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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
Pub Date : 2022-01-01 Epub Date: 2022-06-27
Lingyun Pan, Yu Lin, Jianhui Zhu, Jie Zhang, Zhijing Tan, David M Lubman

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.

质谱法糖肽分析为发现生物标记物提供了重要机会,有助于早期检测阿尔茨海默病(AD)。在这项研究中,我们利用纳米液相色谱分离-HCD-DDA-MS/MS平台和纳米液相色谱分离-HCD-PRM-MS平台大规模筛选和定量分析了新型N-糖肽生物标记物,用于早期检测患者血清中的AD。经过胰蛋白酶消化、糖肽富集、分馏、NanoLC-Stepped-HCD-DDA-MS/MS 或 NanoLC-Stepped-HCD-PRM-MS 分析,分别从轻度认知障碍(MCI,AD 的前驱期)患者和正常对照组的 10 μL 血清中提取了 N-糖肽。通过结合使用 Byonic、Byologic 和 Skyline 软件,我们完成了 MCI 和正常对照组之间特定位点 N-糖肽的鉴定和无标记定量。Byologic的差异定量分析显示,与正常对照组相比,MCI患者中来自16种糖蛋白的29种N-糖肽发生了显著变化。此外,对所选 N-糖肽候选物进行的 HCD-PRM-MS 定量分析证实,来自 CERU 的 EHEGAIYPDN138TTDFQR_HexNAc(4)Hex(5)-Fuc(2)NeuAc(1) 和来自 AHSG 的 VCQDCPLLAPLN156DTR_HexNAc(4)Hex(5)NeuAc(2) 可显著区分 MCI 和正常对照组。这两种糖肽的接收者操作特征曲线下面积(AUC)分别为 0.850(95% CI,0.66-1.0)和 0.867(95% CI,0.68-1.0)(p
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引用次数: 0
Technologies and Their Applications in Proteomics 蛋白质组学技术及其应用
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E124
M. Aslam
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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
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.527
V. Bastikar, Pramodkumar P. Gupta, J. Sangshetti, Alpana Bastikar, S. Chhajed
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.
冠状病毒大流行COVID - 19自2019年12月在中国武汉爆发以来,在全球范围内造成了广泛的危害。到目前为止,还没有发现有希望治疗疾病的药物。鉴于此,科学家们已经阐明了SARS-CoV-2病毒蛋白质的x射线结构。这些可以作为药物设计急需的可能靶点。该病毒的主要蛋白质之一是其主要蛋白酶Mpro,它负责产生病毒的多蛋白。在本研究中,我们将主要蛋白酶作为新冠病毒药物设计和再利用的靶点。为了开发一种快速有效的病毒治疗方法,采用了两种方法。通过对现有FDA批准的药物进行计算机对接分析来进行药物再利用是一种方法,另一种方法是对锌数据库中针对主要蛋白酶的分子进行高通量筛选。采用两种对接方案——快速对接算法筛选命中点或先导分子,基于模拟的分子动力学对接程序优化获得的命中点。我们可以观察到明确的基于支架的对主要蛋白酶的结合亲和力。这些支架是叶黄素,类固醇,吗啡和喹诺酮,CPT。Thiotepa是最佳的对接分子,具有最高的结合亲和力。发现了叶黄素、β -胡萝卜素、丁丙诺啡等独特分子,可作为抗SARS-CoV-2的靶向药物。此外,这些支架显示出独特的药效团,可用于设计潜在的针对SARS-CoV-2的新型导联剂,用于未来的治疗。
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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
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
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.
盐度是影响植物生长发育的主要非生物胁迫。油菜(Brassica napus L.)是世界上重要的油料作物,其产量随着盐度的升高而急剧下降。迄今为止,对其盐胁迫反应和耐受性的分子机制知之甚少。本研究将生理分析与比较蛋白质组学相结合,以了解甘蓝型油菜对盐胁迫的反应。分析了不同NaCl浓度下甘蓝型油菜植株的相对含水量、电导、气孔导度、胞间CO2浓度、蒸腾速率、光合速率、水分利用效率、呼吸速率、叶绿素荧光、抗氧化酶活性、可溶性糖、脯氨酸和甜菜碱的变化。采用基于iTRAQ LC-MS/MS的定量蛋白质组学技术,获得了100,200和400 mM NaCl处理7 d和14 d甘蓝型油菜植株的蛋白质组学特征。在甘蓝型油菜叶片中共鉴定出2316个蛋白,其中614个蛋白在盐胁迫下表现出差异表达。这些蛋白主要参与10个过程,其中胁迫与防御、代谢和光合作用途径中的蛋白排名前三位。亚细胞定位分析表明,大多数蛋白质位于叶绿体、细胞质、线粒体和细胞核中。预计共有138个差异表达蛋白相互作用。这些结果为油菜叶片在盐胁迫下发生的生理和分子过程提供了全面的认识,揭示了油菜耐盐性的分子机制。
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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
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
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.
盐胁迫是制约世界作物生产的主要非生物胁迫之一。甜菜单体附加系M14是一种独特的耐盐胁迫种质,根系在土壤中直接受到盐胁迫。本研究利用iTRAQ LC-MS/MS定量蛋白质组学技术,报道了M14植株在0、200和400 mM NaCl处理下根膜蛋白质组学的变化。共鉴定出115个差异表达膜蛋白(96个升高,19个降低),bbb2.0显著翻倍变化。这些蛋白主要参与转运、信号转导、应激和防御、能量、蛋白质降解和转录等过程。利用实时荧光定量PCR分析了编码差异膜蛋白的10个基因的转录变化,其中7个基因的转录与蛋白水平呈正相关。这些结果揭示了M14根系对盐胁迫响应的有趣机制,可能在通过基因工程和分子育种提高作物耐盐性方面具有潜在的应用价值。
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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
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
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).
数据共享对开放科学至关重要,资助组织和期刊经常要求数据共享。NCI开发了蛋白质组学数据共享(PDC),作为癌症研究数据共享的一部分,这是一个允许用户共享、分析和存储结果的基础设施,利用云的存储和计算资源。迄今为止,各种数据共享中可用的大多数数据都是由NCI资助的大型多机构研究项目提交的,这些项目由来自多个科学学科的专家团队组成。在这里,我们描述了我们的经验,并总结了分享一组蛋白质组学和相关生物标本数据的推荐最佳实践,以及在学术医疗中心核心设施中使用肺腺癌患者样本进行的小规模蛋白质组学研究的分析结果。以本文描述的方式映射和存储数据将用户数据与公共数据模型和社区标准相协调,从而可以与PDC中其他高价值的癌症研究一起查看数据。可用性:数据、元数据、多肽和蛋白质鉴定协议可在PDC获得。(https:// pdc.cancer.gov / pdc /研究/ PDC000231)。
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引用次数: 0
Overview of Neuroproteomics 神经蛋白质组学综述
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E127
S. Eswaran
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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
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.549
M. Shah
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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
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.E125
Paul Anderson
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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
Pub Date : 2021-01-01 DOI: 10.35248/0974-276X.21.14.539
Michal Ben
{"title":"A Commentary on Plasma Membrane Derived Extracellular Vesicles(PMEVs)","authors":"Michal Ben","doi":"10.35248/0974-276X.21.14.539","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.539","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961525","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
期刊
Journal of proteomics & bioinformatics
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