Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra

	Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra
	Zhang, JF ; Gao, W ; Cai, JJ ; He, SM ; Zeng, R ; Chen, RS
	2005-07-01
发表期刊	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN	1545-5963
卷号	2 期号:3 页码:217-230
摘要	A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.
关键词	isotope patterns peptide sequencing tandem mass spectra
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS类目	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000235704200005
出版者	IEEE COMPUTER SOC
引用统计	被引频次：20[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/2XEOYT63/10058
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhang, JF
作者单位	1.Chinese Acad Sci, Inst Comp Technol, JDL, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Inst Biophys, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Zhang, JF,Gao, W,Cai, JJ,et al. Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2005,2(3):217-230.
APA	Zhang, JF,Gao, W,Cai, JJ,He, SM,Zeng, R,&Chen, RS.(2005).Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2(3),217-230.
MLA	Zhang, JF,et al."Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2.3(2005):217-230.