环境蛋白质组学：分子水平上表征微生物活性的范式转变。
Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level.
作者信息
Keller Martin, Hettich Robert
机构信息
Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, MS-6026, Oak Ridge, TN 37831, USA.
出版信息
Microbiol Mol Biol Rev. 2009 Mar;73(1):62-70. doi: 10.1128/MMBR.00028-08.
Abstract
The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.
摘要
测序能力的提升引发了新一轮宏基因组项目，为环境蛋白质组学技术的应用创造了条件并奠定了基础。本综述描述了环境蛋白质组学的现状。它介绍了样品制备以及该领域应用的两种主要技术：基于二维电泳的环境蛋白质组学和基于液相色谱 - 质谱联用的环境蛋白质组学。它还重点介绍了当前的出版物并描述了主要的科学发现。综述最后讨论了在将实验质谱技术与生物信息学整合以及改进样品处理方面的关键进展。
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本文引用的文献
1
Solvent-programmed microchip open-channel electrochromatography.溶剂程序控制微芯片开通道电色谱法
Anal Chem. 1998 Aug 1;70(15):3291-7. doi: 10.1021/ac971367y.
2
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea.在马尾藻海低营养极端条件下，转运功能在SAR11元蛋白质组中占主导地位。
ISME J. 2009 Jan;3(1):93-105. doi: 10.1038/ismej.2008.83. Epub 2008 Sep 4.
3
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.群落蛋白质基因组学揭示了在进行强化生物除磷的活性污泥中微生物菌株变体的蛋白质表达情况。
ISME J. 2008 Aug;2(8):853-64. doi: 10.1038/ismej.2008.38. Epub 2008 May 1.
4
Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics.采用传统分析和SameSpots分析，对差异凝胶电泳（DIGE）和染色后凝胶电泳进行定量蛋白质组学比较。
Proteomics. 2008 Mar;8(5):948-60. doi: 10.1002/pmic.200700812.
5
The biological impact of mass-spectrometry-based proteomics.基于质谱的蛋白质组学的生物学影响。
Nature. 2007 Dec 13;450(7172):991-1000. doi: 10.1038/nature06525.
6
Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses.用于蛋白质组学分析中最大化通量的全自动四元毛细管液相色谱-质谱联用系统。
Anal Chem. 2008 Jan 1;80(1):294-302. doi: 10.1021/ac701727r. Epub 2007 Nov 29.
7
Functional metaproteome analysis of protein extracts from contaminated soil and groundwater.对受污染土壤和地下水中蛋白质提取物进行的功能宏蛋白质组分析。
ISME J. 2007 Jul;1(3):224-34. doi: 10.1038/ismej.2007.39. Epub 2007 May 31.
8
Chip-LC-MS for label-free profiling of human serum.用于人血清无标记分析的芯片液相色谱-质谱联用技术
Electrophoresis. 2007 Dec;28(23):4493-505. doi: 10.1002/elps.200600719.
9
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.翻译后修饰的全蛋白质组分析：质谱技术在蛋白质基因组注释中的应用
Genome Res. 2007 Sep;17(9):1362-77. doi: 10.1101/gr.6427907. Epub 2007 Aug 9.
10
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J Sep Sci. 2007 Aug;30(13):2046-52. doi: 10.1002/jssc.200700053.
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