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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)
KeywordPhosphoproteome Analysis Ms2/ms3 Target-decoy Search Automatic Validation
Source PublicationJOURNAL OF PROTEOME RESEARCH
2008-04-01
ISSN1535-3893
DOI10.1021/pr700675j
Volume7Issue:4Pages:1640-1649
Indexed BySCI
SubtypeArticle
Department18
Funding Project1809
Contribution Rank1;1
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
WOS SubjectBiochemical Research Methods
WOS Research AreaBiochemistry & Molecular Biology
WOS KeywordMETAL AFFINITY-CHROMATOGRAPHY ; SPECTROMETRY-BASED PROTEOMICS ; TANDEM MASS-SPECTROMETRY ; PHOSPHOPROTEOME ANALYSIS ; PHOSPHORYLATION ANALYSIS ; ION-TRAP ; ENRICHMENT ; DATABASE ; FRAGMENTATION ; NANOPARTICLES
AbstractManual 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.
Language英语
URL查看原文
WOS IDWOS:000254711000028
Citation statistics
Cited Times:34[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/99961
Collection中国科学院大连化学物理研究所
Corresponding AuthorZou HF(邹汉法); Zou HF(邹汉法)
Affiliation1.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
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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