DICP OpenIR
学科主题物理化学
Data mining algorithms to improve the sensitivity and reliability for protein and protein phosphorylation identification in shotgun proteomics
Jiang XN(江新宁); Ye ML(叶明亮); Han GH(韩广辉); Zou HF(邹汉法)
会议名称The 24th International Symposium on Micro-scale Bioseparation,
会议日期2009-10-19
2009-10-19
会议地点中国
页码76/1
部门归属十八室
主办者大连化物所
英文摘要In order to overcome the high rick resulting from the model based algorithm while processing dataset with very different characteristics, data mining algorithms were developed to improve the sensitivity for peptide and protein identifications safely. A filtering criteria optimization strategy using genetic algorithm was developed for the determination of tailored filtering criteria for different datasets; and an instance based algorithm using local false discovery rate (local FDR) was developed for the estimation of peptide identification posterior probability by incorporating of k nearest neighbors algorithm and Shannon information entropy strategy. By combining phosphopeptide identification information from MS2 and its consecutive MS3 spectra, an automatic phosphopeptide identification algorithm was developed to overcome the difficulties for phosphopeptide identifications, high FDR and the fact that manual validation is highly relied for the generation of high confident phosphopeptide identifications. By using this strategy, high confidence and sensitivity were achieved for phosphopeptide identification and phosphorylation site localization without the need of manual validation even for low accuracy mass spectrometry. Then a software suite targeted for the validating and processing of phosphoproteome dataset was established to help researchers to generate high confident phosphopeptide/phosphoprotein identifications and prepare phosphoproteome dataset with sufficient information easily. Keywords: Shotgun proteomics/ data mining/ bioinformatics/ phosphorylation/ References 1. Jiang, X. N., Jiang, X. G., Han, G. H., Ye, M. L. and Zou, H. F. Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics BMC Bioinformatics 2007, 8:323. 2. Jiang, X. N., Han, G. H., Feng, S., Jiang, X. G., Ye, M. L., Yao, X. B. and Zou, H. F. Automatic Validation of Phosphopeptide Identifications by the MS2/MS3 Target-Decoy Search Strategy J. Proteome Res. 2008, 7, 1640-1649. 3. Jiang, X. N., Dong, X. L., Ye, M. L. and Zou, H. F. Instance Based Algorithm for Posterior Probability Calculation by Target-Decoy Strategy to Improve Protein Identifications Anal. Chem. 2008, 80, 9326-9335.
语种中文
文献类型会议论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/113824
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)
推荐引用方式
GB/T 7714
Jiang XN,Ye ML,Han GH,et al. Data mining algorithms to improve the sensitivity and reliability for protein and protein phosphorylation identification in shotgun proteomics[C],2009:76/1.
条目包含的文件
条目无相关文件。
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[江新宁]的文章
[叶明亮]的文章
[韩广辉]的文章
百度学术
百度学术中相似的文章
[江新宁]的文章
[叶明亮]的文章
[韩广辉]的文章
必应学术
必应学术中相似的文章
[江新宁]的文章
[叶明亮]的文章
[韩广辉]的文章
相关权益政策
暂无数据
收藏/分享
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。