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
Saccharomyces cerevisiae Y70 is supposed to be potentially used as a source of alternative ingredient due to its high protein content and pleasant flavor.The purpose of this study was to determine the nutritional valu...Saccharomyces cerevisiae Y70 is supposed to be potentially used as a source of alternative ingredient due to its high protein content and pleasant flavor.The purpose of this study was to determine the nutritional value,peptidome profile,and antioxidant activities of hydrolysates with various molecular weights from specific S.cerevisiae Y70 obtained by autolysis and enzymatic methods.In the current study,the analysis of nutritional components indicated that all extractive hydrolysates were rich source of proteins,essential amino acids,flavor amino acids,RNA,phenols and carbohydrates,with low fat.The analysis of peptidome revealed differences in the number and composition among extractive hydrolysates,which exhibited their potential biological activities.The low molecular weight hydrolysates showed good 1,1-diphenyl-2-picrylhydrazyl,2,2'-diazobis(3-ethyl-benzothiazole-6-sulfonic acid)cation,hydroxyl radicals scavenging activity and ferrous ion chelating activity.These findings revealed that the hydrolysates of S.cerevisiae Y70 have nutritional value and could provide useful information for their potential application as alternative and functional ingredients in the food and pharmaceutical industries.展开更多
A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides h...A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides have been identified within transcripts annotated as non-coding RNAs or in intergenic regions.These sORF-encoded peptides(SEPs)were previously overlooked due to their small size and difficulties in detection,both experimentally and computationally.However,analyses of translating RNAs(ribosome profiling)and proteomics(mass spectrometry)have provided growing evidence for the existence of numerous novel‘non-conventional’peptides in eukaryotic organisms,including plants.In animals,mounting evidence indicates that long non-coding RNAs are an important source of SEPs,and that SEPs participate in crucial cellular and physiological processes and can mediate the evolution of novel characteristics.Similar findings are now emerging in plants.The SEP-coding capacity and the full repertoire of functional SEPs within eukaryotic genomes remain unclear,but systematic,large-scale molecular screenings are beginning to address this gap.Here,we review current progress in understanding the plant non-conventional peptidome,explore parallels between plants and animals,and illustrate how findings in animals can help guide plant research on this topic.展开更多
Peptidomics draws more and more attention in discovering useful biomarkers for early diagnosis of disease. However, there is lack of efficient quantification strategy in peptidome analysis. In this study, a strategy w...Peptidomics draws more and more attention in discovering useful biomarkers for early diagnosis of disease. However, there is lack of efficient quantification strategy in peptidome analysis. In this study, a strategy with label-free quantification of the targeted endogenous peptides based on peak intensity using μUPLC-Q-TOF-MS/MS was developed for quantitative peptidome analysis of human serum. Different amounts of standard BSA tryptic digesting peptides were added into the same serum extracts for evaluation of the developed strategy, and it was observed that the average relative error of the targeted peptides was 6.42%, which was superior to the result obtained directly by commercially available software PLGS. It was also demonstrated that this quantification strategy could obviously increase the detection sensitivity of the peptide by DDA analysis. Then, this strategy was applied to comparatively analyze the peptides extracted from the serum of HCC or breast cancer patients and healthy individuals, respectively. Peptides with charge states up to 5 and molecular weight over 4000 can be reliably identified and quantified. This quantitative analysis method based on μUPLC-Q-TOF-MS/MS exhibited superior sensitivity than that by MALDI-TOF-MS commonly used in peptidome analysis. Finally, some interesting endogenous peptides related to corresponding diseases were successfully obtained.展开更多
Hemp is the term commonly used to refer to the variety of Cannabis sativa L.cultivated for industrial purposes.The seeds have gained interest in recent years as functional foods due to their nutritional composition an...Hemp is the term commonly used to refer to the variety of Cannabis sativa L.cultivated for industrial purposes.The seeds have gained interest in recent years as functional foods due to their nutritional composition and high content of protein and bioactive compounds.In this study,ten hemp protein hydrolysates(HPHs)were obtained by enzymatic hydrolysis with Alcalase and Flavourzyme from hemp protein isolate(HPI)and their antioxidant properties(DPPH radical scavenging activity,beta-carotene activity and ferric ion reducing antioxidant power(FRAP))were evaluated.Shorter peptide sequences,mainly obtained with Flavourzyme,were found to react with free radicals more easily.The peptidome of all the hydrolysates was characterized,identifying,and quantifying the peptides.Furthermore,19 unique peptides were assessed by in silico tools to hypothesize those that could be responsible of the bioactivity reported for the hydrolysates.From the identified peptides,based on the molecular features and the predictions,the peptides KNAIYTPH,EERPGHF,and KNGMMAPH,among others,are proposed to be highly contributing to the antioxidant activity of the hydrolysates.展开更多
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
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
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
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
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
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
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
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
Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, s...Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, salt, high temperature,and other environmental challenges. In drought conditions, specific peptides such as CLE25 and CLE9 were foundto regulate stomatal closure and root architecture to enhance the efficiency of water utilization. Salt stress inducesthe expression of CAPE1 and CEP3, which are involved in ion homeostasis and osmoregulation, thereby contributingto salt tolerance in plants. Heat stress triggers the expression of peptides such as CEL45, which contributes to the heattolerance of cells. Besides, we have also verified a new class of non-conventional peptides, and a large numberof non-conventional peptides have been identified in rice seedlings. Understanding the origin and functions of thesepeptides presents both challenges and opportunities for developing stress-resistant crops. Future research shouldfocus on elucidating the precise molecular mechanisms of peptide-mediated stress responses and exploring theirpotential applications in agriculture and biotechnology.展开更多
Objective:As an important food therapy product with traditional Chinese medicine(TCM) applications,donkey-hide gelatin(Asini Corii Colla,ACC) has been used for thousands of years.However,till now few effective strateg...Objective:As an important food therapy product with traditional Chinese medicine(TCM) applications,donkey-hide gelatin(Asini Corii Colla,ACC) has been used for thousands of years.However,till now few effective strategy had been proposed to distinguish ACC from other animal hide gelatins,especially closely related horse-and mule-hide gelatins,which was an embarrassment of ACC quality control.Methods:Combined mass spectrometry and bioinformatic methods have been applied to identify and verify two ACC-specific peptides(Pep-1 and Pep-2) capable of distinguishing ACC from other closely related animal gelatins with high selectivity.Results:It confirmed that these two peptides could be not only used for distinguishing ACC from highly homologous horse-hide and mule-hide gelatins as well as other animal hide gelatins.Conclusion:The present study provides a simple method for species-specific peptides discovery,which can be used for assessing the quality of animal gelatin products,and ensure they are authenticable and traceable.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
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 grants from the National Natural Science Foundation of China(32102016)Taishan Industrial Experts ProgramBeijing Postdoctoral Research Foundation(2323ZZ122)。
文摘Saccharomyces cerevisiae Y70 is supposed to be potentially used as a source of alternative ingredient due to its high protein content and pleasant flavor.The purpose of this study was to determine the nutritional value,peptidome profile,and antioxidant activities of hydrolysates with various molecular weights from specific S.cerevisiae Y70 obtained by autolysis and enzymatic methods.In the current study,the analysis of nutritional components indicated that all extractive hydrolysates were rich source of proteins,essential amino acids,flavor amino acids,RNA,phenols and carbohydrates,with low fat.The analysis of peptidome revealed differences in the number and composition among extractive hydrolysates,which exhibited their potential biological activities.The low molecular weight hydrolysates showed good 1,1-diphenyl-2-picrylhydrazyl,2,2'-diazobis(3-ethyl-benzothiazole-6-sulfonic acid)cation,hydroxyl radicals scavenging activity and ferrous ion chelating activity.These findings revealed that the hydrolysates of S.cerevisiae Y70 have nutritional value and could provide useful information for their potential application as alternative and functional ingredients in the food and pharmaceutical industries.
基金supported by grant PID2022-139578NB-I00(funded by MCIN/AEI/10.13039/501100011033 and by“ERDF A way of making Europe”)and 2021SGR00792(from the Agencia de Gestio d’Ajuts Universitaris i de Recerca)(to J.L.R.)by institutional grants SEV-2015-0533 and CEX2019-000902-S(funded by MCIN/AEI/10.13039/501100011033)+3 种基金by the CERCA Program/Generalitat de Catalunyasupported by fellowship PRE2018-084278funded by MCIN/AEI/10.13039/501100011033by“ESF Investing in your future.”。
文摘A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins(the peptidome).In recent years,short open reading frames(sORFs)capable of encoding functional peptides have been identified within transcripts annotated as non-coding RNAs or in intergenic regions.These sORF-encoded peptides(SEPs)were previously overlooked due to their small size and difficulties in detection,both experimentally and computationally.However,analyses of translating RNAs(ribosome profiling)and proteomics(mass spectrometry)have provided growing evidence for the existence of numerous novel‘non-conventional’peptides in eukaryotic organisms,including plants.In animals,mounting evidence indicates that long non-coding RNAs are an important source of SEPs,and that SEPs participate in crucial cellular and physiological processes and can mediate the evolution of novel characteristics.Similar findings are now emerging in plants.The SEP-coding capacity and the full repertoire of functional SEPs within eukaryotic genomes remain unclear,but systematic,large-scale molecular screenings are beginning to address this gap.Here,we review current progress in understanding the plant non-conventional peptidome,explore parallels between plants and animals,and illustrate how findings in animals can help guide plant research on this topic.
基金support from the National Natural Science Foundation of China (Grant Nos. 20735004 & 20975101)the State Key Basic Research Program of China (Grant Nos. 2005CB522701 & 2007CB914102)+3 种基金the High Technology Research Pro-gram of China (Grant Nos. 2006AA02A309 & 2008ZX10002-017)the Knowledge Innovation Program of Chinese Academy of Sciences (Grant Nos. KJCX2.YW.HO9 & KSCX2-YW-R-079)the Knowledge Innova-tion Program of Dalian Institute of Chemical Physics to Zou HF and the China High Technology Research Program (Grant No. 2008ZX1002-020)the National Natural Science Foundation of China (Grant Nos. 20605022 & 90713017) to Ye ML
文摘Peptidomics draws more and more attention in discovering useful biomarkers for early diagnosis of disease. However, there is lack of efficient quantification strategy in peptidome analysis. In this study, a strategy with label-free quantification of the targeted endogenous peptides based on peak intensity using μUPLC-Q-TOF-MS/MS was developed for quantitative peptidome analysis of human serum. Different amounts of standard BSA tryptic digesting peptides were added into the same serum extracts for evaluation of the developed strategy, and it was observed that the average relative error of the targeted peptides was 6.42%, which was superior to the result obtained directly by commercially available software PLGS. It was also demonstrated that this quantification strategy could obviously increase the detection sensitivity of the peptide by DDA analysis. Then, this strategy was applied to comparatively analyze the peptides extracted from the serum of HCC or breast cancer patients and healthy individuals, respectively. Peptides with charge states up to 5 and molecular weight over 4000 can be reliably identified and quantified. This quantitative analysis method based on μUPLC-Q-TOF-MS/MS exhibited superior sensitivity than that by MALDI-TOF-MS commonly used in peptidome analysis. Finally, some interesting endogenous peptides related to corresponding diseases were successfully obtained.
基金funded by grant P20_00661 from the Andalusian Plan for Research,Development and Innovation(PAIDI)2020by grant US-1381492 from the European Regional Development Fund(ERDF).
文摘Hemp is the term commonly used to refer to the variety of Cannabis sativa L.cultivated for industrial purposes.The seeds have gained interest in recent years as functional foods due to their nutritional composition and high content of protein and bioactive compounds.In this study,ten hemp protein hydrolysates(HPHs)were obtained by enzymatic hydrolysis with Alcalase and Flavourzyme from hemp protein isolate(HPI)and their antioxidant properties(DPPH radical scavenging activity,beta-carotene activity and ferric ion reducing antioxidant power(FRAP))were evaluated.Shorter peptide sequences,mainly obtained with Flavourzyme,were found to react with free radicals more easily.The peptidome of all the hydrolysates was characterized,identifying,and quantifying the peptides.Furthermore,19 unique peptides were assessed by in silico tools to hypothesize those that could be responsible of the bioactivity reported for the hydrolysates.From the identified peptides,based on the molecular features and the predictions,the peptides KNAIYTPH,EERPGHF,and KNGMMAPH,among others,are proposed to be highly contributing to the antioxidant activity of the hydrolysates.
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.
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 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.
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 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.
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.
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 Hubei Provincial Natural Science Foundation of China(202310701201614).
文摘Plant peptides play crucial roles in various biological processes, including stress responses. This study investigatesthe functions of plant peptides in response to different adversity stresses, focusing on drought, salt, high temperature,and other environmental challenges. In drought conditions, specific peptides such as CLE25 and CLE9 were foundto regulate stomatal closure and root architecture to enhance the efficiency of water utilization. Salt stress inducesthe expression of CAPE1 and CEP3, which are involved in ion homeostasis and osmoregulation, thereby contributingto salt tolerance in plants. Heat stress triggers the expression of peptides such as CEL45, which contributes to the heattolerance of cells. Besides, we have also verified a new class of non-conventional peptides, and a large numberof non-conventional peptides have been identified in rice seedlings. Understanding the origin and functions of thesepeptides presents both challenges and opportunities for developing stress-resistant crops. Future research shouldfocus on elucidating the precise molecular mechanisms of peptide-mediated stress responses and exploring theirpotential applications in agriculture and biotechnology.
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.
基金funded by the National Natural Science Foundation of China (No.81973450)the National Key R&D Program of China (No.2018YFC1706100)+4 种基金the Jiangsu Qinglan Projectthe Jiangsu “333” Projectthe Young Researchers Training Project of China Association of Traditional Chinese Medicine (No.QNRC2C14)the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (No.19KJB360020)the Open Project of Chinese Materia Medica First-Class Discipline of Nanjing University of Chinese Medicine (2020YLXK009)。
文摘Objective:As an important food therapy product with traditional Chinese medicine(TCM) applications,donkey-hide gelatin(Asini Corii Colla,ACC) has been used for thousands of years.However,till now few effective strategy had been proposed to distinguish ACC from other animal hide gelatins,especially closely related horse-and mule-hide gelatins,which was an embarrassment of ACC quality control.Methods:Combined mass spectrometry and bioinformatic methods have been applied to identify and verify two ACC-specific peptides(Pep-1 and Pep-2) capable of distinguishing ACC from other closely related animal gelatins with high selectivity.Results:It confirmed that these two peptides could be not only used for distinguishing ACC from highly homologous horse-hide and mule-hide gelatins as well as other animal hide gelatins.Conclusion:The present study provides a simple method for species-specific peptides discovery,which can be used for assessing the quality of animal gelatin products,and ensure they are authenticable and traceable.
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.
