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
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
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
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
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
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 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.
