蛋白质组学研究方法学进展

蛋白质组学是针对蛋白质组研究的一门新兴学科,近年来发展迅速,其相应方法学也取得很大进 展。文章介绍了近年来差异表达蛋白质研究的方法学进展,包括双向凝胶电泳技术、凝胶内差别电泳、同 位素亲和标签技术、蛋白质芯片和蛋白质组的多维液相分离-质谱分析等方法。     

人晶状体上皮细胞蛋白质组的双向电泳和质谱鉴定

目的： 建立人晶状体上皮细胞蛋白质组研究体系，探讨双向电泳和质谱鉴定技术在人晶状体上皮细胞蛋白质组研究中的作用。 方法: 体外培养人晶状体上皮细胞株，用两种不同方法提取总蛋白，进行固相pH梯度(IPG)等电聚焦双向凝胶电泳，凝胶通过GS-800扫描仪（Bio-Rad）获取图像并使用PDQuest专业图像分析软件分析。在此基础之上，胰酶消化蛋白质斑点并进行质谱分析。 结果: 获得了重复性较好的人晶状体上皮细胞蛋白质组电泳图谱。晶状体蛋白质斑点在等电点pH值为4-7、相对分子质量为17-72 kD之间均有分布。其中高丰度蛋白点主要分布于分子量19-50 kD、PI 5-7范围内。2个蛋白点通过质谱分析和数据库的检索得到了初步的鉴定。 结论: 建立起了一个稳定的分析人晶状体上皮细胞蛋白质组学实验体系；为进一步研究人类晶状体在生理状态及白内障等病理条件下的改变提供了蛋白质组学的研究方法和途径。     

HCV患者外周血单个核细胞蛋白质表达质谱分析

目的:应用比较蛋白质组学的方法分析丙型肝炎患者外周血单个核细胞蛋白质表达模式的变化及寻找丙型肝炎相关生物标记分子,进一步识别鉴定其差异表达蛋白质,分析其对丙型肝炎慢性化机制的意义.方法:应用固相化pH梯度双向凝胶电泳(2-DE)分离健康者(10)及HCV患者(28)PBMC的总蛋白质,凝胶银染显色后,PDQuest图像分析软件进行比较分析、识别差异表达的蛋白质,应用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)获得差异蛋白点的肽质指纹图谱,通过SWISS-PROT数据库鉴定蛋白质.结果:得到两张2-DE图谱,HCV患者及健康者PBMC凝胶的蛋白质点数分别为625及614;初步筛选出HCV患者与健康者存在明显差异的12个蛋白点,经质谱分析,初步鉴定了10种蛋白质.这些差异蛋白质包括病毒蛋白、蛋白质合成与分解、三大代谢相关酶类、细胞结构相关蛋白质以及信号转导相关蛋白质.结论:应用2-DE及MALDI-TOF-MS方法建立了HCV患者PBMC双向凝胶电泳图谱,分离并初步鉴定了10种与HCV感染相关的差异表达的蛋白质,为研究HCV慢性化相关机制提供新的线索.     

蛋白质组学在肺癌研究中的应用进展

蛋白质组学(proteomics)指的是在大规模水平上研究细胞内动态变化的蛋白质的翻译后修饰、组成与表达水平,探究蛋白质之间的相互作用,揭示蛋白质功能与细胞活动规律的学科.蛋白质组学技术主要包括蛋白质的分离、质谱鉴定及生物信息学等技术.     

蛋白质组学研究

目前 ,蛋白质组学已从早期用双向电泳和凝胶蛋白鉴定进行蛋白质表达谱研究扩展到蛋白质研究的几乎所有方面 ,如蛋白质相互作用、翻译后修饰、蛋白质结构和蛋白质胞内移位等 ,可以理解为大规模研究蛋白质相关问题的学科     

脑瘤患者脑脊液肿瘤相关蛋白的蛋白质组学初步研究

通过比较脑肿瘤患者和正常人脑脊液的二维凝胶电泳图谱（two-dimensional electrophoresis,2DE）,并对差异蛋白进行质谱鉴定,以寻找肿瘤特异脑脊液蛋白。以脑肿瘤患者和正常人的脑脊液为研究对象,采用固相pH梯度（immobilized pH gradient,IPG）2DE分离总蛋白质,凝胶经银染显后,用ImageMaster2D图像分析软件进行比较分析、识别差异表达的蛋白质。结果得到肿瘤患者脑脊液蛋白点924个,正常脑组织蛋白点507个,匹配512个,匹配率分别为55．4％和84．3％,去冗余后发现,有35个蛋白点只在脑肿瘤患者脑脊液图谱中出现。肿瘤患者脑脊液和正常对照脑脊液双向电泳图谱有明显差别,但是本实验尚未对这些差异蛋白进行质谱鉴定,所以未找出肿瘤特异蛋白。     

胆囊癌组织的蛋白质组研究

目的: 通过分离并鉴定胆囊癌和胆囊良性组织的差异表达蛋白质,以发现可能用于早期诊断的胆囊癌肿瘤标志物。方法: 提取人胆囊癌和胆囊良性组织的总蛋白质,用双向电泳分离蛋白并进行比较。选择在胆囊癌组织中明显差异表达的蛋白点,行质谱分析。结果: 获得了分辨率和重复性均很好的凝胶蛋白图谱。对筛选出的在胆囊癌组织中明显差异表达的46个蛋白点,共有17个蛋白点被成功鉴定,其中在胆囊癌组织中高表达的为9个,低表达的为8个。结论: 胆囊癌组织相对于胆囊良性组织蛋白存在明显的差异,通过蛋白质组学方法筛选并鉴定出的这些蛋白质可能成为用于胆囊癌早期诊断和治疗的分子靶点。     

催乳素在Jurkat细胞中信号传导分子的蛋白质组分析

目的：利用蛋白质组学分析催乳素（PRL）在人T淋巴白血病细胞株JurkatD1．1细胞中所激活的信号传导分子。方法：应用重组人催乳素（rhPRL）刺激JurkatD1．1细胞。利用磷酸化金属亲和层析法（PMAC）和免疫沉淀法（IP）富集磷酸化蛋白，单向凝胶电泳（1DE）或者双向凝胶电泳（2DE）分离磷酸化蛋白。分析不同组的凝胶，获取有差异的蛋白质条带和斑点。质谱分析并与蛋白质数据库进行匹配鉴定。结果：PMAC法获取的磷酸化蛋白用1DE分离，胶扫描分析发现对照组和rhPRL刺激组之间存在五条明显差别的条带，其中三条条带在rhPRL刺激组，两条在对照组。质谱分析并与数据库匹配，成功鉴定刺激组中一条条带的蛋白质，为热休克蛋白90（Hsp90）。IP法获取的磷酸化蛋白，经过2DE分离，胶扫描分析后，挖取rhPRL刺激组凝胶的九个蛋白质点。质谱分析并与数据库匹配，成功鉴定三个斑点的蛋白质分别是核内受体辅助抑制因子2变异体、半乳糖-1-磷酸尿苷酰转移酶和锌指蛋白ZIM3。结论：催乳素上调磷酸化热休克蛋白90（Hsp90），Hsp90可能参与催乳素的信号传导。催乳素信号分子调节目的基因的表达可能有核内受体辅助抑制因子2变异体和锌指蛋白ZIM3的参与。     

系统性红斑狼疮患者血清蛋白质组学研究

目的 运用蛋白质组学的方法,分析正常人及SLE患者血清蛋白质的差异表达,寻找与SLE疾病发病机制相关的蛋白质.方法 分别收集健康人及SLE患者血清各9例,同组血清等量混合,用试剂盒除去血清中的白蛋白和免疫球蛋白,再经除盐浓缩后,将血清样品采用固相pH梯度（IPG）双向凝胶电泳（2-DE）分离正常人及SLE患者血清的总蛋白质.凝胶经考马斯亮蓝染色显色后,利用Analysis2d软件对获得的蛋白图谱进行分析,寻找差异表达的蛋白质,利用基质辅助激光解析电离飞行时间质谱（MALDI-TOF-MS）进行鉴定,分析差异蛋白点.结果 对照组凝胶共检出蛋白点648个,患者组检出639个.对照组凝胶蛋白点匹配率84.5％,患者组凝胶蛋白点匹配率82.5％.通过比较分析,差异表达蛋白质点数为92个,有52个蛋白点在SLE患者组表达上调,40个表达下调,有14个点的表达水平在组间差异有统计学意义,质谱鉴定共鉴定5个蛋白质.通过文献研究显示,我们鉴定的部分蛋白在SLE的发病机制中起潜在的作用.结论 在SLE患者血清中存在着差异血清蛋白质,这些蛋白质可能是SLE发病的内在因素,并且在SLE的疾病发展过程中发挥重要作用,可能作为新的血清标志物和潜在的自身抗原.     

肺腺癌和癌旁组织蛋白质表达谱差异的研究

通过比较肺癌患者癌组织和癌旁组织的二维凝胶电泳图谱(two-dimensional electrophoresis,2DE),以寻找肺癌相关蛋白、肺癌患者癌组织和癌旁组织,采用固相pH梯度(immobilized pH gradient,IPG)2DE分离总蛋白质,凝胶经银染显后,ImageMaster 2D图像分析软件进行比较分析、识别差异表达的蛋白质并进行质谱鉴定获取肺癌相关蛋白信息。结果分析得到肺癌组织蛋白点709个,癌旁组织蛋白点722个,选择表达量差异达3倍以上的40个,进行胶内酶解,基质辅助电离解析飞行时间质谱(MALDI TOF MS)获得肽质量指纹图谱(PMF),搜寻蛋白质数据库,得到7个肺癌标志物的候选蛋白,但这些差异蛋白点在肺癌发生发展中的作用需要进一步研究。     

突触蛋白质组学分析中双向电泳技术的优化

背景：双向电泳是突触蛋白质组学分析中最流行最通用的蛋白质分离方法之一。但文献中突触蛋白双向电泳对线性固相pH梯度(immobilized pH gradients,IPG)胶条和十二烷基磺酸钠聚丙烯酰胺凝胶电泳(sodium dodecyl sulfate-polyacrylamide gel electroph-oresis,SDS-PAGE)浓度的选择很多,尚未见统一标准。 目的：对突触蛋白双向电泳的IPG胶条和SDS-PAGE凝胶浓度进行优化,以获得高质量的突触蛋白双向电泳图谱。 方法：以大鼠海马突触蛋白为试材,比较pH 5.0-8.0与pH 3.0-10.0线性IPG胶条,线性与非线性pH 3.0-10.0 IPG胶条,以及单一浓度10%与12% SDS-PAGE对双向电泳的影响。此外,还使用计算机检索了1989至2013年中国知网及PubMed数据库中关于突触蛋白双向电泳的文献,对文献中选择的IPG胶条、SDS-PAGE凝胶浓度进行了统计和评价,并总结了突触蛋白在不同pH值IPG胶条和不同浓度SDS-PAGE凝胶的双向电泳图谱上的分布特征。 结果与结论：结果表明,使用pH 3.0-10.0的非线性胶条及单一浓度10% SDS-PAGE凝胶进行突触蛋白双向电泳较为适宜,电泳图谱质量好,实验操作便利;同时还推荐合并使用pH 4.0-7.0和pH 6.0-11.0的IPG胶条,以及线性梯度浓度9%-16% SDS-PAGE凝胶,也适用于突触蛋白双向电泳分析。 中国组织工程研究杂志出版内容重点：组织构建;骨细胞;软骨细胞;细胞培养;成纤维细胞;血管内皮细胞;骨质疏松;组织工程全文链接：     

Polygalacturonase (pectinase), a new oilseed rape allergen

BACKGROUND: Type I hypersensitivity to rapeseed pollen allergens was described as the result of a cross-sensitization with various pollens that could constitute an aggravating factor in birch or grass pollen allergies. Recently, a few rapeseed pollen allergens were described. The aim of the present work was to identify new rapeseed pollen allergens by using two-dimensional gel analysis, microsequencing, and mass spectrometry. METHODS: Water extractable proteins from oilseed rape pollen or stamen were separated by two-dimensional gel electrophoresis. The proteins were then electroblotted onto a nitrocellulose (NC) sheet. The NC sheets were successively incubated with (1) individual human sera pre-selected for their immunoglobulin E (IgE) reactivity to rapeseed pollen proteins, (2) alkaline phosphatase (AP)-conjugated goat anti-human IgE and (3) AP substrate. The allergens localized by this method were then identified by microsequencing and MALDI-TOF mass spectrometry analysis. RESULTS: Of the 18 sera studied, five recognized a wide multispot zone with a molecular mass around 43 kD and pIs between 6.5 and 8.5. The results obtained with two representative sera are shown. From this zone, two isoforms of the polygalacturonase enzyme were identified by microsequencing. Confirmation was obtained through MALDI-TOF mass spectrometry analysis. CONCLUSION: The present results allow the identification of a new rapeseed allergen that can be the main allergen for some patients.     

Human neuronal encoding of English syntactic violations as revealed by both L1 and L2 speakers

Glycosylation influences the biological activity of proteins and affects their folding and stability. Because aberrant glycosylation is associated with Alzheimer's disease (AD), we applied proteome analysis together with Pro-Q Emerald 300 glycoprotein staining to investigate changes in glycosylated cytosolic proteins in AD and control brain. Frontal cortex proteins from 10 AD patients and 7 non-demented controls were subjected to separation by two-dimensional gel electrophoresis and subsequently stained with carbohydrate-specific Pro-Q Emerald 300 dye. Changes in glycosylation of separated proteins were quantified, and proteins of interest identified by mass spectrometry. Approximately 30% of all detectable proteins in the human frontal cortex appeared glycosylated, including heat shock cognate 71 stress protein and beta isoform of creatine kinase. The glycosylation of collapsin response mediator protein 2 (CRMP-2) and an unknown protein was reduced in AD, while the glycosylation of glial fibrillary acidic protein was increased. CRMP-2 regulates the assembly and polymerization of microtubules and is associated with neurofibrillary tangles in AD. Aberrant glycosylations in AD may help understand the mechanisms of neurodegenerative diseases.     

蛋白质组学技术鉴定吉兰-巴雷综合征患者血清急性期反应蛋白的表达

背景：吉兰-巴雷综合征患者血液中存在与发病有关的抗体、补体和细胞因子,以蛋白质组学技术分离鉴定这些标志蛋白,可为寻找新的药物靶标提供依据。 目的：以蛋白质组技术比较吉兰-巴雷综合征患者与正常对照组血清的差异表达蛋白。 方法：采集确诊的吉兰-巴雷综合征患者和正常者血清各30例,提取血清蛋白质以固相pH梯度等电聚焦为第一向,SDS-PAGE垂直电泳为第二向进行双向电泳,图象分析软件Imagemaster 2D分析电泳图谱,MALDI-TOF/TOF串联质谱鉴定差异表达蛋白。 结果与结论：在吉兰-巴雷综合征患者与正常者中24种蛋白质的表达量显著不同,其中α-2-巨球蛋白,血浆铜蓝蛋白,血清淀粉样P物质,丛生蛋白,抗糜蛋白酶,触珠蛋白,血红素蛋白,α-1-抗胰蛋白酶,血清转铁蛋白等9种蛋白质被鉴定为急性期反应蛋白。结果说明吉兰-巴雷综合征患者血清中急性期反应蛋白表达量发生了明显变化,加深了对吉兰-巴雷综合征发病分子机制的理解。     

Analysis of the Proteomic Profiling of Brain Tissue in Alzheimer's Disease

In proteome analysis, it is necessary to separate proteins as a first step prior to characterization. Thus, the overall performance of the analysis depends strongly on the separation tool, which is usually two-dimensional electrophoresis (2DE). We have utilized 2DE to begin characterization of the complex pathologic processes in Alzheimer''s disease (AD). In the present study, we show how a reliable 2-DE database of brain proteins in Alzheimer''s disease was created, improving reproducibility by using an immobilized pH gradient (IPG) for the first dimension gel electrophoresis. The recent progress in this field, and future prospects in this area are also discussed. Preparation of brain proteins into a suitable solubilized state enabled us to separate over 1000 well-defined protein spots in each 2-DE. A comparison of the density of the spots identified on the reference map between the AD and control group, showed that 5 protein spots were significantly increased, 28 spots were significantly decreased and 7 spots were specifically detected in AD. Two spots among those significantly increased and one spot among those significantly decreased were identified as GFAP related. It is hoped that comparative studies to identify, quantitate, and characterize the proteins differentially expressed in normal brain versus diseased brain will give insight into the mechanisms of pathogenesis and allow the development of a strategy to control both the etiology and course of the diseases.     

结肠癌的蛋白质组学研究

目的： 通过比较结肠癌组织与正常结肠组织的蛋白质组表达差异，寻找结肠癌相关的蛋白质，选择敏感的分子标志物。方法： 运用蛋白质组学技术，对8例结肠癌患者的结肠癌组织和正常结肠组织进行胶内差异双向电泳（2-D），选择差异表达超过2倍的蛋白质进行MALDI-TOF质谱分析和生物学信息分析。结果： 成功建立结肠癌和正常结肠组织的双向凝胶电泳图谱，结肠癌组织和正常组织凝胶电泳图谱中平均蛋白质斑点数分别为3289和3066，其中表达差异超过2倍的斑点共有31个，质谱分析和数据库检索共鉴定出18种蛋白质，包括keratin 8、S100A6、protein disulfide isomerase等。从功能分析，这些差异蛋白质与癌细胞的发生、增殖、分化、转移等相关。结论： 蛋白质组学能很好地显示结肠癌组织与正常结肠组织间的蛋白质表达差异，本研究鉴定的18种差异蛋白质有可能为研究结肠癌的生物学行为提供新的分子标记物。     

Proteome studies of CSF in AD patients

Proteins in cerebrospinal fluid (CSF) may often serve as indicators of neurodegenerative diseases, and are a rich source for biomarker discovery. However, a large dynamic range of proteins in CSF makes the analysis very challenging because high abundant proteins tend to mask those of lower abundance. Therefore, advances in the proteomic analysis had to be applied in the screen for new specific biomarkers for Alzheimer's disease (AD). In this study, we have summarised the studies regarding two-dimensional gel electrophoresis (2-DE), and surface enhanced laser desorption/ionisation mass spectrometry (SELDI) technology that have been used in CSF of AD patients. Many proteins have shown to be altered in CSF of AD patients compared to controls, by using a protein pattern, from 2-D gel analysis or from SELDI analysis. Several studies show that the use of a panel of biomarkers derived from proteomic analysis is an advantageous way to distinguish AD from normal, and other dementia subjects.     

凡纳滨对虾新过敏原烯醇化酶的鉴定

目的：鉴定凡纳滨对虾分子量为47 kD过敏原的性质。方法：采用丙酮沉淀法提取凡纳滨对虾总蛋白,通过SDS-PAGE、11例虾过敏患者血清IgE的Western blot。分析凡纳滨对虾中过敏原组份,运用基质辅助激光解析串联飞行时间质谱仪(Matrix-Assisted laser desorption ionization/time of flight mass spectrometry,MALDI-TOF/TOF-MS)鉴定凡纳滨对虾47 kD未知过敏原组分。结果：通过 SDS-PAGE电泳证明所提取的凡纳滨对虾总蛋白组分完全。Western blot 结果显示,凡纳滨对虾至少有14种与阳性血清反应的组分,其中,55%的虾过敏患者IgE与分子量为47 kD的蛋白分子发生特异性反应,质谱分析结果显示47 kD蛋白为烯醇化酶。结论：烯醇化酶是凡纳滨对虾的一种新的过敏原。     

Proteomic profiling and neurodegeneration in West-Nile-virus-infected neurons

West Nile virus, a mosquito-borne flavivirus, is a human, equine, and avian pathogen. High-resolution two-dimensional differential-gel electrophoresis (2D-DIGE) was used to characterize protein expression in primary rat neurons and to examine the proteomic profiling to understand the pathogenesis of West-Nile-associated meningoencephalitis. Three pH ranges, 3-10, 4-7, and 5-6, were used to analyze the protein spots. The proteins are labeled with fluorescent dyes Cy3 and Cy5 before being separated on the basis of charge and size respectively on a two-dimensional platform. About 55 proteins showed altered expression levels. These were then subsequently digested and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis using peptide mass fingerprinting and database searching. These cellular proteins could represent distinct roles during infection related to apoptosis. Our findings show that two-dimensional differential gel electrophoresis combined with mass spectrometry is a powerful approach that permits the identification of proteins whose expression was altered due to West Nile virus infection.