质谱技术及其在后基因组时代中的应用

蛋白质组学的建立开辟了功能基因组学研究的新领域,为研究蛋白质水平的生命活动展现了更为崭新的思路和广阔的前景.质谱技术能准确测量肽和蛋白质的相对分子质量、氨基酸序列及翻译后修饰,成为连接蛋白质与基因的重要技术.质谱技术联合蛋白质组学多角度、深层次探索生命系统分子本质成为现阶段生命科学研究领域.简要综述了肽和蛋白质等生物大分子质谱分析的原理、方式和应用,并对其发展前景做出展望.     

生物质谱与蛋白质组学

蛋白质组学是后基因组学时代最受关注的研究领域之一,其核心的鉴定技术——生物质谱近年来在仪器设计以及鉴定通量、分辨率和灵敏度等各方面均有质的飞跃,促进了蛋白质表达谱作图、定量蛋白质组分析、亚细胞器蛋白质组作图、蛋白质翻译后修饰以及蛋白质相互作用等蛋白质组研究各个领域的飞速发展。本综述了生物质谱技术的最新进展,及其在蛋白质组学研究中的应用。     

蛋白质组学研究技术及其在植物抗渗透胁迫研究中的应用

蛋白质组学是功能基因组学研究的热点领域之一。该文介绍了蛋白质组学的基本的和新兴的研究技术方法如蛋白质组样品的制备、双向凝胶电泳、生物质谱技术、蛋白质芯片技术、酵母双杂交系统和生物信息学等,以及蛋白质组学技术在植物抗干旱、盐渍等渗透胁迫研究中的应用。     

蛋白质组学技术及其在心血管疾病研究中的应用

蛋白质组学是旨在研究蛋白质表达谱和蛋白质与蛋白质之间相互作用的新的领域。蛋白质组学的研究必须依赖高通量、自动化程度很高的技术。双向电泳、液相色谱和生物质谱技术的发展推动了蛋白质组学的研究。蛋白质组学为疾病发病机制的研究提供了新的思路和方法 ,本文重点介绍了蛋白质组学技术在心血管疾病研究中的应用     

以胶原蛋白为例浅述古蛋白质组学研究现状与未来*

蛋白质作为参与构建生物体的重要生物大分子,是生物功能与代谢的物质基础,同时蛋白质的序列信息又源自生物的遗传编码信息,因此是认识生物演化本质的重要研究对象。近年来,随着质谱技术的发展,获取生物化石中的古蛋白质序列信息不再遥不可及,这为在形态学与DNA序列信息缺乏的条件下对古生物的认识提供了一条新途径。胶原蛋白(Collagen)在动物骨骼中极为丰富,又因为其特殊的结构,易于在化石中保存,故已成为古蛋白质组学研究的重要对象。本文将以胶原蛋白为例,对古蛋白质组学现有的研究方法与已经取得的研究成果进行总结,并对古蛋白质组学目前面临的挑战与困难及未来研究趋势进行讨论,旨在展示古蛋白质组学的应用潜力,并探讨其在生物演化研究中的意义。     

生物质谱及其在蛋白质组学研究中的应用

生物质谱是蛋白质组学研究必不可少的关键技术。近年来,生物质谱在鉴定通量、分辨率和灵敏度等方面均有质的飞跃,从而促进了蛋白质组研究各个领域的飞速发展。本文就生物质谱技术的原理、技术和仪器发展现状,及其在蛋白质组学研究中的应用进展作一简要的综述。     

蛋白质组学研究中的双向电泳技术

蛋白质组学研究已经成为后基因组时代的研究热点,其两大支柱是双向凝胶电泳技术和生物质谱技术。尽管双向电泳技术近几年已经取得了突破性进展,是当前蛋白质分离的最常用技术,但其本身还有一些难以克服的问题。随着质谱技术的快速发展,双向电泳逐渐成为蛋白质组学研究的瓶颈。本综述双向电泳主要技术步骤的现状、存在问题及其改进方向。     

基于电感耦合等离子体质谱的蛋白质定量技术研究进展

综述了ICP-MS法应用于蛋白质定量技术方面的研究进展.蛋白质定量研究已成为蛋白质组学研究领域的热点,它是解析生物体蛋白质功能的重要途径.基于同位素标记和生物质谱分析技术是蛋白质定量最常用的方法之一,近年来,随着质谱技术的发展,电感耦合等离子体质谱(ICP-MS)技术成为元素测量的重要手段,这使其在蛋白质定量中具一定的应用前景.     

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。     

蛋白质组学相关概念与技术及其研究进展

随着后基因组时代的到来,蛋白质组学得到了空前的发展。包括蛋白质组、蛋白质组学、功能蛋白质组学和结构基因组学等新的概念和学科不断涌现,并相应改进和发燕尾服了许多新的技术和研究手段,如双向凝胶电泳、生物质谱、生物传感芯片质谱、蛋白质芯片、和生物信息学等。     

Challenges in mass spectrometry-based proteomics

During the last decade, protein analysis and proteomics have been established as new tools for understanding various biological problems. As the identification of proteins after classical separation techniques, such as two-dimensional gel electrophoresis, have become standard methods, new challenges arise in the field of proteomics. The development of "functional proteomics" combines functional characterization, like regulation, localization and modification, with the identification of proteins for deeper insight into cellular functions. Therefore, different mass spectrometric techniques for the analysis of post-translational modifications, such as phosphorylation and glycosylation, have been established as well as isolation and separation methods for the analysis of highly complex samples, e.g. protein complexes or cell organelles. Furthermore, quantification of protein levels within cells is becoming a focus of interest as mass spectrometric methods for relative or even absolute quantification have currently not been available. Protein or genome databases have been an essential part of protein identification up to now. Thus, de novo sequencing offers new possibilities in protein analytical studies of organisms not yet completely sequenced. The intention of this review is to provide a short overview about the current capabilities of protein analysis when addressing various biological problems.     

Eicosanomics: targeted lipidomics of eicosanoids in biological systems

Recent advancements in mass spectrometry, especially the development of electrospray tandem mass spectrometry (ESI/LC/MS2) and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI/TOF), have greatly facilitated analysis of complex biomolecules. It has now become possible to profile, in relatively short periods of time, large multicomponent groups of compounds biosynthesized by biological systems. The efficiency and accuracy of analysis have led to the development of new concepts of mass spectrometric profiling, mapping, and imaging. Profiling of proteins in biological material (proteomics) has become a widely accepted strategy for identification of mechanisms involved in the biochemistry of disease processes, and has become a novel tool for unraveling new drug targets. Evolution of proteomics has relied on ESI/LC/MS2 and MALDI/TOF, techniques that are also useful in the novel area of quantitative proteomics.     

Application of Mass Spectrometry in Proteomics

Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.     

Towards the analysis of protein species: an overview about strategies and methods

The deciphering of the relationship between function and exact chemical composition of a defined protein species in the context of the proteome is one of the major challenges in proteomics and molecular cell physiology. In the Special Issue of Amino Acids about the analysis of protein species current approaches are reviewed and new methods described focusing on the investigation of protein species. On the basis of the articles in this Special Issue it can be summarized that first important and promising steps towards the comprehensive analysis of protein species have been done. It is already possible to obtain full (100%) sequence coverage of proteins by mass spectrometry, if the amount of proteins available for their analysis allows their proteolytic degradation by more than one protease and the subsequent mass spectrometric analysis of the resulting peptides. Employing affinity chromatography helps to analyse proteins with defined post-translational modifications thus opening a targeted view on e.g. the phosphoproteome. In the future the aim to identify the exact chemical composition including not one but every posttranslational modification and complete sequence coverage on the protein species level should be achievable with further progress in sample preparation techniques, especially concerning separation techniques on the protein level, mass spectrometry and algorithms for mass spectrometric data processing. For determining the function of defined protein species a closer cooperation between cell biologists and proteomics experts is desirable.     

利用串联质谱鉴定氨基酸突变的生物信息学算法

氨基酸突变能够改变蛋白的结构和功能,影响生物体的生命过程.基于串联质谱的鸟枪法蛋白质组学是目前大规模研究蛋白质组学的主要方法,但是现有的质谱数据鉴定流程为了提高鉴定结果的灵敏度往往会有意压缩数据库中的氨基酸突变信息.因此,如何挖掘数据中的氨基酸突变信息成为当前质谱数据鉴定的一个重要部分.当前应用于氨基酸突变鉴定的串联质谱鉴定方法大致可以分为3大类:基于序列数据库搜索的方法、基于序列标签搜索的算法以及基于图谱库搜索的算法.本文首先详细介绍了这3种氨基酸突变鉴定算法,并分析了各种方法的特点和不足,然后介绍了氨基酸突变鉴定的研究现状和发展方向.随着基于串联质谱的蛋白质组学的不断发展,蛋白序列中的氨基酸突变信息将被更好地解析出来,从而得以深入探讨由氨基酸突变引起的蛋白结构和功能改变,为揭示氨基酸突变的生物学意义奠定基础.     

Schizophrenia proteomics: biomarkers on the path to laboratory medicine?

Over two million Americans are afflicted with schizophrenia, a debilitating mental health disorder with a unique symptomatic and epidemiological profile. Genomics studies have hinted towards candidate schizophrenia susceptibility chromosomal loci and genes. Modern proteomic tools, particularly mass spectrometry and expression scanning, aim to identify both pathogenic-revealing and diagnostically significant biomarkers. Only a few studies on basic proteomics have been conducted for psychiatric disorders relative to the plethora of cancer specific experiments. One such proteomic utility enables the discovery of proteins and biological marker fingerprinting profiling techniques (SELDI-TOF-MS), and then subjects them to tandem mass spectrometric fragmentation and de novo protein sequencing (MALDI-TOF/TOF-MS) for the accurate identification and characterization of the proteins. Such utilities can explain the pathogenesis of neuro-psychiatric disease, provide more objective testing methods, and further demonstrate a biological basis to mental illness. Although clinical proteomics in schizophrenia have yet to reveal a biomarker with diagnostic specificity, methods that better characterize the disorder using endophenotypes can advance findings. Schizophrenia biomarkers could potentially revolutionize its psychopharmacology, changing it into a more hypothesis and genomic/proteomic-driven science.     

Virion proteomics of large DNA viruses

Large DNA viruses normally have complex structures with many of protein components derived from both viral and host origins. The development in proteomics, especially mass spectrometry identification techniques provide powerful tools for analyzing large viruses. In this review, we have summarized the recent achievements on proteomic studies of large DNA viruses, such as herpesvirus, poxvirus, nimavirus and baculoviruse. The proteomics of baculovirus occlusion-derived virions (ODV) were emphasized. Different mass spectrometry techniques used on ,carious baculoviruses were introduced, and the identified structurally associated proteins of baculoviruses are summarized.     

Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data

In recent years, proteomics research has gained importance due to increasingly powerful techniques in protein purification, mass spectrometry and identification, and due to the development of extensive protein and DNA databases from various organisms. Nevertheless, current identification methods from spectrometric data have difficulties in handling modifications or mutations in the source peptide. Moreover, they have low performance when run on large databases (such as genomic databases), or with low quality data, for example due to bad calibration or low fragmentation of the source peptide. We present a new algorithm dedicated to automated protein identification from tandem mass spectrometry (MS/MS) data by searching a peptide sequence database. Our identification approach shows promising properties for solving the specific difficulties enumerated above. It consists of matching theoretical peptide sequences issued from a database with a structured representation of the source MS/MS spectrum. The representation is similar to the spectrum graphs commonly used by de novo sequencing software. The identification process involves the parsing of the graph in order to emphasize relevant sections for each theoretical sequence, and leads to a list of peptides ranked by a correlation score. The parsing of the graph, which can be a highly combinatorial task, is performed by a bio-inspired algorithm called Ant Colony Optimization algorithm.     

Review of application of mass spectrometry for analyses of anterior eye proteome

Proteins have important functional roles in the body, which can be altered in disease states. The eye is a complex organ rich in proteins; in particular, the anterior eye is very sophisticated in function and is most commonly involved in ophthalmic diseases. Proteomics, the large scale study of proteins, has greatly impacted our knowledge and understanding of gene function in the post-genomic period. The most significant breakthrough in proteomics has been mass spectrometric identification of proteins, which extends analysis far beyond the mere display of proteins that classical techniques provide. Mass spectrometry functions as a "mass analyzer" which simplifies the identification and quantification of proteins extracted from biological tissue. Mass spectrometric analysis of the anterior eye proteome provides a differential display for protein comparison of normal and diseased tissue. In this article wepresent the key proteomic findings in the recent literature related to the cornea, aqueous humor, trabecular meshwork, iris, ciliary body and lens. Through this we identified unique proteins specific to diseases related to the anterior eye.     

Protein-protein interactions in plants

The study of protein-protein interactions (PPIs) is essential to uncover unknown functions of proteins at the molecular level and to gain insight into complex cellular networks. Affinity purification and mass spectrometry (AP-MS), yeast two-hybrid, imaging approaches and numerous diverse databases have been developed as strategies to analyze PPIs. The past decade has seen an increase in the number of identified proteins with the development of MS and large-scale proteome analyses. Consequently, the false-positive protein identification rate has also increased. Therefore, the general consensus is to confirm PPI data using one or more independent approaches for an accurate evaluation. Furthermore, identifying minor PPIs is fundamental for understanding the functions of transient interactions and low-abundance proteins. Besides establishing PPI methodologies, we are now seeing the development of new methods and/or improvements in existing methods, which involve identifying minor proteins by MS, multidimensional protein identification technology or OFFGEL electrophoresis analyses, one-shot analysis with a long column or filter-aided sample preparation methods. These advanced techniques should allow thousands of proteins to be identified, whereas in-depth proteomic methods should permit the identification of transient binding or PPIs with weak affinity. Here, the current status of PPI analysis is reviewed and some advanced techniques are discussed briefly along with future challenges for plant proteomics.