Identification of specific peptides from Bubali Cornu by ultra-performance liquid chromatography-tandem mass spectrometry / 中国中药杂志

This paper explored the specific peptides from Bubali Cornu by ultra-performance liquid chromatography-tandem mass spectrometry and based on mathematics set theory. Following the profile analysis of peptides from Bubali Cornu, Bovis Grunniens Cornu, Caprae Hircus Cornu, and Suis Cornu by nano LC-LTQ-Obitrap-MS after digestion with trypsin, the relationship of peptide composition among different samples was analyzed using the mathematics set theory. The ones that existed only in the Bubali Cornu set rather than in any other set were considered as the specific peptides of Bubali Cornu. The further bioinformatic analysis revealed four specific peptides from Bubali Cornu, whose specificity was verified by UPLC-QQQ-MS. The results showed that these four peptides could be used for distinguishing Bubali Cornu from Caprae Hircus Cornu and Suis Cornu. This study has provided a rapid and simple method for seeking the specific peptides in animal medicines, which can be utilized for quality evaluation of animal medicines, thus making them authenticable and traceable.

Label-free quantitative peptidomics-based analysis on glycopeptides in deerhorn gelatin and deer-hide gelatin / 中国中药杂志

Nano-LC-MS/MS was used to analyze trypsin digested deer-horn gelatin( DCG) and deer-hide gelatin( DHG) samples.The glycopeptides in DCG and DHG were quantified by Label-free quantitative( LFQ) peptidomics,on the basis of which the glycopeptides with significant difference in DCG and DHG were determined. As a result,5 736 peptides were identified from DCG samples,including 213 galactosyl-hydroxylysine containing peptides( Gal-Hyl-peptides) and 102 glucosyl-galactosyl-hydroxylysine containing peptides( Glc-Gal-Hyl-peptides),while 6 836 peptides were identified from DHG samples,among which there were 250 Gal-Hyl-peptides and 98 Glc-Gal-Hyl-peptides. With over 3-fold peak area difference and highly significant intergroup difference( P < 0. 01) as the screening criteria,444 differential peptides were determined in DCG and DHG,including 16 Gal-Hyl-peptides and 5 Glc-Gal-Hyl-peptides. Then XIC peak shapes,standard deviation of peak area,and fold change were applied for further screening and 5 glycopeptides with significant differences in DCG and DHG were confirmed,which could serve as potential biomarkers for distinguishing DCG and DHG. The present study provided ideas and strategies for the in-depth investigation on the discrimination of DCG and DHG and is of good theoretical significance and application value for the further research on chemical constituents and quality control of gelatin derived Chinese medicinals.

Quantity - but not diversity - of secreted peptides and proteins increases with age in the tree frog Pithecopus nordestinus

Amphibians inhabit the terrestrial environment, a conquest achieved after several evolutionary steps, which were still insufficient to make them completely independent of the aquatic environment. These processes gave rise to many morphological and physiological changes, making their skin (and cutaneous secretion) rich in bioactive molecules. Among the tree frogs, the secretion is composed mainly of peptides; but alkaloids, proteins and steroids can also be found depending on the species. The most known class of biologically active molecules is the antimicrobial peptides (AMPs) that act against bacteria, fungi and protozoans. Although these molecules are well-studied among the hylids, AMPs ontogeny remains unknown. Therefore, we performed peptidomic and proteomic analyses of Pithecopus nordestinus (formerly Phyllomedusa nordestina) in order to evaluate the peptide content in post-metamorphosed juveniles and adult individuals. Methods: Cutaneous secretion of both life stages of individuals was obtained and analyzed by LC-MS/MS after reduction and alkylation of disulfide bonds or reduction, alkylation and hydrolysis by trypsin. Results: Differences in the TIC profile of juveniles and adults in both treatments were observed. Moreover, the proteomic data revealed known proteins and peptides, with slight differences in the composition, according to the life stage and the treatment. AMPs were identified, and bradykinin-potentiating peptides were observed in trypsin-treated samples, which suggests a protein source of such peptide (cryptide). Conclusion: In general, skin secretion contents were similar between juveniles and adults, varying in quantity, indicating that the different stages of life are reflected in the number of molecules and not on their diversity.(AU)

Collagen derived species-specific peptides for distinguishing donkey-hide gelatin (Asini Corii Colla) / 中草药·英文版

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.

Comparative gender peptidomics of Bothrops atrox venoms: are there differences between them?

Bothrops atrox is known to be the pit viper responsible for most snakebites and human fatalities in the Amazon region. It can be found in a wide geographical area including northern South America, the east of Andes and the Amazon basin. Possibly, due to its wide distribution and generalist feeding, intraspecific venom variation was reported by previous proteomics studies. Sex-based and ontogenetic variations on venom compositions of Bothrops snakes were also subject of proteomic and peptidomic analysis. However, the venom peptidome of B. atrox remains unknown. Methods: We conducted a mass spectrometry-based analysis of the venom peptides of individual male and female specimens combining bottom-up and top-down approaches. Results: We identified in B. atrox a total of 105 native peptides in the mass range of 0.4 to 13.9 kDa. Quantitative analysis showed that phospholipase A2 and bradykinin potentiating peptides were the most abundant peptide families in both genders, whereas disintegrin levels were significantly increased in the venoms of females. Known peptides processed at non-canonical sites and new peptides as the Ba1a, which contains the SVMP BATXSVMPII1 catalytic site, were also revealed in this work. Conclusion: The venom peptidomes of male and female specimens of B. atrox were analyzed by mass spectrometry-based approaches in this work. The study points to differences in disintegrin levels in the venoms of females that may result in distinct pathophysiology of envenomation. Further research is required to explore the potential biological implications of this finding.(AU)

Comparative analysis of chemical constituents of deer hide and deer hide gelatin by "peptidomics-modifications" methods / 药学学报

Collagen is the main constituent of gelatinous Chinese medicine, with deer hide gelatin (Cervi Corii Colla, DHG) made from deer hide (DH) through a complex thermal and high-pressure processing procedure. During this procedure some amino acids in collagen undergo hydroxylation and deamidation. In the present study, comparative analysis of proteins and peptides in DH and DHG was carried out using "peptidomics-modifications" methods. Nano-LC-MS/MS was used to analyze proteins and peptides in DH and DHG, and the number and sites of modification were determined as well. The amount of hydroxylation and deamidation that occurred in DHG was significantly greater than that in DH, suggesting that under thermal and high-pressure processing these modifications occurred more frequently on certain amino acids in collagen, and might be correlated with hydrophobicity. The occurrence and mechanism of hydroxylation and deamidation in DH processing procedures should be explored in further research. The present study provides important evidence of the chemical constituents and the correlation of processing procedures with these modifications, and also suggests some investigative ideas for DHG processing optimization and improvement of quality standards.

Advances in effectively screening anti-tumor peptides / 药学学报

Malignant tumor is a disease that severely threaten human health. Common chemotherapeutical drugs currently used in clinical practice have some problems in severe side effects and chemoresistance. In contrast, natural venom peptides and artificially designed targeting peptides have excellent biological activities and potential druggability due to their small molecular weights and high affinity to tumor tissues. Thus, the methods for the discovery of anti-tumor peptides have attracted much attention. In this paper, we summarized the types of anti-tumor peptides from recent literatures. Then, we systematically reviewed screening theories, methods and applications based on traditional chromatographic separation, peptidomics, phage display, phenotypic screening, and artificial intelligence. These strategies and technologies will provide a methodological reference for accelerating anti-tumor peptides research.

Preliminary Study on the Biological Markers for I-IIb Stage Non-small Cell Lung Cancer Based on a Serum-peptidomics / 中国肺癌杂志

BACKGROUND@#Non-small cell lung cancer (NSCLC) have the highest incidence of lung cancer which treatment principles are diagnosis and treatment as early as possible. Because of its insidious onset and lack of specific markers for early screening, most patients are at an advanced stage when diagnosed which results in a low 5-year survival rate and poor prognosis. Therefore Exploring a sensitive biomarker is the focus of current diagnosis and treatment of lung cancer. The aim of this study is to investigate the biological markers in serum of patients with I-IIb stage NSCLC by differential peptidomics analysis.@*METHODS@#The serum peptidome was compared and analyzed among the groups of normal health controls, benign lung diseases and early stage NSCLC patients using a nano ultra-performance liquid chromatography combined with a quadrupole-orbitrap mass spectrometer. The differentially expressed polypeptides were identified and analyzed quantitatively to screen the tumor biomarkers for the early diagnosis of NSCLC patients.@*RESULTS@#According to the Swiss-Prot database, a total of 545 polypeptides originated from 118 proteins were identified. The spectral numbers of serum polypeptides in each group were compared and a total of 201 polypeptides differentially expressed were found. Following a quantitative analysis of the above peptides, we found that there were 7 peptides with the coefficient of variation (CV) less than 30% and among them the peptide of QGAKIPKPEASFSPR from ITIH4 was down-regulated and the peptide of CDDYRLC from MGP was up-regulated in NSCLC group.@*CONCLUSIONS@#The tumor biomarkers obtained by serum peptidome technology can provide a new clue for early diagnosis of NSCLC and the specific peptides hydrolyzed from ITIH4 and MGP may be the serum biological markers for early NSCLC patients.

Research ideas and methods of protein and peptides in animal medicine based on transcriptomics-proteomics-peptidomics integrated association analysis strategy / 中草药

Animal medicine is an important part of traditional Chinese medicine, and its unique efficacy is irreplaceable in clinical application. In consideration of the main problems in the research of animal medicine, such as the uncertainty of chemical composition, pharmacodynamic components and toxic components, and the inadequacy of quality control system, this article established a research method of protein and peptides in animal medicine based on transcriptomics-proteomics-peptidomics integrated association analysis strategy, which mainly include the construction of protein database based on transcriptomics, high resolution mass spectrometry analysis, identification and activity evaluation of protein and peptide components. It attempts to provide a practical research method for the analysis and identification of protein and peptide components in animal medicine and technical support for further solving the key issues of animal medicine research.

Peptidomic investigation of Neoponera villosa venom by high-resolution mass spectrometry: seasonal and nesting habitat variations

Background: Advancements in proteomics, including the technological improvement in instrumentation, have turned mass spectrometry into an indispensable tool in the study of venoms and toxins. In addition, the advance of nanoscale liquid chromatography coupled to nanoelectrospray mass spectrometry allows, due to its high sensitivity, the study of venoms from species previously left aside, such as ants. Ant venoms are a complex mixture of compounds used for defense, predation or communication purposes. The venom from Neoponera ants, a genus restricted to Neotropical regions, is known to have cytolytic, hemolytic, antimicrobial and insecticidal activities. Moreover, venoms from several Neoponera species have been compared and differences in their toxicity related to nesting habitat variation were reported. Therefore, the present study aimed to perform a deep peptidomic analysis of Neoponera villosa venom and a comparison of seasonal and nesting habitat variations using high-resolution mass spectrometry. Methods: Specimens of N. villosa ants were captured in Panga Natural Reserve (Uberlândia, MG, Brazil) from arboreal and ground-dwelling nests during summer and winter time. The venom glands were dissected, pooled and disrupted by ultra-sonic waves. The venom collected from different habitats (arboreal and ground-dwelling) and different seasons (summer and winter) was injected into a nanoACQUITY ULPC hyphened to a Q-Exactive Orbitrap mass spectrometer. The raw data were analyzed using PEAKS 7. Results: The results showed a molecular diversity of more than 500 peptides among these venoms, mostly in the mass range of 8004000 Da. Mutations and post-translational modifications were described and differences among the venoms were observed. Part of the peptides matched with ponericins, a well-known antimicrobial peptide family...

Peptidomic investigation of Neoponera villosa venom by high-resolution mass spectrometry: seasonal and nesting habitat variations

Advancements in proteomics, including the technological improvement in instrumentation, have turned mass spectrometry into an indispensable tool in the study of venoms and toxins. In addition, the advance of nanoscale liquid chromatography coupled to nanoelectrospray mass spectrometry allows, due to its high sensitivity, the study of venoms from species previously left aside, such as ants. Ant venoms are a complex mixture of compounds used for defense, predation or communication purposes. The venom from Neoponera ants, a genus restricted to Neotropical regions, is known to have cytolytic, hemolytic, antimicrobial and insecticidal activities. Moreover, venoms from several Neoponera species have been compared and differences in their toxicity related to nesting habitat variation were reported. Therefore, the present study aimed to perform a deep peptidomic analysis of Neoponera villosa venom and a comparison of seasonal and nesting habitat variations using high-resolution mass spectrometry. Methods: Specimens of N. villosa ants were captured in Panga Natural Reserve (Uberlândia, MG, Brazil) from arboreal and ground-dwelling nests during summer and winter time. The venom glands were dissected, pooled and disrupted by ultra-sonic waves. The venom collected from different habitats (arboreal and ground-dwelling) and different seasons (summer and winter) was injected into a nanoACQUITY ULPC hyphened to a Q-Exactive Orbitrap mass spectrometer. The raw data were analyzed using PEAKS 7. Results: The results showed a molecular diversity of more than 500 peptides among these venoms, mostly in the mass range of 800-4000 Da. Mutations and post-translational modifications were described and differences among the venoms were observed. Part of the peptides matched with ponericins, a well-known antimicrobial peptide family. In addition, smaller fragments related to ponericins were also identified, suggesting that this class of antimicrobial peptide might undergo enzymatic cleavages. Conclusion: There are substantial differences among the venom of N. villosa ants collected in different seasons and from different nest habitats. The venom composition is affected by climate changes that influence prey availability and predator presence. Clearly, nano-LC-MS boosted the knowledge about ant venom, a rich source of unexplored and promising bioactive compounds.(AU)

Study of Alzheimer′s Disease Biomarkers Based onSerum Peptidomics / 分析化学

Early diagnosis and intervention is an important way to delay the progress of Alzheimer′s disease (AD).Compared with cerebrospinal fluid, blood sampling is not invasive and easy to be obtained in clinic practice.In this study, the serum samples of 9 controls, 10 AD and 12 mild cognitive dysfunction (MCI) patients were analyzed and compared through one by one analysis to screen potential markers for AD diagnosis.The experimental results showed that VGFYESDVMGR of α-2-macroglobulin peptide was closely related to the late stage of AD disease, and the large amount degradation of apolipoprotein C-Ⅲ, histone H1.2 and histone H1.4 was significantly related to early stages of AD progression.The characteristics of serum peptidome were different for the early and late AD, and these four proteins may be used as potential biomarkers of AD disease.In addition, the obvious ladder sequence characteristic was observed for apolipoprotein C-Ⅲ and histone H1, which could partly explain why the peptides distribution in different samples was somewhat contingent.On the contrary, the distribution at protein level was more stable.Finally, it was confirmed that the peptides of proteins such as fibrinogen α-chain, thymosin β-4 and patchy proteins were the dominant peptides in all serum samples.Overall, this study showed that the method of using serum peptidomics to diagnose AD was possible.The results may provide evidence and references for the large-scale clinical validation of AD.

Effect of Reproducibility of Nano-liquid Chromatography-Mass Spectrometry on Analysis of Urinary Peptidomics / 分析化学

As an extension of proteomics, peptidomics has been widely used in medical and biological researches. However, the effect of reproducibility of identification method on peptidomics is not yet clear. In this work, the urine sample of a healthy people was analyzed for seven times in parallel by nano-liquid chromatography-high-resolution tandem mass spectrometry. To illustrate the variability and stability among these experiments, the number of spectra, the utilization of total spectra, the number of identified peptides, the number of proteins, and the ionic strength and retention time of peptides were counted and compared. The average number of peptides was 208 and the standard deviation was 38. 7. After all of data were combined, 426 peptides belonging to 114 proteins were obtained, while only 109 peptides coming from 35 proteins were identified in each experiment, indicating that there were both an randomness and a relative stability for LC-MS analysis. Increasing the number of parallel experiments would expand the data set of peptidomics, but the rate of increase would decrease over 3 or more measurements. Compared with peptides, the results of peptidomics were more stable at protein level, indicating that proteins were more robustly peptidomics biomarker than the peptides.

Effect of Reproducibility of Nano-liquid Chromatography-Mass Spectrometry on Analysis of Urinary Peptidomics / 分析化学

As an extension of proteomics, peptidomics has been widely used in medical and biological researches. However, the effect of reproducibility of identification method on peptidomics is not yet clear. In this work, the urine sample of a healthy people was analyzed for seven times in parallel by nano-liquid chromatography-high-resolution tandem mass spectrometry. To illustrate the variability and stability among these experiments, the number of spectra, the utilization of total spectra, the number of identified peptides, the number of proteins, and the ionic strength and retention time of peptides were counted and compared. The average number of peptides was 208 and the standard deviation was 38. 7. After all of data were combined, 426 peptides belonging to 114 proteins were obtained, while only 109 peptides coming from 35 proteins were identified in each experiment, indicating that there were both an randomness and a relative stability for LC-MS analysis. Increasing the number of parallel experiments would expand the data set of peptidomics, but the rate of increase would decrease over 3 or more measurements. Compared with peptides, the results of peptidomics were more stable at protein level, indicating that proteins were more robustly peptidomics biomarker than the peptides.

Initial peptidomic profiling of Brazilian sea urchins: Arbacia lixula, Lytechinus variegatus and Echinometra lucunter

Background Sea urchins can be found throughout the Brazilian coast and are reported to be one of the major causes of marine accidents on the shoreline. Although not lethal, these accidents are reported to be extremely painful. In order to understand the toxinology of the Brazilian urchins, a peptidomic approach was performed aiming to characterize the naturally occurring peptides in both the coelomic fluid and the spine. Methods Animals were collected without gender distinction and samples of the coelomic fluid and spines extracted were analyzed by RP-HPLC and mass spectrometry for peptide de novo sequencing. Results Several peptides were identified either in the coelomic fluid or the spine extract (except for E. lucunter). The peptide sequences were aligned with public deposited sequences and possible functions were inferred. Moreover, some peptides can be cryptides, since their sequences were identified within functional proteins, for example thymosin from Strongylocentrotus purpuratus. Conclusions Although preliminary, the peptidomic approach presented here reports, for the first time, the abundance of novel biological molecules derived from these animals. The discovery of such molecules may be of potential biotechnological application, as described for other organisms; nevertheless, further studies are required.(AU)

Initial peptidomic profiling of Brazilian sea urchins: Arbacia lixula, Lytechinus variegatus and Echinometra lucunter

Sea urchins can be found throughout the Brazilian coast and are reported to be one of the major causes of marine accidents on the shoreline. Although not lethal, these accidents are reported to be extremely painful. In order to understand the toxinology of the Brazilian urchins, a peptidomic approach was performed aiming to characterize the naturally occurring peptides in both the coelomic fluid and the spine. Methods Animals were collected without gender distinction and samples of the coelomic fluid and spines extracted were analyzed by RP-HPLC and mass spectrometry for peptide de novo sequencing. Results Several peptides were identified either in the coelomic fluid or the spine extract (except for E. lucunter). The peptide sequences were aligned with public deposited sequences and possible functions were inferred. Moreover, some peptides can be cryptides, since their sequences were identified within functional proteins, for example thymosin from Strongylocentrotus purpuratus. Conclusions Although preliminary, the peptidomic approach presented here reports, for the first time, the abundance of novel biological molecules derived from these animals. The discovery of such molecules may be of potential biotechnological application, as described for other organisms; nevertheless, further studies are required.

Neuropeptidomics: Mass Spectrometry-Based Identification and Quantitation of Neuropeptides

Neuropeptides produced from prohormones by selective action of endopeptidases are vital signaling molecules, playing a critical role in a variety of physiological processes, such as addiction, depression, pain, and circadian rhythms. Neuropeptides bind to post-synaptic receptors and elicit cellular effects like classical neurotransmitters. While each neuropeptide could have its own biological function, mass spectrometry (MS) allows for the identification of the precise molecular forms of each peptide without a priori knowledge of the peptide identity and for the quantitation of neuropeptides in different conditions of the samples. MS-based neuropeptidomics approaches have been applied to various animal models and conditions to characterize and quantify novel neuropeptides, as well as known neuropeptides, advancing our understanding of nervous system function over the past decade. Here, we will present an overview of neuropeptides and MS-based neuropeptidomic strategies for the identification and quantitation of neuropeptides.

Characterization of Leiurus abdullahbayrami (Scorpiones: Buthidae) venom: peptide profile, cytotoxicity and antimicrobial activity

Background Scorpion venoms are rich bioactive peptide libraries that offer promising molecules that may lead to the discovery and development of new drugs.Leiurus abdullahbayrami produces one of the most potent venoms among Turkish scorpions that provokes severe symptoms in envenomated victims.Methods In the present study, the peptide profile of the venom was investigated by electrophoretic methods, size-exclusion and reversed-phase chromatography and mass spectroscopy. Cytotoxic and antimicrobial effects were evaluated on a breast cancer cell line (MCF-7) and various bacterial and fungal species.Results Proteins make up approximately half of the dry weight of L. abdullahbayrami crude venom. Microfluidic capillary electrophoresis indicated the presence of 6 to 7 kDa peptides and proved to be a highly practical peptidomics tool with better resolution when compared to conventional polyacrylamide gel electrophoresis. Mass spectroscopy analysis helped us to identify 45 unique peptide masses between 1 to 7 kDa with a bimodal mass distribution peaking between molecular weights of 1 to 2 kDa (29%) and 3 to 4 kDa (31%). L. abdullahbayrami crude venom had a proliferative effect on MCF-7 cells, which may be explained by the high concentration of polyamines as well as potassium and calcium ions in the arachnid venoms. Antimicrobial effect was stronger on gram-negative bacteria.Conclusions This work represents the first peptidomic characterization of L. abdullahbayrami venom. Considering the molecular weight-function relationship of previously identified venom peptides, future bioactivity studies may lead to the discovery of novel potassium and chloride ion channel inhibitors as well as new antimicrobial peptides fromL. abdullahbayrami venom.(AU)

Characterization of Leiurus abdullahbayrami (Scorpiones: Buthidae) venom: peptide profile, cytotoxicity and antimicrobial activity

Background Scorpion venoms are rich bioactive peptide libraries that offer promising molecules that may lead to the discovery and development of new drugs.Leiurus abdullahbayrami produces one of the most potent venoms among Turkish scorpions that provokes severe symptoms in envenomated victims.Methods In the present study, the peptide profile of the venom was investigated by electrophoretic methods, size-exclusion and reversed-phase chromatography and mass spectroscopy. Cytotoxic and antimicrobial effects were evaluated on a breast cancer cell line (MCF-7) and various bacterial and fungal species.Results Proteins make up approximately half of the dry weight of L. abdullahbayrami crude venom. Microfluidic capillary electrophoresis indicated the presence of 6 to 7 kDa peptides and proved to be a highly practical peptidomics tool with better resolution when compared to conventional polyacrylamide gel electrophoresis. Mass spectroscopy analysis helped us to identify 45 unique peptide masses between 1 to 7 kDa with a bimodal mass distribution peaking between molecular weights of 1 to 2 kDa (29%) and 3 to 4 kDa (31%). L. abdullahbayrami crude venom had a proliferative effect on MCF-7 cells, which may be explained by the high concentration of polyamines as well as potassium and calcium ions in the arachnid venoms. Antimicrobial effect was stronger on gram-negative bacteria.Conclusions This work represents the first peptidomic characterization of L. abdullahbayrami venom. Considering the molecular weight-function relationship of previously identified venom peptides, future bioactivity studies may lead to the discovery of novel potassium and chloride ion channel inhibitors as well as new antimicrobial peptides fromL. abdullahbayrami venom.