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Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy
Jiang, Xinning1,2; Han, Guanghui1,2; Feng, Shun1; Jiang, Xiaogang1; Ye, Mingliang1; Yao, Xuebiao3; Zou, Hanfa1; Zou HF(邹汉法); Zou HF(邹汉法)
关键词Phosphoproteome Analysis Ms2/ms3 Target-decoy Search Automatic Validation
刊名JOURNAL OF PROTEOME RESEARCH
2008-04-01
ISSN1535-3893
DOI10.1021/pr700675j
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
关键词[WOS]METAL AFFINITY-CHROMATOGRAPHY ; SPECTROMETRY-BASED PROTEOMICS ; TANDEM MASS-SPECTROMETRY ; PHOSPHOPROTEOME ANALYSIS ; PHOSPHORYLATION ANALYSIS ; ION-TRAP ; ENRICHMENT ; DATABASE ; FRAGMENTATION ; NANOPARTICLES
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.
语种英语
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WOS记录号WOS:000254711000028
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文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/99961
专题中国科学院大连化学物理研究所
通讯作者Zou HF(邹汉法); Zou HF(邹汉法)
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
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GB/T 7714
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.
APA Jiang, Xinning.,Han, Guanghui.,Feng, Shun.,Jiang, Xiaogang.,Ye, Mingliang.,...&邹汉法.(2008).Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy.JOURNAL OF PROTEOME RESEARCH,7(4),1640-1649.
MLA Jiang, Xinning,et al."Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy".JOURNAL OF PROTEOME RESEARCH 7.4(2008):1640-1649.
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