Iterative Non-m/z-sharing Rule for Confident and Sensitive Protein Identification of Non-shotgun Proteomics
Selecting reasonable matches from the database search results is crucial to mass spectrometry-based proteomics identification. However, the current score-based filter solution and decoy database methods are not effective enough to prevent all false positive and false negative selections. In this study, a systematic search strategy named iterative non-m/z-sharing (INMZS) analysis was proposed to address the problem. In the strategy, all search results were screened based on the share status of corresponding matched m/z, only the proteins that matched with exclusive m/z information were reserved for the confident matches. The researchers did further iterative search to improve the identification of minor components in a spot. Finally, identifications were confirmed by decoy database evaluation for the final phase of protein identification. Simulation and application tests of INMZS were implemented on a large human liver data set and standard protein cocktails. The result shows that INMZS plus decoy database evaluation is efficient in ensuring the confidence and sensitivity of 2-DE or similar non-shotgun based proteome identification.
作 者: YUN Dong LU Haojie WANG Haijian ZHANG Yang CHENG Gang JIN Hong YU Yanbao XU Yawei YANG Pengyuan HE Fuchu 作者单位: YUN Dong,YU Yanbao,XU Yawei(Department of Chemistry, Fudan University, Shanghai 200433, China)LU Haojie,JIN Hong,YANG Pengyuan(Department of Chemistry, Fudan University, Shanghai 200433, China;Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China)
WANG Haijian,ZHANG Yang,CHENG Gang(Institutes of Biomedical Sciences,Fudan University,Shanghai 200032,China)
HE Fuchu(Department of Chemistry, Fudan University, Shanghai 200433, China;Institutes of Biomedical Sciences,Fudan University,Shanghai 200032,China;State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine,Beijing 102206, China)
刊 名: 中国化学(英文版) SCI 英文刊名: CHINESE JOURNAL OF CHEMISTRY 年,卷(期): 2009 27(2) 分类号: O6 关键词: iterative search proteome mass spectrometry quality control database search