大鼠海马的表达蛋白质组学实验研究

目的：用蛋白质组学方法初步分析大鼠海马蛋白质的表达。方法：提取大鼠海马蛋白质样品后,用双向凝胶电泳对其分离,经考马斯亮蓝染色后,产生大鼠海马蛋白质双向凝胶电泳图谱。从凝胶上切割分离的蛋白质,经胰蛋白酶胶内酶解,通过基质辅助激光解吸／电离飞行时间质谱（MALDI-TOF-MS）对酶解后的肽段进行分析。根据肽段质谱数据,经数据库（NCBI）检索,对蛋白质进行鉴定。结果：鉴定了37种具有明确功能的蛋白质,它们分别属于代谢酶、细胞骨架蛋白、热休克蛋白、抗氧化蛋白、信号传导蛋白、蛋白酶体相关蛋白、神经元特异蛋白及神经胶质蛋白。另外,鉴定了3种未知功能蛋白。结论：为建立大鼠海马蛋白质组数据库提供必要的资料,为在大鼠模型上研究神经疾病发病机理奠定基础。     

Type 1 diabetes: entering the proteomic era

During the last decade, a major breakthrough in the field of proteomics has been achieved. This review describes available techniques for proteomic analyses, both gel and non-gel based, particularly concentrating on relative quantification techniques. The principle of the different techniques is discussed, highlighting the advantages and drawbacks of recently available visualization methods in gel-based assays. In addition, recent developments for quantitative analysis in non-gel-based approaches are summarized. This review focuses on applications in Type 1 diabetes. These mainly include proteomic studies on pancreatic islets in animal models and in the human situation. Also discussed are mass spectrometry-based studies on T-cells, and studies on the development of diagnostic markers for diabetic nephropathology by capillary electrophoresis coupled to mass spectrometry.     

蛋白质组学技术在感染研究中的应用

蛋白质组学的目标在于阐明特定生物体、组织、细胞或亚细胞结构中全部蛋白质的表达模式和功能模式,其技术平台由高通量的蛋白质分离技术、鉴定技术和生物信息学组成。在许多研究领域,蛋白质组学技术为阐明疾病过程和生命现象的分子机制提供了全面、网络和动态的蛋白质组信息。感染是重要的基本致病因素之一,蛋白质组学的研究策略和技术方法有利于快速分离鉴定病原体蛋白质组、宿主免疫细胞蛋白质组、感染相关蛋白、疫苗候：选抗原蛋白、生物标志物和药物靶标,从而明显加快病原体、宿主反应、感染发病机制以及感染预防、诊断和治疗等相关研究的进程。     

大鼠不同发育时期胰腺相关蛋白的差异表达

探讨大鼠胰腺不同发育时期相关蛋白的差异表达,应用显微技术分离了大鼠孕15.5天,孕18.5天胚胎胰腺和新生鼠及成年鼠的胰腺,提取其蛋白质后,用固相pH梯度双向聚丙烯酰胺凝胶电泳和质谱分析等蛋白质组学方法,得到了4个不同发育时期的蛋白质表达谱.对其中的6个在孕18.5天胚胎胰腺中有高丰度表达,而在成年鼠胰腺中缺失的蛋白质点,4个在成年胰腺中特异表达的蛋白质点, 8个在成年胰腺中表达明显下调的蛋白质点和1个在成年中表达上调的点,进行了肽质量指纹分析和蛋白质鉴定,共获得18个点的肽质量指纹图.经BIOWORK等软件搜索大鼠非冗余蛋白质数据库来鉴定其身份,发现其中7个点为大鼠甲胎蛋白（AFP）、5个点为胰脂酶相关蛋白1前体、1个点为微管蛋白β、2个点为蛋白二硫异构酶、1个为FLN29基因产物的类似物、1个为胰蛋白酶V-A前体、1个为过氧化物氧化还原酶4.其中AFP为特异表达于大鼠胚胎期及新生期胰腺的蛋白质,在孕18.5天的胰腺中表达量最高,在成年胰腺中极低表达.对它们的功能和与胚胎胰腺代谢调节功能完善过程的可能关系进行了初步探讨.     

One-dimensional proteomic mapping of human liver cytochromes P450

A method for constructing one-dimensional proteomic maps (1D-PM) based on mass spectrometric identification of proteins from adjacent slices of one-dimensional electrophoregram has been developed. For the proteomic mapping, gel lanes were sectioned into slices less than 0.2 mm thick and each slice was subjected to enzymatic hydrolysis. The resultant mixture of peptide fragments was analyzed by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF) and liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS/MS). Proteins were identified by the mass spectra obtained. Data on peptide fragments and corresponding identified proteins were presented as a 1D-PM. Proteomic maps were constructed by assigning individual proteins to gel slices based on number of matching peptides in a corresponding MS-data. On 1D-PM of human liver microsomal fraction, 18 proteins were identified in the region of 40–65 kDa. These included 12 membrane proteins belonging to the superfamily of cytochromes P450. Pooling of mass spectrometric data, obtained from several adjacent gel slices (molecular zooming) increased sequence coverage of CYP2A (cytochrome P450 family 2A). The maximal coverage of 66% significantly exceeded the level of 48% that could be obtained using one (even the most informative) slice. This method can be applied to the proteomic profiling of membrane-bound proteins.     

磷蛋白组的研究技术及其进展

真核细胞中蛋白质磷酸化是一个重要事件。真核细胞利用可逆的蛋白磷酸化来控制许多细胞过程包括信号转换、基因表达、细胞周期等。磷蛋白组的研究涉及磷蛋白的分离和鉴定 ,磷酸化残基定位和定量分析。由于蛋白质磷酸化是一个动态过程 ,在细胞中磷蛋白含量低 ,磷酸化位点可变 ,且磷酸肽的质谱信号常常会受到抑制 ,所以磷蛋白的分析存在更多的困难。本文介绍了国内外在磷酸蛋白的分离鉴定及定量分析方面的研究技术以及进展情况。目前 ,质谱仍然是核心的鉴定技术 ,寻找更好富集方法是最大的挑战。定量蛋白组学是对蛋白质的差异表达进行精确的定量分析。目前还不存在一种独立的方法可以完成磷蛋白的分离、鉴定 ,以及磷酸位点的定位和定量分析。随着样品分离技术和相关仪器的发展 ,磷酸蛋白快速、准确、全面分析鉴定将能够实现。     

Proteomic tools for cell biology

Acquisition of large bodies of genomic sequence is facilitating the use of global techniques to assay cellular function. DNA microarrays have enabled the measurement of global mRNA levels and are able to detect changes in gene expression between different cellular states. Since much of the regulation of physiolgical processes happens post-translationally, measuring only the mRNA levels gives an incomplete picture. Strategies to assay global expression, localization, or interaction of proteins fall into the emerging field of proteomics, with various combinations of techniques being utilized to separate and identify proteins. In this review, we will present a general overview of the currently available proteomic tools and then give examples of how these tools are being utilized to answer questions in cell biology.     

正常精子和圆头精子差异表达蛋白的分离与鉴定

圆头精子症是一种表现为顶体缺失的男性不育症.为了研究正常精子和圆头精子的蛋白质组成差异,用固相pH梯度双向凝胶电泳和质谱分析等蛋白质组学方法,分离了30份正常和3份圆头精子标本的蛋白质.对其中16个在正常精子中有高丰度表达而在圆头精子中缺失,和1个在圆头精子中表达明显下调的蛋白质点,以及在圆头精子中存在而在正常精子中缺失的蛋白质簇W和点X,进行了肽质指纹分析和蛋白质鉴定,获得8个点的肽质量指纹图,经MS-Fit软件搜索SWISS-PROT数据库来鉴定其身分.发现其中3个点与高尔基体相关、2个点与蛋白酶体相关、2个点为锌指蛋白,对其功能和与圆头精子形成的可能关系进行了初步探讨.     

Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat

The recent introduction of fluorescent two-dimensional difference gel electrophoresis, combined with mass spectrometry, has greatly simplified the analysis and identification of differentially expressed proteins by eliminating intergel variability. In this report, we describe the successful application of this functional proteomics approach to compare protein expression levels in visual cortical area 17 of adult cats and 30-day-old kittens, in order to identify proteins expressed in an age-related fashion. We identified 16 proteins that were more abundantly expressed in kitten striate cortex and 12 proteins with a pronounced expression in adult cat area 17. Among those isolated from kitten area 17 were proteins related to axon growth and growth cone guidance and to the formation of cytoskeletal filaments. Glial fibrillary acidic protein, as identified in adult cat area 17, has been implicated previously in the termination of the critical period for cortical plasticity in kittens. In situ hybridization experiments for two of the identified proteins, glial fibrillary acidic protein and collapsin response mediator protein 5, confirmed and extended their differential expression to the mRNA level. Our findings show that two-dimensional difference gel electrophoresis combined with mass spectrometry is a powerful approach that permits the identification of small protein expression differences correlated to different physiological conditions.     

The Use of Ammonium Formate as a Mobile-Phase Modifier for LC-MS/MS Analysis of Tryptic Digests

A major challenge facing current mass spectrometry (MS)-based proteomics research is the large concentration range displayed in biological systems, which far exceeds the dynamic range of commonly available mass spectrometers. One approach to overcome this limitation is to improve online reversed-phase liquid chromatography (RP-LC) separation methodologies. LC mobile-phase modifiers are used to improve peak shape and increase sample load tolerance. Trifluoroacetic acid (TFA) is a commonly used mobile-phase modifier, as it produces peptide separations that are far superior to other additives. However, TFA leads to signal suppression when incorporated with electrospray ionization (ESI), and thus, other modifiers, such as formic acid (FA), are used for LC-MS applications. FA exhibits significantly less signal suppression, but is not as effective of a modifier as TFA. An alternative mobile-phase modifier is the combination of FA and ammonium formate (AF), which has been shown to improve peptide separations. The ESI-MS compatibility of this modifier has not been investigated, particularly for proteomic applications. This work compares the separation metrics of mobile phases modified with FA and FA/AF and explores the use of FA/AF for the LC-MS analysis of tryptic digests. Standard tryptic-digest peptides were used for comparative analysis of peak capacity and sample load tolerance. The compatibility of FA/AF in proteomic applications was examined with the analysis of soluble proteins from canine prostate carcinoma tissue. Overall, the use of FA/AF improved online RP-LC separations and led to significant increases in peptide identifications with improved protein sequence coverage.     

Proteomic analysis of two functional states of the Golgi complex in mammary epithelial cells

Organellar compartments involved in secretion are expanded during the transition from late pregnancy (basal secretory state) to lactation (maximal secretory state) to accommodate for the increased secretory function required for copious milk production in mammary epithelial cells. The Golgi complex is a major organelle of the secretory pathway and functions to sort, package, distribute, and post-translationally modify newly synthesized proteins and membrane lipids. These complex functions of the Golgi are reflected in the protein complement of the organelle. Therefore, using proteomics, the protein complements of Golgi fractions isolated at two functional states (basal and maximal) were compared to identify some of the molecular changes that occur during this transition. This global analysis has revealed that only a subset of the total proteins is up-regulated from steady state during the transition. Identification of these proteins by tandem mass spectrometry has revealed several classes of proteins involved in the regulation of membrane fusion and secretion. This first installment of the functional proteomic analysis of the Golgi complex begins to define the molecular basis for the transition from basal to maximal secretion.     

Towards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas reinhardtii

Functional proteomics of membrane proteins is an important tool for the understanding of protein networks in biological membranes but structural studies on this part of the proteome are limited. In this study we undertook such an approach to analyse photosynthetic thylakoid membranes isolated from wild-type and mutant strains of Chlamydomonas reinhardtii. Thylakoid membrane proteins were separated by high-resolution two-dimensional gel electrophoresis (2-DE) and analysed by immuno-blotting and mass spectrometry for the presence of membrane-spanning proteins. Our data show that light-harvesting complex proteins (LHCP), that cross the membrane with three transmembrane domains, can be separated using this method. We have identified more than 30 different LHCP spots on our gels. Mass spectrometric analysis of 2-DE separated Lhcb1 indicates that this major LHCII protein can associate with the thylakoid membrane with part of its putative transit sequence. Separation of isolated photosystem I (PSI) complexes by 2-DE revealed the presence of 18 LHCI protein spots. The use of two peptide-specific antibodies directed against LHCI subunits supports the interpretation that some of these spots represent products arising from differential processing and post-translational modifications. In addition our data indicate that the reaction centre subunit of PSI, PsaA, that possesses 11 transmembrane domains, can be separated by 2-DE. Comparison between 2-DE maps from thylakoid membrane proteins isolated from a PSI-deficient (Deltaycf4) and a crd1 mutant, which is conditionally reduced in PSI and LHCI under copper-deficiency, showed the presence of most of the LHCI spots in the former but their absence in the latter. Our data demonstrate that (i) hydrophobic membrane proteins like the LHCPs can be faithfully separated by 2-DE, and (ii) that high-resolution 2-DE facilitates the comparative analysis of membrane protein complexes in wild-type and mutants cells.     

一种适用于质谱分析的简化胶内酶解方法

在常规方法的基础上,设计了一种适于质谱分析的简化胶内酶解方法。改进的步骤包括:(1)通过加大洗涤所用超纯水量、延长涡混时间来强化凝胶洗涤的环节;(2)加入酸化处理来提高胰蛋白酶的活性;(3)在预酶解时不加CaCl_2,减少了酶的自切作用;(4)省略了蛋白质样品脱盐、脱SDS的步骤;(5)直接吸取酶解液进行质谱分析。系统比较该简化酶解法和最新报道的一种酶解方法的质谱鉴定效果,简化法能有效减少酶解后肽段的损失,增加质谱数据库搜索的信息量,得到更可靠的蛋白质鉴定结果。     

蛋白质组学研究中的分离分析技术及其研究进展

在后基因组时代,蛋白质组学成为新的研究热点。蛋白质组学的研究目标是为复杂蛋白质样品建立一个高通量、大规模、自动化的分离分析技术平台,从而实现准确、快速地筛选功能蛋白质。蛋白质的分离分析在蛋白组学研究中起着非常重要的作用。本文主要综述在蛋白质组学研究中二维凝胶电泳、毛细管电泳及其与质谱联用、多维液相分离技术及其与质谱联用和蛋白质芯片等高效分离分析技术的应用研究进展。     

双向凝胶电泳缺陷胶及其原因

双向凝胶电泳是蛋白质组学研究中的关键技术之一,涉及较多的实验步骤和试剂,常出现缺陷胶而导致实验失败。从数千张电泳胶图中选取了21张典型的缺陷胶图,对它们进行了归类和总结,分析和讨论了形成缺陷胶的多种原因,提出了实验改进的方法和注意事项。     

帕金森病患者脑脊液蛋白质组学分析

帕金森病（Parkinson′s disease,PD）是一种中枢神经系统慢性进展性疾病.本研究采用双向凝胶电泳（two-dimensional gel electrophoresis,2-DE）分离脑脊液（cerebrospinal fluid,CSF）蛋白,获得2-DE图谱,通过ImageMaster 2D Elite软件分析寻找两组的差异蛋白点.结果显示,PD患者CSF中有4个蛋白点丰度下降,22个蛋白点丰度上升.还利用电喷雾质谱（electrospray ionization-tandem mass spectrometric,ESI-MS）对差异蛋白点进行鉴定,发现丰度上升的蛋白点有电压依赖性钙通道α2/δ1亚基,结合珠蛋白,β2-微球蛋白和阿朴脂蛋白A-IV前体,丰度下降的蛋白点为转铁蛋白和转甲状腺蛋白.研究发现,PD患者与对照组CSF蛋白质表达有明显差异,对差异蛋白进行质谱鉴定并了解它们的功能,为以后进一步研究他们在PD发病机制和病程进展中的作用奠定基础.