Iterative Non-m/z-sharing Rule for Confident and Sensitive Protein Identification of Non-shotgun Proteomics (pages 331–337)
Dong YUN, Haojie LU, Haijian WANG, Yang ZHANG, Gang CHENG, Hong JIN, Yanbao YU, Yawei XU, Pengyuan YANG and Fuchu HE
Version of Record online: 3 MAR 2009 | DOI: 10.1002/cjoc.200990053
In this study, a systematic search strategy named iterative non-m/z-sharing (INMZS) analysis was proposed to address this problem. In the strategy, all search results were screened based on the share status of corresponding matched m/z, only the proteins matched with exclusive m/z information were reserved for the confident matches. Furthermore the researchers did 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 search results. Simulation and application tests of INMZS were implemented on human liver data set and standard protein cocktails. The results show that INMZS plus decoy database evaluation is efficient in ensuring the confidence and sensitivity of 2-DE or similar non-shotgun based proteome identification.