Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry
Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry
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DOI：
10.1039/c2an35891c
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发表时间：
2012-01-01
期刊：
影响因子：
4.2
通讯作者：
Yan, Guangli
中科院分区：
文献类型：
--
作者：
Wang, Xijun;Zhang, Aihua;Yan, Guangli
蛋白质组学技术的最新进展使我们能够在疾病中创建详细的蛋白质-蛋白质相互作用图。随着交互数据集的大小增加，需要强大的计算方法来有效地解释大规模交互组数据中的网络模型。在这项研究中，我们进行了比较蛋白质组学，以构建和鉴定与肝损伤(HI)相关的蛋白质网络，作为一个案例研究。用双向凝胶电泳法(2-DE)和基质辅助激光解吸电离飞行时间-飞行时间质谱仪(MALDI-TOF/TOF-MS)对表达的蛋白质进行分离和鉴定。使用字符串分析程序绘制蛋白质相互作用网络和路径图。我们首次对HI大鼠蛋白质表达的变化进行了全面的分析，以揭示CCl4处理后改变的网络。用MALDI-TOF/TOF MS鉴定了15个蛋白质点(7个过度表达，8个低表达)，利用STRING软件对这些蛋白质进行了功能途径分析，以更好地了解所鉴定蛋白质的生物学背景。这表明，DNA修复过程、细胞凋亡、氧化还原、信号转导、代谢过程、细胞内信号级联、生物过程调控、细胞通讯、细胞过程调控和分子运输等多种重要生理途径的调控。综上所述，本研究提供了第一个蛋白质相互作用网络图，并对HI的生物学反应和潜在途径提供了新的见解。蛋白质相互作用网络的产生明显增强了对蛋白质组数据的解释，特别是在理解组蛋白生物标记物的分子机制方面。
Recent advances in proteomic technologies have enabled us to create detailed protein-protein interaction maps in diseases. As the size of the interaction dataset increases, powerful computational methods are required in order to effectively interpret network models from large scale interactome data. In this study, we carried out comparative proteomics to construct and identify the proteins networks associated with hepatic injury (HI) which are largely unknown, as a case study. All proteins expressed were separated and identified by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry (MALDI-TOF/TOF MS). Protein-interacting networks and pathways were mapped using STRING analysis program. We have performed for the first time a comprehensive profiling of changes in protein expression of HI rats, to uncover the networks altered by treated with CCl4. Identification of fifteen spots (seven over-expressed and eight under-expressed) were established by MALDI-TOF/TOF MS. These proteins were subjected to functional pathway analysis using STRING software for better understanding of the biological context of the identified proteins. It suggested that modulation of multiple vital physiological pathways including DNA repair process, cell apoptosis, oxidation reduction, signal transduction, metabolic process, intracellular signaling cascade, regulation of biological processes, cell communication, regulation of cellular process, and molecular transport. In summary, the present study provides the first protein-interacting network maps and novel insights into the biological responses and potential pathways of HI. The generation of protein interaction networks clearly enhances the interpretation of proteomic data, particularly in respect of understanding molecular mechanisms of panel protein biomarkers.