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Proteomics provides important information--that may not be inferable from indirect sources such as RNA or DNA--on key players in biological systems or disease states. However, it suffers from coverage and consistency problems. The advent of network-based analysis methods can help in overcoming these problems but requires careful application and interpretation. This review considers briefly current trends in proteomics technologies and understanding the causes of critical issues that need to be addressed--i.e., incomplete data coverage and inter-sample inconsistency. On the coverage issue, we argue that holistic analysis based on biological networks provides a suitable background on which more robust models and interpretations can be built upon; and we introduce some recently developed approaches. On consistency, group-based approaches based on identified clusters, as well as on properly integrated pathway databases, are particularly useful. Despite that protein interactions and pathway networks are still largely incomplete, given proper quality checks, applications and reasonably sized data sets, they yield valuable insights that greatly complement data generated from quantitative proteomics. 相似文献
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Proteomics research focuses on the identification and quantification of "all" proteins present in cells, organisms or tissue. Proteomics is technically complicated because it encompasses the characterization and functional analysis of all proteins that are expressed by a genome. Moreover, because the expression levels of proteins strongly depend on complex regulatory systems, the proteome is highly dynamic. This review focuses on the two major proteomics methodologies, one based on 2D gel electrophoresis and the other based on liquid chromatography coupled to mass spectrometry. The recent developments of these methodologies and their application to quantitative proteomics are described. The model system Saccharomyces cerevisiae is considered to be the optimal vehicle for proteomics and we review studies investigating yeast adaptation to changes in (nutritional) environment. 相似文献
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Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies. 相似文献
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Describing the connectivity of chemical and/or biological systems using networks is a straight gate for the introduction of mathematical tools in proteomics. Networks, in some cases even very large ones, are simple objects that are composed at least by nodes and edges. The nodes represent the parts of the system and the edges geometric and/or functional relationships between parts. In proteomics, amino acids, proteins, electrophoresis spots, polypeptidic fragments, or more complex objects can play the role of nodes. All of these networks can be numerically described using the so-called Connectivity Indices (CIs). The transformation of graphs (a picture) into CIs (numbers) facilitates the manipulation of information and the search for structure-function relationships in Proteomics. In this work, we review and comment on the challenges and new trends in the definition and applications of CIs in Proteomics. Emphasis is placed on 1-D-CIs for DNA and protein sequences, 2-D-CIs for RNA secondary structures, 3-D-topographic indices (TPGIs) for protein function annotation without alignment, 2-D-CIs and 3-D-TPGIs for the study of drug-protein or drug-RNA quantitative structure-binding relationships, and pseudo 3-D-CIs for protein surface molecular recognition. We also focus on CIs to describe Protein Interaction Networks or RNA co-expression networks. 2-D-CIs for patient blood proteome 2-DE maps or mass spectra are also covered. 相似文献
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Gangadharan B Antrobus R Chittenden D Rossa J Bapat M Klenerman P Barnes E Dwek RA Zitzmann N 《Journal of proteome research》2011,10(5):2643-2650
Despite many shortcomings, liver biopsy is regarded as the gold standard for assessing liver fibrosis. A less invasive and equally or more reliable approach would constitute a major advancement in the field. Proteomics can aid discovery of novel serological markers and these proteins can be measured in patient blood. A major challenge of discovering biomarkers in serum is the presence of highly abundant serum proteins, which restricts the levels of total protein loaded onto gels and limits the detection of low abundance features. To overcome this problem, we used two-dimensional gel electrophoresis (2-DE) over a narrow pH 3-5.6 range since this lies outside the range of highly abundant albumin, transferrin and immunoglobulins. In addition, we used in-solution isoelectric focusing followed by SDS-PAGE to find biomarkers in hepatitis C induced liver cirrhosis. Using the pH 3-5.6 range for 2-DE, we achieved improved representation of low abundance features and enhanced separation. We found in-solution isoelectric focusing to be beneficial for analyzing basic, high molecular weight proteins. Using this method, the beta chains of both complement C3 and C4 were found to decrease in serum from hepatitis C patients with cirrhosis, a change not observed previously by 2-DE. We present two proteomics approaches that can aid in the discovery of clinical biomarkers in various diseases and discuss how these approaches have helped to identify 23 novel biomarkers for hepatic fibrosis. 相似文献
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Molecular biologist's guide to proteomics. 总被引:26,自引:0,他引:26
Paul R Graves Timothy A J Haystead 《Microbiology and molecular biology reviews》2002,66(1):39-63; table of contents
The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems. 相似文献
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The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems. 相似文献
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Advances in proteomics have fundamentally changed the paradigm of discovery for drug targets and novel biomarkers. Proteomics methodologies currently used will be reviewed in this paper, including structural proteomics, quantitative proteomics, and functional proteomics. A strategy to identify differentially expressed cell surface proteins as monoclonal therapeutic targets in oncology will be discussed. 相似文献
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Strzeżek J Wysocki P Kordan W Kuklińska M Mogielnicka M Soliwoda D Fraser L 《Reproductive biology》2005,5(3):279-290
Proteomics is critical to identify the properties and functions of proteins involved in the mechanism regulating the male reproductive tract function. This approach is important in male fertility assessment and clinical diagnosis of the physiological state of individual reproductive organs. Proteomics also provides a tool to understand the interactions of seminal plasma proteins with spermatozoa, which could provide a useful model for studying ligand-cell interaction occurring at the sperm cell surface. This review covers a selection of advances in the realm of functional proteomics of boar seminal plasma proteins and is focused on some fundamental proteomic technologies. Also, this review explores key themes in proteomics and their application in animal reproductive techniques. 相似文献
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Proteomics in Argentina ‐ limitations and future perspectives: A special emphasis on meat proteomics
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André M. Almeida 《Proteomics》2015,15(21):3676-3687
Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case‐study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics‐based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. 相似文献
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蛋白质组学是系统鉴定、定量蛋白质及其翻译后修饰形式,并研究这些蛋白质生物学功能的学科。目前,基于质谱的鸟枪法蛋白质组学技术是蛋白质组学研究的主要手段之一,其技术流程是先将蛋白质组样品经位点特异性蛋白酶消化形成肽组,再进行高效液相色谱分离和质谱检测。而位点特异性蛋白酶对蛋白质样品的消化是质谱检测的前提和基础。随着蛋白质组学研究的深入,多种位点特异性蛋白酶被先后开发利用;而切割发生在相应氨基酸的N端,与传统的C端蛋白酶互为镜像的蛋白酶的鉴定、开发、特性研究和广泛使用更是为蛋白质组学研究提供了新的工具。文中对最近发现的胰蛋白酶的镜像酶——赖氨酸精氨酸N端蛋白酶(LysargiNase)的特点及其应用进行综述,为国内外学者更加广泛的使用创造条件。 相似文献
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蛋白质组学的产生及其重要意义 总被引:20,自引:0,他引:20
蛋白质组学是在后基因组时代出现的一个新的研究领域,它是对机体或组织或细胞的全部蛋白质的表达和功能模式进行研究。本文简要介绍蛋白质组学产生的科学背景及其重要意义。 相似文献
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Agrawal GK Job D Zivy M Agrawal VP Bradshaw RA Dunn MJ Haynes PA van Wijk KJ Kikuchi S Renaut J Weckwerth W Rakwal R 《Proteomics》2011,11(9):1559-1568
Given the essential role of proteomics in understanding the biology of plants, we are establishing a global plant proteomics organization to properly organize, preserve and disseminate collected information on plant proteomics. We call this organization 'International Plant Proteomics Organization (INPPO; http://www.inppo.com).' Ten initiatives of INPPO are outlined along with how to address them in multiple phases. As our vision is global, we sincerely hope the scientific communities around the world will come together to support and join INPPO. 相似文献
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Proteomics is a new scientific field aimed at the large-scale characterization of the protein constituents of biologic systems. It facilitates comparisons between different protein preparations by searching for minute differences in their protein expression repertoires and the patterns of their post-translational modifications. These attributes make proteomics perfectly suited for searching for proteins and peptides expressed exclusively or preferentially in cancer cells as candidates for cancer vaccines. The main proteomics technologies include 2D polyacrylamide gel electrophoresis, multidimensional high-performance liquid chromatography, mass spectrometry and protein arrays. Proteomics technologies used to analyze cancer culture cells, fresh tumor specimens, human leukocyte antigen peptides, serum and serum antibodies (serologic proteomics) have successfully identified tumor markers. Turning the potential vaccine candidates identified by proteomics technologies into clinical treatments awaits demonstration. 相似文献
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血浆蛋白质组学是研究血浆蛋白质的功能和变化的一门科学。血浆中蕴藏着生命机体的所有信息,因此只有彻底了解血浆中存在哪些蛋白质,才能知道如何利用血浆来预测人体对疾病的易感性并监控疾病的进程,以期达到对疾病进行早诊断早治疗。由于血浆蛋白质组动态范围大,给研究带来了很大的困难。尤其是高丰度蛋白质的存在影响了低丰度蛋白质的检测率。而低丰度蛋白质都是有意义的具有临床诊断价值的蛋白质。因此去除高丰度蛋白质的干扰成了血浆蛋白质组学研究的关键。近年来,血浆蛋白质组学相关研究技术也得到了长足进展,为深入研究血浆蛋白质做出了重要贡献。血浆蛋白质组学作为一种无创性的研究方法,值得我们去探讨。本文就血浆蛋白质组学研究进展情况做一简要综述。 相似文献