Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
Proteomics. 2013 Oct;13(18-19):2700-30. doi: 10.1002/pmic.201300175.
The steadily increasing amount of (meta-)genomic sequence information of diverse organisms and habitats has a strong impact on research in microbial physiology and ecology. In-depth functional understanding of metabolic processes and overall physiological adaptation to environmental changes, however, requires application of proteomics, as the context specific proteome constitutes the true functional output of a cell. Considering the enormous structural and functional diversity of proteins, only rational combinations of various analytical approaches allow a holistic view on the overall state of the cell. Within the past decade, proteomic methods became increasingly accessible to microbiologists mainly due to the robustness of analytical methods (e.g. 2DE), and affordability of mass spectrometers and their relative ease of use. This review provides an overview on the complex portfolio of state-of-the-art proteomics and highlights the basic principles of key methods, ranging from sample preparation of laboratory or environmental samples, via protein/peptide separation (gel-based or gel-free) and different types of mass spectrometric protein/peptide analyses, to protein identification and abundance determination.
不断增加的（宏）基因组序列信息来自不同的生物和生境，对微生物生理学和生态学的研究具有重要影响。然而，要深入了解代谢过程的功能和整体对环境变化的生理适应，需要应用蛋白质组学，因为特定于环境的蛋白质组是细胞的真实功能输出。考虑到蛋白质结构和功能的巨大多样性，只有合理组合各种分析方法，才能全面了解细胞的整体状态。在过去十年中，由于分析方法（例如 2-DE）的稳健性以及质谱仪的价格合理和易于使用，蛋白质组学方法越来越多地被微生物学家所采用。本综述概述了最先进的蛋白质组学的复杂组合，并重点介绍了关键方法的基本原理，范围从实验室或环境样品的样品制备，通过蛋白质/肽分离（基于凝胶或无凝胶）和不同类型的质谱蛋白质/肽分析，到蛋白质鉴定和丰度测定。
