Journal of proteomics & bioinformatics最新文献

Large Scale Screening and Quantitative Analysis of Site-Specific N-Glycopeptides from Human Serum in Early Alzheimer's Disease Using LC-HCD-PRM-MS. 利用 LC-HCD-PRM-MS 大规模筛查和定量分析早期阿尔茨海默氏症患者血清中的特定位点 N-糖肽

Journal of proteomics & bioinformatics Pub Date : 2022-01-01 Epub Date: 2022-06-27

Lingyun Pan, Yu Lin, Jianhui Zhu, Jie Zhang, Zhijing Tan, David M Lubman

{"title":"Large Scale Screening and Quantitative Analysis of Site-Specific N-Glycopeptides from Human Serum in Early Alzheimer's Disease Using LC-HCD-PRM-MS.","authors":"Lingyun Pan, Yu Lin, Jianhui Zhu, Jie Zhang, Zhijing Tan, David M Lubman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Glycopeptide analysis by mass spectrometry may provide an important opportunity in discovery of biomarkers to aid in early detection of Alzheimer's Disease (AD). In this work, we have used a NanoLC-Stepped-HCD-DDA-MS/MS platform and a NanoLC-Stepped-HCD-PRM-MS platform for large-scale screening and quantification of novel N-glycopeptide biomarkers for early detection of AD in patient serum. N-glycopeptides were retrieved from 10 μL of serum in patients with mild cognitive impairment (MCI, a prodromal phase of AD) and normal controls, respectively, after trypsin digestion, glycopeptide enrichment, fractionation, and NanoLC-Stepped-HCD-DDA-MS/MS or NanoLC-Stepped-HCD-PRM-MS analysis. Using a combination of Byonic, Byologic and Skyline softwares, we were able to accomplish both identification and label-free quantitation of site-specific N-glycopeptides between MCI and normal controls. Differential quantitation analysis by Byologic showed that 29 N-glycopeptides derived from 16 glycoproteins were significantly changed in MCI compared to normal controls. Further, HCD-PRM-MS quantitative analysis of the selected N-glycopeptide candidates confirmed that EHEGAIYPDN138TTDFQR_HexNAc(4)Hex(5)-Fuc(2)NeuAc(1) from CERU, and VCQDCPLLAPLN156DTR_HexNAc(4)Hex(5)NeuAc(2) from AHSG can significantly discriminate MCI from normal controls. These two glycopeptides had the area under the receiver operating characteristic curve (AUC) of 0.850 (95% CI, 0.66-1.0) and 0.867 (95% CI, 0.68-1.0), respectively (p<0.05). The result demonstrates that changes in the expression level of the N-glycopeptides provide potential serum biomarkers for detection of AD at a very early stage.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"15 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10289803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10075311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Technologies and Their Applications in Proteomics 蛋白质组学技术及其应用

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E124

M. Aslam

引用次数: 0

Drug Repurposing Approach Targeting Main Protease Using HTVS and Pharmacophoric Mapping: Exceptional Reassuring Itinerary for Most Insolvent Anti-SARS-CoV-2 Drug 利用HTVS和药效学作图靶向主要蛋白酶的药物重新利用方法:大多数破产抗sars - cov -2药物的特殊可靠行程

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.527

V. Bastikar, Pramodkumar P. Gupta, J. Sangshetti, Alpana Bastikar, S. Chhajed

{"title":"Drug Repurposing Approach Targeting Main Protease Using HTVS and Pharmacophoric Mapping: Exceptional Reassuring Itinerary for Most Insolvent Anti-SARS-CoV-2 Drug","authors":"V. Bastikar, Pramodkumar P. Gupta, J. Sangshetti, Alpana Bastikar, S. Chhajed","doi":"10.35248/0974-276X.21.14.527","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.527","url":null,"abstract":"Coronavirus pandemic COVID 19 has caused a wide range of harm worldwide with its inception in December 2019 in Wuhan, China. Till date there is no promising drug identified for the treatment of disease. In the view of this, scientists have elucidated X-ray structures of the proteins in SARS-CoV-2 virus. These can act as probable drug targets for the designing of drugs which is urgent need. One of the main proteins of the virus is its main protease Mpro which is responsible for producing polyproteins of the virus. In this study we have used main protease as the target for drug design and repurposing for COVID-19. Two approaches were applied in order to develop a fast and effective treatment against the virus. Drug repurposing through in-silico docking analysis of existing FDA approved drugs was one method and high throughput screening of molecules from the ZINC database against main protease was the other technique applied. Two docking protocols were utilized- a fast docking algorithm to screen the hits or lead molecules followed by simulation based molecular dynamics docking procedure to optimize the obtained hits. We could observe a definite scaffold based binding affinity against the main protease. These scaffolds were lutein, steroids, morphine and quinolone, CPT. Thiotepa was identified as the best docked molecule with highest binding affinity. Unique molecules like lutein, beta carotene, Buprenorphine etc. were identified which can be used as repurposed drugs against SARS-CoV-2. Also these scaffolds show unique pharmacophores which can be utilized to design potential novel leads against SARS-CoV-2 for future treatment.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"14 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Physiological and Proteomic Analysis of Brassica napus in Response to Salt Stress 甘蓝型油菜对盐胁迫的生理和蛋白质组学分析

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.523

Bing-Yun Yu, Gang Chen, Hui-zi DuanMu, D. Dufresne, J. Erickson, J. Koh, Haiying Li, Sixue Chen

{"title":"Physiological and Proteomic Analysis of Brassica napus in Response to Salt Stress","authors":"Bing-Yun Yu, Gang Chen, Hui-zi DuanMu, D. Dufresne, J. Erickson, J. Koh, Haiying Li, Sixue Chen","doi":"10.35248/0974-276X.21.14.523","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.523","url":null,"abstract":"Salinity is a major abiotic stress that adversely affects plant growth and development. Canola (Brassica napus L.) is an important oilseed crop in the world, and its yield decreases drastically with increasing salinity. To date, little is known about the molecular mechanisms underlying its salt stress response and tolerance. This study combines physiological assays with comparative proteomics to understand how B. napus plants respond to salt stress. The changes in relative water content, electrical conductance, stomata conductance, intercellular CO2 concentration, transpiration rate, photosynthesis rate, water usage efficiency, respiration rate, chlorophyll fluorescence, antioxidant enzyme activities, soluble sugar, proline and betaine in B. napus plants under different NaCl concentrations were analyzed. Proteomic profiles of B. napus plants under 100, 200 and 400 mM NaCl treatment at 7 day and 14 day were acquired using iTRAQ LC-MS/MS based quantitative proteomics. A total of 2316 proteins were identified in B. napus leaves, of which 614 proteins showed differential expression under salt stress. These proteins were mainly involved in 10 processes, of which proteins in stress and defense, metabolism and photosynthesis pathways ranked the top three. Subcellular localization analysis showed that most proteins were located in chloroplast, cytoplasm, mitochondria and nucleus. A total of 138 differentially expressed proteins were predicted to interact with each other. These results have provided a comprehensive view of the physiological and molecular processes taken place in B. napus leaves under salt stress, and revealed the molecular mechanisms underlying salt tolerance of B. napus plants.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"14 1","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Membrane Proteomic Responses in Sugar Beet Roots to Salt Stress 甜菜根膜蛋白质组学对盐胁迫的响应

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.541

Jinna Li, Jianing Kang, P. Liao, Bing-Yun Yu, Sixue Chen, Haiying Li, Chunquan Ma

{"title":"Membrane Proteomic Responses in Sugar Beet Roots to Salt Stress","authors":"Jinna Li, Jianing Kang, P. Liao, Bing-Yun Yu, Sixue Chen, Haiying Li, Chunquan Ma","doi":"10.35248/0974-276X.21.14.541","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.541","url":null,"abstract":"Salt stress as one of the major abiotic stresses limits the world crop production. Sugar beet monosomic addition line M14 is a unique germplasm with salt stress tolerance, and root is directly exposed to salt stress in the soil. Here we report changes in root membrane proteome of the M14 plants in response to 0, 200 mM and 400 mM NaCl treatment using iTRAQ LC-MS/MS quantitative proteomics. A total of 115 differentially expressed membrane proteins (96 increased and 19 decreased) were identified with a significant fold change of >2.0. The proteins were mainly involved in the processes of transport, signaling, stress and defense, energy, protein degradation, and transcription. Transcriptional changes of 10 genes encoding the differential membrane proteins were analyzed using real-time PCR, and seven genes showed a positive correlation between transcriptional and protein levels. These results have revealed interesting mechanisms underlying the M14 root response to the salt stress, which may have potential applications toward improving crop salt tolerance through genetic engineering and molecular breeding.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"14 1","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Sharing Data from an Academic Cancer Center Biospecimen and Proteomic Core Facilities through the Proteomics Data Commons 通过蛋白质组学数据共享共享来自学术癌症中心生物标本和蛋白质组学核心设施的数据

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.529

P. McGarvey, Ratna R. Thangudu, Junfeng Ma, Ci Wu, Shabeeb Kannattikuni, Krysta Chaldekas, D. Berry, Alicia Francis, D. Singhal, P. Rudnick, An, Basu, Subha Madhavan

{"title":"Sharing Data from an Academic Cancer Center Biospecimen and Proteomic Core Facilities through the Proteomics Data Commons","authors":"P. McGarvey, Ratna R. Thangudu, Junfeng Ma, Ci Wu, Shabeeb Kannattikuni, Krysta Chaldekas, D. Berry, Alicia Francis, D. Singhal, P. Rudnick, An, Basu, Subha Madhavan","doi":"10.35248/0974-276X.21.14.529","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.529","url":null,"abstract":"Data sharing is critical for open science and often required by funding organizations and journals. NCI has developed the Proteomics Data Commons (PDC) as part of the Cancer Research Data Commons, an infrastructure that allows users to share, analyze, and store results, utilizing the storage and compute resources of the cloud. To date most of the data available in the various Data Commons are submitted from large multi-institution research programs funded by NCI with teams of specialists from multiple scientific disciplines. Here we describe our experiences and summarize the recommended best practices for sharing a set of proteomics and related biospecimen data and analyses results from smaller scale proteomics studies conducted in an academic medical center core facility using patient samples of lung adenocarcinoma. Mapping and depositing data in the manner described here harmonizes user’s data to a common data model and community standards, making it possible to view the data alongside other high value cancer studies available in the PDC. Availability: Data, metadata, protocols with peptide and protein identifications are available at the PDC. (https:// pdc.cancer.gov/pdc/study/PDC000231).","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"14 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overview of Neuroproteomics 神经蛋白质组学综述

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E127

S. Eswaran

引用次数: 0

Recent Advances in the Field of Protein Sequencing 蛋白质测序领域的最新进展

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.549

M. Shah

引用次数: 0

An Editorial on ActDES: A Curated Actinobacterial Database for Evolutionary Studies 一篇关于ActDES的社论:一个用于进化研究的放线菌数据库

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E125

Paul Anderson

引用次数: 0

A Commentary on Plasma Membrane Derived Extracellular Vesicles(PMEVs) 质膜源性细胞外囊泡(pmev)研究进展

Journal of proteomics & bioinformatics Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.539

Michal Ben

引用次数: 0