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In recent years, proteomics including mass §spectrometry-based technologies become method of §choice for detection of new proteins including §biomarkers as well for pathway discovery in§large-scale. The role of bioinformatics is one of§unrecognized issues in proteomics. For correct§definition, identification and detection of§hypothetical proteins (HPs) as well as experimental§characterization of these proteins, §bioinformatic plays an essential role. In this §book, the basics of bioinformatics in proteomics are §discussed and several practical examples are given §to understand the importance of proteomic §methodology together with bioinformatic tools §for identification as well as characterization of §HPs.