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题名: Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy
作者: Jiang, Xinning1, 2;  Han, Guanghui1, 2;  Feng, Shun1;  Jiang, Xiaogang1;  Ye, Mingliang1;  Yao, Xuebiao3;  Zou, Hanfa1
通讯作者: 邹汉法
关键词: phosphoproteome analysis ;  MS2/MS3 ;  target-decoy search ;  automatic validation
刊名: JOURNAL OF PROTEOME RESEARCH
发表日期: 2008-04-01
DOI: 10.1021/pr700675j
卷: 7, 期:4, 页:1640-1649
收录类别: SCI
文章类型: Article
部门归属: 18
项目归属: 1809
产权排名: 1;1
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine
类目[WOS]: Biochemical Research Methods
研究领域[WOS]: Biochemistry & Molecular Biology
英文摘要: Manual checking is commonly employed to validate the phosphopeptide identifications from database searching of tandem mass spectra. It is very time-consuming and labor intensive as the number of phosphopeptide identifications increases greatly. In this study, a simple automatic validation approach was developed for phosphopeptide identification by combining consecutive stage mass spectrometry data and the target-decoy database searching strategy. Only phosphopeptides identified from both MS2 and its corresponding MS3 were accepted for further filtering, which greatly improved the reliability in phosphopepticle identification. Before database searching, the spectra were validated for charge state and neutral loss peak intensity, and then the invalid MS2/MS3 spectra were removed, which greatly reduced the database searching time. It was found that the sensitivity was significantly improved in MS2/MS3 strategy as the number of identified phosphopeptides was 2.5 times that obtained by the conventional filter-based MS2 approach. Because of the use of the target-decoy database, the false-discovery rate (FDR) of the identified phosphopeptides could be easily determined, and it was demonstrated that the determined FDR can precisely reflect the actual FDR without any manual validation stage.
关键词[WOS]: METAL AFFINITY-CHROMATOGRAPHY ;  SPECTROMETRY-BASED PROTEOMICS ;  TANDEM MASS-SPECTROMETRY ;  PHOSPHOPROTEOME ANALYSIS ;  PHOSPHORYLATION ANALYSIS ;  ION-TRAP ;  ENRICHMENT ;  DATABASE ;  FRAGMENTATION ;  NANOPARTICLES
语种: 英语
原文出处: 查看原文
WOS记录号: WOS:000254711000028
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/99961
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, Natl Chromatog R&A Ctr, Dalian 116023, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
3.Univ Sci & Technol China, Lab Cell Dynam, Sch Life Sci, Hefei 230027, Peoples R China

Recommended Citation:
Jiang, Xinning,Han, Guanghui,Feng, Shun,et al. Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy[J]. JOURNAL OF PROTEOME RESEARCH,2008,7(4):1640-1649.
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