Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy
文献类型：期刊论文
| 作者 | Jiang, Xinning1,2; Han, Guanghui1,2; Feng, Shun1; Jiang, Xiaogang1; Ye, Mingliang1; Yao, Xuebiao3; Zou, Hanfa1 |
| 刊名 | journal of proteome research
 |
| 出版日期 | 2008-04-01 |
| 卷号 | 7期号:4页码:1640-1649 |
| 关键词 | phosphoproteome analysis MS2/MS3 target-decoy search automatic validation |
| ISSN号 | 1535-3893 |
| 产权排序 | 1;1 |
| 通讯作者 | 邹汉法 |
| 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. |
| 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 |
| 收录类别 | SCI |
| 原文出处 | true |
| 语种 | 英语 |
| WOS记录号 | WOS:000254711000028 |
| 公开日期 | 2010-11-30 |
| 源URL | [http://159.226.238.44/handle/321008/99961]  |
| 专题 | 大连化学物理研究所_中国科学院大连化学物理研究所 |
| 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 |
| 推荐引用方式 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.,...&Zou, Hanfa.(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. |
入库方式： OAI收割
来源：大连化学物理研究所
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