A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data

doi:10.1186/1471-2105-7-222

	A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
	Zhang, Z ; Sun, SW ; Zhu, XP ; Chang, SH ; Liu, XF ; Yu, CG ; Bu, DB ; Chen, RS
	2006-04-26
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	7 页码:8
摘要	Background: Tandem mass spectrometry ( MS/ MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass spectra and an amino acid sequence database, improvements could be made in three aspects, including characterization ofpeaks in spectra, adoption of effective scoring functions and access to thereliability of matching between peptides and spectra. Results: A novel scoring function is presented, along with criteria to estimate the performance confidence of the function. Through learning the typesof product ions and the probability of generating them, a hypothetic spectrum was generated for each candidate peptide. Then relative entropy was introduced to measure the similarity between the hypothetic and the observed spectra. Based on the extreme value distribution ( EVD) theory, a threshold was chosen to distinguish a true peptide assignment from a random one. Tests on a public MS/ MS dataset demonstrated that this method performs better than the well-known SEQUEST. Conclusion: A reliable identification of proteins from the spectra promises a more efficient application of tandem mass spectrometry to proteomes with high complexity.
关键词	t
DOI	10.1186/1471-2105-7-222
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000237641500001
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：10[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/2XEOYT63/10757
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu, DB
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Z,Sun, SW,Zhu, XP,et al. A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data[J]. BMC BIOINFORMATICS,2006,7:8.
APA	Zhang, Z.,Sun, SW.,Zhu, XP.,Chang, SH.,Liu, XF.,...&Chen, RS.(2006).A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.BMC BIOINFORMATICS,7,8.
MLA	Zhang, Z,et al."A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data".BMC BIOINFORMATICS 7(2006):8.