No.2022YFD2101204).
文摘Taste peptides are crucial food flavor compounds,but how the extraction method affects their characteristics remains unclear.Here,the taste profiles and sequence composition of Huangjiu peptides obtained by different extraction methods were studied by sensory evaluation,label-free peptidomics and computational peptidology.The target peptide fractions were prepared by four methods.Cationic resin extraction(CX)was superior to ul-trafiltration(UF)alone,with the highest peptide yield(65.44%),purity(82.04%)and umami,followed by ethanol precipitation(ETP).Macroporous resin extraction(MR)exhibited the highest bitterness(score 7.3).A total of 3131 peptides were identified from the CX,UF,ETP,and MR extracted fractions,80.18%of the peptides were 2-4 amino acid in length,and umami peptides accounted for 24.24%.Further analysis revealed that the intensity,hydrophobicity,isoelectric point values,and amino acid types of peptides affected the taste of the four extract peptide fractions.Moreover,molecular simulation revealed that the taste mechanism of the identified umami and bitter peptides are related to interaction with T1R1-T1R3 and TAS2R receptors through hydrogen bonding and hydrophobic forces.Overall,this study provides a reference for the extraction of taste peptides.
基金supported by the National Natural Science Foundation of China(32572484)Natural Science Foundation of Hunan Province(2022JJ30587,2022JJ50218)Science and Technology Innovation Program of Hunan Province(2024JK2145).
文摘Rice-derived peptides are a sustainable protein source with emerging lipid regulation functions.In this study,peptides with novel pancreatic lipase(PL)and cholesterol esterase(CE)inhibition from rice protein hydrolysates(RPHs)were identified by peptidomics.Then their alleviating effects and mechanisms on lipid accumulation in cells were investigated.55 peptides were identified,showing significant enrichment of Phe,Pro,Arg,and Leu,with hydrophobic/polar amino acids at terminal positions.Among them,five peptides(WQ7,FR6,GF6,GA7,and GY7)exhibited potent inhibitory activity against PL and CE,with IC_(50)values of 0.19-0.70μg/mL and 0.22-0.25μg/mL,respectively.Molecular docking studies revealed that five peptides bind stably to the active sites of PL(Phe77,Tyr114,Phe215,and His263)and CE(Ser194 and His435)through hydrogen bonding,PIalkyl,and PI-PI interactions.Dynamic simulations demonstrated that three peptides(WQ7,FR6,and GF6)form stable complexes with both CE and PL,exhibiting strong binding affinity.In vitro study confirmed that these peptides reduced levels of TC,TG,and LDL-c while increasing HDL-c content,with WQ7 showing superior efficacy.Western blot and qPCR results indicated WQ7 regulated lipid metabolism by suppressing the PPARγpathway and downregulating the protein expression of related factors,such as ACS,FASN,and SREBP-1c.This study showed that the WQ7,a multifunctional bioactive peptide,demonstrates direct enzyme-inhibitory activity and regulates core transcriptional pathways,providing theoretical support for utilizing rice protein in the development of lipid-lowering functional food.
基金supported by grants from the Intramural Research Program of the NIH,NIA,NIH,Department of Health and Human Services(Grant No.ZIAAG000534)as well as the National Institute of Neurological Disorders and Stroke,the NIH,USA(Grant Nos.R01 NS120992 and U54 NS123743)to Mercedes Prudencio.
文摘This is a correction to:Ziyi Li,Cory A.Weller,Syed Shah,Nicholas L.Johnson,Ying Hao,Paige B.Jarreau,Jessica Roberts,Deyaan Guha,Colleen Bereda,Sydney Klaisner,Pedro Machado,Matteo Zanovello,Mercedes Prudencio,Bjorn Oskarsson,Nathan P.Staff,Dennis W.Dickson,Pietro Fratta,Leonard Petrucelli,Priyanka Narayan,Mark R.Cookson,Michael E.Ward,Andrew B.Singleton,Mike A.Nalls,Yue A.Qi,ProtPipe:A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics,Genomics,Proteomics Bioinformatics,Volume 22,Issue 6,December 2024,qzae083,https://doi.org/10.1093/gpbjnl/qzae083.
文摘The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large data sets of proteins or peptides involved in various biologic and disease progression processes generating testable hypothesis for complex biologic questions. This review provides an introduction to relevant topics in proteomics and peptidomics including biologic material selection, sample preparation, separation techniques, peptide fragmentation, post-translational modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature, remaining challenges, and emerging technologies for proteomics and peptidomics are presented.
基金supported in part by the National Natural Science Foundation of China(32202295)Guizhou Provincial Science and Technology Projects(Qian Ke He Ji Chu-ZK[2022]General 051)+1 种基金Scientific Research Foundation for Talent Introduced in Guizhou University(Gui Da Te Gang He Zi[2021]22)Guizhou Provincial Science and Technology Projects(Qian Ke He Support[2019]2292,Qian Ke He NY[2013]3040).
文摘Neuropeptides are crucial in regulation of a rich variety of developmental,physiological,and behavioral functions throughout the life cycle of insects.Using an integrated approach of multiomics,we identified neuropeptide precursors in the greater wax moth Galleria mellonella,which is a harmful pest of honeybee hives with a worldwide distribution.Here,a total of 63 and 67 neuropeptide precursors were predicted and annotated in the G.mellonella genome and transcriptome,in which 40 neuropeptide precursors were confirmed in the G.mellonella peptidome.Interestingly,we identified 12 neuropeptide precursor genes present in G.mellonella but absent in honeybees,which may be potential novel pesticide target sites.Honeybee hives were contaminated with heavy metals such as lead,enabling its bioaccumulation in G.mellonella bodies through the food chain,we performed transcriptome sequencing to analyze the effects of Pb stress on the mRNA expression level of G.mellonella neuropeptide precursors.After treatment by Pb,the expression of neuropeptide F1 was found to be significantly downregulated,implying that this neuropeptide might be associated with responding to the heavy metal stress in G.mellonella.This study comprehensively identified neuropeptide precursors in G.mellonella,and discussed the effects of heavy metals on insect neuropeptides,with the example of G.mellonella.The results are valuable for future elucidation of how neuropeptides regulate physiological functions in G.mellonella and contribute to our understanding of the insect's environmental plasticity and identify potential new biomarkers to assess heavy metal toxicity in insects.
基金supported by the Natural Sciences and Engineering Research Council of Canada(NSERC)Discovery Grants(RGPIN-435865-2013 and RGPIN-2018-06839)Canada Foundation for Innovation(CFI)John R.Evans Leaders Fund Infrastructure Grant(Project number:31305).
文摘Food components possessing zinc ligands can be used to inhibit zinc-dependent enzymes.In this study,zinc-binding peptides were derived from whey protein hydrolysates,and their ultrafiltration(>1 and<1 kDa)fractions,produced with Esperase(WPH-Esp),Everlase and Savinase.Immobilized metal affinity chromatography(IMAC-Zn^(2+))increased the zinc-binding capacity of the peptide fraction(83%)when compared to WPH-Esp(23%)and its<1 kDa fraction(40%).The increased zinc-binding capacity of the sample increased the inhibitory activity against the zinc-dependent“a disintegrin and metalloproteinase 17”.LC-MS/MS analysis using a shotgun peptidomics approach resulted in the identification of 24 peptides originating from bovineβ-lactoglobulin,α-lactalbumin,serum albumin,β-casein,κ-casein,osteopontin-k,and folate receptor-αin the fraction.The identified peptides contained different combinations of the strong zinc-binding group of residues,His+Cys,Asp+Glu and Phe+Tyr,although Cys residues were absent in the sequences.In silico predictions showed that the IMAC-Zn^(2+)peptides were non-toxins.However,the peptides possessed poor drug-like and pharmacokinetic properties;this was possibly due to their long chain lengths(5–19 residues).Taken together,this work provided an array of food peptide-based zinc ligands for further investigation of structure-function relationships and development of nutraceuticals against inflammatory and other zinc-related diseases.
基金supported by LiaoNing Revitalization Talents Project(grant number XLYC1902083).
文摘As a subset of the proteome, peptidomics is the best tool to analyze peptides in different food matrices. Milk peptides are produced by protease hydrolysis in the mammary gland, which plays an important role in the growth and development of infants. However, methods of probing endogenous peptides are limited because the concentration of peptides is low, the peptides are easily lost during extraction/enrichment, and database searches are complicated. Based on the peptidomics analysis process, this paper reviews the research progress and applications of endogenous peptides with a focus on extraction, fractionation, identification, and bioinformatics analysis. Additionally, in-depth analysis of endogenous peptides in milk and milk-related products using joint strategies (a combined analysis of proteome/peptidomics/metabolomic approaches) was also introduced. New methodologies are provided to study peptides through bioinformatics and tracking the release of bioactive peptides from various milk sources by in vitro digestion models, which can better track the utilization of endogenous peptides in vivo. Challenges and future perspectives are also discussed, with a goal of exploring more bioactive peptides in milk and dairy products as well as simulating human milk in formula milk powder in the future.
基金supported by Major Scientific and Technological Innovation Project of Shandong Province(2022CXGC020414)National Key R&D Program of China(2018YFC0311201)Youth Innovation Technology Project of Higher School in Shandong Province(2021KJ090).
文摘Target peptides containing branched-chain amino acids(BCAAs)possess various proven physiologic functions,yet there has been a limited focus on the manufacturing processes associated with these peptides.Herein,target BCAA-containing oligopeptides were purposefully produced from biomacromolecules via the site-complementary perspective based on the combination of peptidomics and chemometrics strategies employing Antarctic krill rich in BCAAs as the material.Based on peptidomics profile and principal component analysis,a portfolio of 566 peptides,with the number and abundance percentage of target oligopeptides being 80.74%and 86.50%respectively,was identified from protein hydrolysate by papain,establishing papain as the most suitable cutting tool under single-enzymatic hydrolysis.Terminal amino acid frequency and chemometric analysis further revealed that alcalase,when employed in conjunction with papain,complemented the hydrolysis of papain and significantly enhanced the content of BCAAs from 13.27%to 15.00%within the target peptides.Another portfolio of 411 peptides was identified,accounting for 90.75%in number and 90.36%in abundance percentage for target oligopeptides,demonstrating strong radical scavenging capacities.This investigation provided a comprehensive understanding of the intricate relationship between enzymatic conversion and the molecular composition of target peptides at a molecular scale,which not only contributed valuable insights into the manufacturing processes but also proposed a promising strategy for the rational combination of proteases in the production of target peptides.
文摘Imaging mass spectrometry (IMS) methodology for biological tissue component distribution map using MALDI-TOF MS and MALDI-TOF/TOF MS was established.Peak density distribution was probed to be quite useful for MS image classification.More than 40 000 spectra from 200 tissue sections were acquired and reproducibility between various of species groups was great than 80%.Tens of differentiately expressed components were detected by t-test (P<0.01).Classification modeling was created based on the differentiate components,blind species were analyzed for model validation,accuracy was above 90%.
文摘A protocol for serum peptidomics using peptide electrophoresis combining with mass spectrometry was reported in this paper.Results showed that the improved peptide electrophoresis and MALDI-TOF MS could evaluate the efficiency of serum peptide processing methods.Our protocol was verified with a high reproducibility.
基金supported and funded by the Gobernación del Cesar-Ministry of Science,Technology,and Innovation through resources for the higher education(grant 736/2015)the Natural Sciences and Engineering Research Council of Canada(NSERC)。
文摘Enzymatic hydrolysis of proteins is a breakdown process of peptide bond in proteins,releasing some peptides with potential biological functions.Previous studies on enzymatic hydrolysis of whey proteins have not identified the complete peptide profiles after hydrolysis.In this study,we reconstructed a profile of peptides from whey hydrolysates with two enzymes and different processing conditions.We also developed an ensemble machine learning predictor to classify peptides obtained from whey hydrolysis.A total of 2572 peptides were identified over three process conditions with two enzymes in duplicate.499 peptides were classified and chosen as potential antioxidant peptides from whey proteins.The peptides classified as antioxidants in the hydrolysates had a proportion of 13.1%-24.5%regarding all peptides identified.These results facilitate the selection of promising peptides involved in the antioxidant properties during the enzymatic hydrolysis of whey proteins,aiding the discovery of novel antioxidant peptides.
基金Supported by The Russian Foundation for Basic Research,No.15-04-01843the Ministry of Science and Education of the Russian Federation,No.RFMEFI58414X0006
文摘Animal venom research is a specialized investigation field, in which a number of different methods are used and this array is constantly expanding. Thus, recently emerged omics and nanotechnologies have already been successfully applied to venom research. Animal venoms have been studied for quite a long time. The traditional reductionist approach has been to isolate individual toxins and then study their structure and function. Unfortunately, the characterization of the venom as a whole system and its multiple effects on an entire organism were not possible until recent times. The development of new methods in mass spectrometry and sequencing have allowed such characterizations of venom, encompassing the identification of new toxins present in venoms at extremely low concentrations to changes in metabolism of prey organisms after envenomation. In particular, this type of comprehensive research has become possible due to the development of the various omics technologies: Proteomics, peptidomics, transcriptomics, genomics and metabolomics. As in other research fields, these omics technologies ushered in a revolution for venom studies, which is now entering the era of big data. Nanotechnology is a very new branch of technology and developing at an extremely rapid pace. It has found application in many spheres and has not bypassed the venom studies. Nanomaterials are quite promising in medicine, and most studies combining venoms and nanomaterials are dedicated to medical applications. Conjugates of nanoparticles with venom components have been proposed for use as drugs or diagnostics. For example, nanoparticles conjugated with chlorotoxin- a toxin in scorpion venom, which has been shown to bind specifically to glioma cells- are considered as potential glioma-targeted drugs, and conjugates of neurotoxins with fluorescent semiconductor nanoparticles or quantum dots may be used to detect endogenous targets expressed in live cells. The data on application of omics and nanotechnologies in venom research are systematized concisely in this paper.
基金financially supported by the National Natural Science Foundation of China(No.21172067)Science and Technology Project of Hunan Province(Nos.2013SK2015,2014SK3017)Scientific Research Key Fund of Hunan Provincal Education Department(No.13A032)
文摘Biomarkers can be used for the screening and clinical diagnosis of cancer,and peptidomics approach has been proven successful in the research of biomarkers.To develop better peptidomic technologies for fast,accurate,and reliable detection of peptides biomarkers for lung cancer,we have improved the procedures of blood collection to minimize the degradation of the blood proteins and optimize the extraction of peptidome peptides from plasma samples based on acetonitrile precipitation associated with size exclusion chromatography（SEC）.Studies show that squamous cell carcinomas are found to express CAGEl,SPAT9 and TEX28 genes at significantly higher rates,and the results suggest that as tumors progress,the level of CAGEl,SPAT9 and TEX28 genes are likely to increase and lead to immunization.This suggests a potentially important therapeutic method for cancer testis-based cancer vaccines.
基金Supported by The National Science and Technology Pillar Program of the Ministry of Science and Technology of the People’s Republic of China during the Eleventh Five-Year plan period,No. 2007BAID4B02
文摘AIM： To investigate the relationship between urinary peptide changes and Helicobacter pylori （H. pylorl） infection using urinary peptidome profiling. METHODS： The study was performed in volunteers （n = 137） who gave informed consent. Urinary peptides were enriched by magnetic beads based weak cation exchange chromatography＇and spectrums acquired by matrix-assisted laser desorption/ionization time-of-flight （MALDI-TOF） mass spectrometry （MS）. ClinProTools bioinformatics software was used for statistical analysis and the recognition of peptide patterns. The marker peptides were identified by LTQ Obitrap XL tandem MS. RESULTS： Approximately 50 proteins or peptides which loaded onto the magnetic beads were detected by MAL-DI-TOF MS. By optimizing the parameters of the model, the Genetic Algorithm model had good recognition capability （97%） and positive predictive value （94%）. Based on the model, 2 markers with molecular masses of 6788 and 1912 Da were found that differentiated between H. pylori positive and negative volunteers. The m/z 1912 sequence was parsed as SKQFTSSTSYN- RGDSTF. The peptide was identified as isoform 1 of the fibrinogen a chain precursor, whose concentration in urine was markedly higher in H. pylori infected volunteers than in H. pylori non-infected ones. CONCLUSION： The appearance of urinary fibrinogen degradation products is caused by an active H. pyloriinduced process.
基金supported by the Fok Ying-Tong Education Foundation (171024)Fundamental Research Funds for the Central Universities (201941005)Fundamental Research Funds for the Central Universities (862001013136)。
文摘Enzymatic hydrolysis has been widely used to produce bioactive hydrolysates from sea cucumber body wall.Here,inspired by the clarification of Apostichopus japonicus genome,we investigated the enzymatic hydrolysis of sea cucumber body wall by using the omics strategy.Shared proteins,including major yolk proteins,collagens,extracellular matrix glycoproteins and muscle proteins,were released from the body wall by different hydrolysis condition.A portfolio of 216 shared peptides were detected in the peptidome by papain with different hydrolysis time,while 32 shared peptides were detected in the peptidome by differing proteases.Unshared peptides and the relative abundance distribution profiles of shared peptides changed depending on hydrolysis approaches,indicating dynamic changes of peptidome during hydrolysis.Moreover,release of sulfated fucan and fucosylated chondroitin sulfate changed with the hydrolysis condition.The monitoring of dynamic enzymatic hydrolysis process at a molecular scale would contribute to production and quality control of sea cucumber hydrolysates.
基金financially supported by National Key R&D Program of China(No.2018YFA0507501)the National Natural Science Foundation of China(Nos.22074019,21425518,22004017)Shanghai Sailing Program(No.20YF1405300)。
文摘As the most common pathological type of nephrotic syndrome,membranous nephropathy(MN)presents diversity in progression trends,facing severe complications.The precise discrimination of MN from healthy people,other types of nephrotic syndrome or those with therapeutic remission has always been huge challenge in clinics,not to mention comprehensive individualized monitoring relied on minimally invasive molecular detection means.Herein,we construct a functionalized pore architecture to couple with machine learning to aid all-round peptidome enrichment and data profiling from hundreds of human serum samples,and finally establish a set of defined peptide panel consisting of 12 specific feature signals.In addition to the realization of above-mentioned precise discrimination with more than 97%of sensitivity,88%of accuracy and f1 score,the simultaneously comprehensive individualized monitoring for MN can also be achieved,including conventionally screening diagnosis,congeneric distinction and prognostic evaluation.This work greatly advances the development of peptidome data-driven individualized monitoring means for complex diseases and undoubtedly inspire more devotion into molecular detection field.
基金Supported by the National Natural Science Foundation of China(No.30600458)
文摘Peptides in shrimp hemolymph play an important role in the innate immune response.Analysis of hemolymph will help to detect and identify potential novel biomarkers of microbial infection.We used magnetic bead-based purification(ClinProt system) and matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF MS) to characterize shrimp hemolymph peptides.Shrimp serum and plasma were used as the source of samples for comparative analysis,and it was found that serum was more suitable for shrimp hemolymph peptidomic analysis.To screen potential specific biomarkers in serum of immune-challenged shrimps,we applied magnetic bead-based MALDI-TOF MS to serum samples from 10 immune-challenged and 10 healthy shrimps.The spectra were analyzed using FlexAnalysis 3.0 and ClinProTools 2.1 software.Thirteen peptide peaks significantly different between the two groups were selected as candidate biomarkers of lipopolysaccharide(LPS)-infection.The diagnostic model established by genetic algorithm using five of these peaks was able to discriminate LPS-challenged shrimps from healthy control shrimps with a sensitivity of 90% and a specificity of 100%.Our approach in MALDITOF MS-based peptidomics is a powerful tool for screening bioactive peptides or biomarkers derived from hemolymph,and will help to enable a better understanding of the innate immune response of shrimps.
