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
刊名	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
	2005
卷号	2 期号:3 页码:217-230
关键词	isotope patterns peptide sequencing tandem mass spectra
通讯作者	Zhang, JF (reprint author), Chinese Acad Sci, Inst Comp Technol, JDL, Room 701,1,Shangdi E Rd, Beijing 100080, Peoples R China.,jfzhang@jdl.ac.cn ; wgao@jdl.ac.cn ; jjcai@jdl.ac.cn ; smhe@jdl.ac.cn ; zr@sibs.ac.cn ; crs@ict.ac.cn
英文摘要	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.
学科主题	Biochemistry & Molecular Biology; Computer Science; Mathematics
类目[WOS]	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
关键词[WOS]	ELEMENTAL ANALYSIS ; PEPTIDES ; SPECTROMETRY ; IDENTIFICATION ; PROGRAM
收录类别	SCI
语种	英语
WOS记录号	WOS:000235704200005
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/1877]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
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.