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   作者單位： 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： 中國化學（英文版）  SCI 英文刊名： CHINESE JOURNAL OF CHEMISTRY  年，卷(期)： 2009 27(2)  分類號： O6  關鍵詞： iterative search   proteome   mass spectrometry   quality control   database search  

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