TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary

doi:10.2174/1574893613666171212160431

	TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary
	Wang, Yaojun 1,2; Zhang, Jingwei 2; Bu, Dongbo 2; Sun, Shiwei 2
	2018
发表期刊	CURRENT BIOINFORMATICS
ISSN	1574-8936
卷号	13 期号:5 页码:444-449
摘要	Background: Tandem mass spectrometry (MS/MS) peptide identification is an important research topic in molecular biology; the comparison between an experimental spectrum and a theoretically predicted spectrum is a crucial step for many identification methods. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the performance of peptide identification and is a significant problem for mass spectrometry-based proteomics. Objective: We studied the mechanism of peptide fragmentation in the mass spectrometer and proposed a strategy for theoretical spectrum simulation. We have proposed a new theoretical spectrum prediction model called TagDict. Method: TagDict built a "tag dictionary" from existing spectrum library and used for theoretical spectrum prediction. This dictionary collected a large number of records that each record comprised of peptide segment and the middle adjacent position fragment ion's intensity. Results: Full theoretical spectrum can derive from the adjacent ion intensity ratios get from query "tag dictionary". Compared with MassAnalyzer, the theoretical spectrum of TagDict simulated is more similar to the real spectrum. Conclusion: The new approach, comparing with another existing spectrum prediction tool MassAnalyzer, not only simplifies the process of theoretical spectrum simulation but also improves the prediction accuracy of the spectrum library searching by using this approach to extend spectrum library.
关键词	Mass spectrometry theoretical spectrum prediction database search peptide identification TagDict MassAnalyzer
DOI	10.2174/1574893613666171212160431
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31671369] ; National Natural Science Foundation of China[31270834] ; National Natural Science Foundation of China[11175224] ; National Natural Science Foundation of China[11121403] ; National Natural Science Foundation of China[61272318]
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:000440847000003
出版者	BENTHAM SCIENCE PUBL LTD
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/5075
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun, Shiwei
作者单位	1.Peking Univ, Guanghua Sch Management, Beijing, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yaojun,Zhang, Jingwei,Bu, Dongbo,et al. TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary[J]. CURRENT BIOINFORMATICS,2018,13(5):444-449.
APA	Wang, Yaojun,Zhang, Jingwei,Bu, Dongbo,&Sun, Shiwei.(2018).TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary.CURRENT BIOINFORMATICS,13(5),444-449.
MLA	Wang, Yaojun,et al."TagDict: Prediction of Theoretical Spectra of Peptides Based on A Tag Dictionary".CURRENT BIOINFORMATICS 13.5(2018):444-449.