Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra
文献类型：期刊论文
| 作者 | Zhang, JF; Gao, W; Cai, JJ; He, SM; Zeng, R; Chen, RS |
| 刊名 | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
 |
| 出版日期 | 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 |
| 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. |
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