PeakSelect: preprocessing tandem mass spectra for better peptide identification

doi:10.1002/rcm.3488

	PeakSelect: preprocessing tandem mass spectra for better peptide identification
	Zhang, Jingfen 1; He, Simin 1; Ling, Charles X.2; Ca, Xingjun 3; Zeng, Rong 3; Gao, Wen 1
	2008-04-01
发表期刊	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
ISSN	0951-4198
卷号	22 期号:8 页码:1203-1212
摘要	We present a new preprocessing method, PeakSelect, to improve the accuracy and efficiency of Tandem Mass-Spec peptide (protein) identification. The fundamental difference between noise and fragment ions in spectra is that ions have isotopes but noise does not. We propose a new and important concept of an Isotope Pattern Vector (IPV) which characterizes the isotope cluster of fragment ions. Then the noise and real peaks can be distinguished by the quantitative IPV values. PeakSelect first uses a new method of the Gaussian Mixture Model and Expectation-Maximization (EM) algorithm to find the base intensity level (baseline) in a spectrum. Then PeakSelect selects features based on the IPV and baseline, and constructs a decision tree to automatically classify the peaks into different categories such as noise, single ion peaks, and overlapping peaks. Experiments show that PeakSelect can help to reduce the Mascot searching time and increase the reliability of peptide identifications. In particular, PeakSelect performs well on complex spectra with a large number of peaks from large peptides, and supports more sequence identification than other well-known systems. Copyright (c) 2008 John Wiley & Sons, Ltd.
DOI	10.1002/rcm.3488
收录类别	SCI
语种	英语
WOS研究方向	Chemistry ; Spectroscopy
WOS类目	Chemistry, Analytical ; Spectroscopy
WOS记录号	WOS:000255362300016
出版者	JOHN WILEY & SONS LTD
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/2XEOYT63/11073
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, Jingfen
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China 2.Univ Western Ontario, Dept Comp Sci, London, ON, Canada 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Shanghai 200031, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jingfen,He, Simin,Ling, Charles X.,et al. PeakSelect: preprocessing tandem mass spectra for better peptide identification[J]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY,2008,22(8):1203-1212.
APA	Zhang, Jingfen,He, Simin,Ling, Charles X.,Ca, Xingjun,Zeng, Rong,&Gao, Wen.(2008).PeakSelect: preprocessing tandem mass spectra for better peptide identification.RAPID COMMUNICATIONS IN MASS SPECTROMETRY,22(8),1203-1212.
MLA	Zhang, Jingfen,et al."PeakSelect: preprocessing tandem mass spectra for better peptide identification".RAPID COMMUNICATIONS IN MASS SPECTROMETRY 22.8(2008):1203-1212.