Lee Tzong-Yi, Horng Jorng-Tzong, Juan Hsueh-Fen, Huang Hsien-Da, Wu Li-Cheng, Tsai Meng-Fong, Huang Hsuan-Cheng
Department of Biological Science and Technology & Institute of Bioinformatics, National Chiao-Tung University, Taiwan, Republic of China.
J Comput Chem. 2006 Jul 15;27(9):1020-32. doi: 10.1002/jcc.20417.
Proteins "work together" by actually binding to form multicomponent complexes that carry out specific functions. Proteomic analyses based on the mass spectrum are now key methods to determine the components in protein complexes. The protein-protein interaction or functional association may be known to exist among the extracted protein spots while analyzing the proteins on the 2D gel. In this study, we develop an agent-based system, namely AgentMultiProtIdent, which integrated two protein identification tools and a variety of databases storing relations among proteins and used to discover protein-protein interactions and protein functional associations, and identify protein complexes and proteins with multiple peptide mass fingerprints as input. The system takes Multiple Peptide Mass Fingerprints (PMFs) as a whole in the protein complex or protein identification. With the relations among proteins, it may greatly improve the accuracy of identification of protein complexes. Also, possible relationship of the multiple peptide mass fingerprints, such as ontology relation, can be discovered by our system, especially in the identification of protein complexes. The agent-based system is now available on the Web at http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/.
蛋白质通过实际结合形成执行特定功能的多组分复合物来“协同工作”。基于质谱的蛋白质组学分析现在是确定蛋白质复合物中组分的关键方法。在分析二维凝胶上的蛋白质时，提取的蛋白质斑点之间可能已知存在蛋白质 - 蛋白质相互作用或功能关联。在本研究中，我们开发了一种基于代理的系统，即AgentMultiProtIdent，它集成了两种蛋白质鉴定工具和各种存储蛋白质之间关系的数据库，并用于发现蛋白质 - 蛋白质相互作用和蛋白质功能关联，以及将具有多个肽质量指纹的蛋白质复合物和蛋白质作为输入进行鉴定。该系统在蛋白质复合物或蛋白质鉴定中整体采用多个肽质量指纹。借助蛋白质之间的关系，它可以大大提高蛋白质复合物鉴定的准确性。此外，我们的系统可以发现多个肽质量指纹之间的可能关系，例如本体关系，特别是在蛋白质复合物的鉴定中。基于代理的系统现在可在网页http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/上获取。
