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An agent‐based system to discover protein–protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints

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/∼protein/NEW2/. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1020–1032, 2006