Plant proteome analysis: a 2004-2006 update

Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.     

2014蛋白质组学专刊序言

蛋白质组学研究是后基因组学时代最重要的功能基因组学研究之一,与医学生物学、化学、物理学、信息学以及现代技术等关系十分密切。为了检阅近年来国内外蛋白质组学某些重要研究进展,探索其可能的应用范围,讨论其存在的问题,展望其发展前景,特组织出版"蛋白质组学专刊"。本期专刊包括综述和研究论文两部分,内容主要涉及不同物种(包括人类、哺乳类动物、原核生物、放线菌等)蛋白质组学研究、蛋白质组学重要方法学与技术研究(包括串联质谱分析、尿蛋白膜保存法、定量蛋白质组学分折、meta分析等)和蛋白质组功能与应用研究(包括蜘蛛毒素蛋白质组、磷酸化蛋白质组、卵母细胞和早期胚胎蛋白质组、肝脏纤维化蛋白质组、分枝杆菌耐药的蛋白质组等)。     

Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity

Computationally aided protein identification of mass spectrometry (MS) data has been a challenge for the proteomic community since the field's inception. As the community attempts to address challenges such as computational site assignment of posttranslational modifications (PTMs), selective reaction monitoring data analysis, and the transition of proteomic assays to the clinic a robust framework with defined metrics is essential. The frameworks used for protein identification are currently score based, not hypothesis driven nor deterministic, resulting in a gradation from poor to good but without the ability to recognize when a given tandem MS spectrum has insufficient information in the context of the proteome to be identified. Means of computing deterministic and pseudodeterministic assays have been proposed by both us and others [Sherman, J., McKay, M.J., Ashman, K., Molloy, M.P., Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062; Kiyonami, R., Schoen, A., Prakash, A., Peterman, S., et al., Increased selectivity, analytical precision, and through-put in targeted proteomics. Mol. Cell. Proteomics 2011, 10, M110.002931]. We believe it is crucial to incorporate the complexity of the proteome into the design of the experiment/data analysis upstream and that by doing so proteomic data analysis will become more robust. The seminal paper by Claude Shannon published in 1948 provides the robust mathematical framework now called Information Theory, to achieve this goal. Information Theory defines appropriate metrics for information and complexity as well as means to account for interference, all of which is directly applicable to peptide identification. We attempt to encourage the adoption of Information Theory as a means to ensure that appropriate metrics are used to measure the uncertainty in a peptide identification with or without PTM site assignment.     

种子蛋白质组的研究进展

蛋白质组学是通过对全套蛋白质动态的研究, 来阐明生物体、组织、细胞和亚细胞全部蛋白质的表达模式及功能模式。大量可用的核苷酸序列信息和灵敏高速的质谱鉴定技术, 使得蛋白质组学方法为分析模式植物和农作物的复杂功能开辟了新的途径。目前, 种子蛋白质组研究主要集中在两个方面: 一方面是鉴定尽可能多的蛋白, 以创建种子特定生命时期的蛋白质组参照图谱; 另一方面主要集中在差异蛋白质组, 通过比较分析不同蛋白质组, 以探明关键功能蛋白。该文综述了近年来种子蛋白质组的研究进展, 内容包括种子发育过程中蛋白质组的变化, 与种子休眠/萌发相关的蛋白质组、翻译后修饰蛋白质组、细胞与亚细胞差异蛋白质组以及环境因子对种子蛋白质组的影响; 并对种子蛋白质组研究的热点问题进行了展望。     

Current trends in computational inference from mass spectrometry-based proteomics

Mass spectrometry offers a high-throughput approach to quantifying the proteome associated with a biological sample and hence has become the primary approach of proteomic analyses. Computation is tightly coupled to this advanced technological platform as a required component of not only peptide and protein identification, but quantification and functional inference, such as protein modifications and interactions. Proteomics faces several key computational challenges such as identification of proteins and peptides from tandem mass spectra as well as their quantitation. In addition, the application of proteomics to systems biology requires understanding the functional proteome, including how the dynamics of the cell change in response to protein modifications and complex interactions between biomolecules. This review presents an overview of recently developed methods and their impact on these core computational challenges currently facing proteomics.     

Rejuvenating rice proteomics: facts, challenges, and visions

Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.     

种子蛋白质组的研究进展

蛋白质组学是通过对全套蛋白质动态的研究,来阐明生物体、组织、细胞和亚细胞全部蛋白质的表达模式及功能模式。大量可用的核苷酸序列信息和灵敏高速的质谱鉴定技术,使得蛋白质组学方法为分析模式植物和农作物的复杂功能开辟了新的途径。目前,种子蛋白质组研究主要集中在两个方面：一方面是鉴定尽可能多的蛋白,以创建种子特定生命时期的蛋白质组参照图谱;另一方面主要集中在差异蛋白质组,通过比较分析不同蛋白质组,以探明关键功能蛋白。该文综述了近年来种子蛋白质组的研究进展,内容包括种子发育过程中蛋白质组的变化,与种子休眠/萌发相关的蛋白质组、翻译后修饰蛋白质组、细胞与亚细胞差异蛋白质组以及环境因子对种子蛋白质组的影响;并对种子蛋白质组研究的热点问题进行了展望。     

Is protein overlap in two‐dimensional gels a serious practical problem?

In a recently published article, Campostrini et al. [Proteomics 2005, 5, 2385-2395] raised questions regarding the utility of 2-D gels in proteomics research. We believe that the authors have overlooked several key issues including the dynamic range of protein expression and the sensitivity of the analytical methods used to explore a proteome. We argue that 2-D gels have and will continue to provide meaningful quantitative data when applied to proteomic analysis and that the practical significance of spot overlap has been overstated.     

Plant redox proteomics

In common with other aerobic organisms, plants are exposed to reactive oxygen species resulting in formation of post-translational modifications related to protein oxidoreduction (redox PTMs) that may inflict oxidative protein damage. Accumulating evidence also underscores the importance of redox PTMs in regulating enzymatic activities and controlling biological processes in plants. Notably, proteins controlling the cellular redox state, e.g. thioredoxin and glutaredoxin, appear to play dual roles to maintain oxidative stress resistance and regulate signal transduction pathways via redox PTMs. To get a comprehensive overview of these types of redox-regulated pathways there is therefore an emerging interest to monitor changes in redox PTMs on a proteome scale. Compared to some other PTMs, e.g. protein phosphorylation, redox PTMs have received less attention in plant proteome analysis, possibly due to technical challenges such as with maintaining the in vivo redox states of proteins and the lability of certain PTMs, e.g. nitrosylations, during sample preparation and mass spectrometric analysis. The present review article provides an overview of the recent developments in the emerging area of plant redox proteomics.     

植物蛋白质组学研究若干重要进展

植物蛋白质组学近年来正从定性向精确定量蛋白质组学的方向发展。国际上近两年发表的约160篇研究论文报道了利用不断改进的双向电泳结合生物质谱技术、多维蛋白质鉴定技术, 以及包括双向荧光差异凝胶电泳、15N体内代谢标记、同位素标记的亲和标签、同位素标记相对和绝对定量等在内的第2代蛋白质组学技术, 对植物组织(器官)与细胞器、植物发育过程和植物响应环境胁迫的蛋白质组特征, 以及植物蛋白质翻译后修饰和蛋白质相互作用等方面的研究成果。该文对上述报道进行总结, 综述了2007年以来植物蛋白质组学若干重要问题研究的新进展。     

Proteomics and the dynamic plasma membrane: Quo Vadis?

Quo Vadis: where are you going? Advances in MS-based proteomics have enabled research to move from obtaining the basic protein inventory of cells and organelles to the ability of monitoring their dynamics, including changes in abundance, location and various PTMs. In this respect, the cellular plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma membrane proteome is crucial for understanding fundamental biological processes, disease mechanisms and for finding drug targets. Protein identification, characterization of dynamic PTMs and protein-ligand interactions, and determination of transient changes in protein expression and composition are among the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies required for detailed functional and comparative analysis of the dynamic plasma membrane proteome.     

Proteomic dissection of plant responses to various pathogens

During their growth and development, plants are vulnerable to the effects of a variety of pathogens. Proteomics technology plays an important role in research studies of plant defense mechanisms by mining the expression changes of proteins in response to various biotic stresses. This review article provides a comprehensive overview of the latest developments in international proteomic research on plant biotic stress. It summarizes the methods commonly used in plant proteomic research to investigate biotic stress, analyze the protein responses of plants in adverse conditions, and reviews the applications of proteomics combined with transgenic technology in plant protection.     

The utility of proteases in proteomics,from sequence profiling to structure and function analysis

In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational modifications (PTMs). Trypsin is the gold standard in digesting intact proteins into small-size peptides, which are more suitable for high-performance liquid chromatography (HPLC) separation and tandem MS (MS/MS) characterization. However, protein sequences lacking Lys and Arg cannot be cleaved by trypsin and may be missed in conventional proteomic analysis. Proteases with cleavage sites complementary to trypsin are widely applied in proteomic analysis to greatly improve the coverage of proteome sequences and PTM sites. In this review, we survey the common and newly emerging proteases used in proteomics analysis mainly in the last 5 years, focusing on their unique cleavage features and specific proteomics applications such as missing protein characterization, new PTM discovery, and de novo sequencing. In addition, we summarize the applications of proteases in structural proteomics and protein function analysis in recent years. Finally, we discuss the future development directions of new proteases and applications in proteomics.     

Proteomic databases and tools to decipher post-translational modifications

Post-translational modifications (PTMs) are vital cellular control mechanism, which affect protein properties, including folding, conformation, activity and consequently, their functions. As a result they play a key role in various disease conditions, including cancer and diabetes. Proteomics as a rapidly growing field has witnessed tremendous advancement during the last decade, which has led to the generation of prodigious quantity of data for various organisms' proteome. PTMs being biologically and chemically dynamic process, pose greater challenges for its study. Amidst these complexities connecting the modifications with physiological and cellular cascade of events are still very challenging. Advancement in proteomic technologies such as mass spectrometry and microarray provides HT platform to study PTMs and help to decipher role of some of the very essential biological phenomenon. To enhance our understanding of various PTMs in different organisms, and to simplify the analysis of complex PTM data, many databases, software and tools have been developed. These PTM databases and tools contain crucial information and provide a valuable resource to the research community. This article intends to provide a comprehensive overview of various PTM databases, software tools, and analyze critical information available from these resources to study PTMs in various biological organisms.     

Exploring the diversity of plant proteome

The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.     

Study of the urine proteome in healthy humans

A new branch of molecular biology, proteomics, has been developed recently due to a success in genomics and informatics. Proteomics is currently solving problems of the full proteome mapping of various biological substances, e.g., body fluids, cells, and tissues in the normal state and pathology; and also search for biomarkers of pathologies, including tumors. Data on the urine proteome have been analyzed in this review. Analysis of the methods used in proteomics, including sample preparation, study strategy, as well as published data on urine proteome over the past five years are presented.     

3rd Annual FinnProt Meeting: from cells to systems

The Finnish Proteomics Society, FinnProt ( www.finnprot.org ), was founded in November 2004 as the Proteomics Division of the Societas biochemica, biophysica et microbiologica Fenniae ( www.biobio.org ). The mission of FinnProt is to make proteomics research readily available for the large scientific community in Finland, promote research and education in proteomics and protein chemistry, and act as the official Finnish collaborative body to international proteomics organizations such as the European Proteomics Association.