pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

doi:10.1021/acs.analchem.5b03963

	pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification
	Sun, Rui-Xiang 1; Luo, Lan 1,2; Wu, Long 1,2; Wang, Rui-Min 1,2; Zeng, Wen-Feng 1,2; Chi, Hao 1; Liu, Chao 1; He, Si-Min 1
	2016-03-15
发表期刊	ANALYTICAL CHEMISTRY
ISSN	0003-2700
卷号	88 期号:6 页码:3082-3090
摘要	There has been tremendous progress in top-down proteomics (TDP) in the past 5 years, particularly in intact protein separation and high resolution mass spectrometry. However, bioinformatics to deal with large-scale mass spectra has lagged behind, in both algorithmic research and software development. In this study, we developed pTop 1.0, a novel software tool to significantly improve the accuracy and efficiency of mass spectral data analysis in TDP. The precursor mass offers crucial clues to infer the potential post translational modifications co-occurring on the protein, the reliability of which relies heavily on its mass accuracy. Concentrating on detecting the precursors more accurately, a machine-learning model incorporating a variety of spectral features was trained online in pTop via a support vector machine (SVM). pTop employs the sequence tags extracted from the MS/MS spectra and a dynamic programming algorithm to accelerate the search speed, especially for those spectra with multiple post-translational modifications. We tested pTop on three publicly available data sets and compared it with ProSight and MS-Align+ in terms of its recall, precision, running time, and so on. The results showed that pTop can, in general, outperform ProSight and MS-Align+. pTop recalled 22% more correct precursors, although it exported 30% fewer precursors than Xtract (in ProSight) from a human histone data set. The running speed of pTop was about 1 to 2 orders of magnitude faster than that of MS-Align+. This algorithmic advancement in pTop, including both accuracy and speed, will inspire the development of other similar software to analyze the mass spectra from the entire proteins.
DOI	10.1021/acs.analchem.5b03963
收录类别	SCI
语种	英语
资助项目	National Basic Research Program of China[2013CB911203]
WOS研究方向	Chemistry
WOS类目	Chemistry, Analytical
WOS记录号	WOS:000372391500016
出版者	AMER CHEMICAL SOC
引用统计	被引频次：53[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/2XEOYT63/8681
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun, Rui-Xiang
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Sun, Rui-Xiang,Luo, Lan,Wu, Long,et al. pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification[J]. ANALYTICAL CHEMISTRY,2016,88(6):3082-3090.
APA	Sun, Rui-Xiang.,Luo, Lan.,Wu, Long.,Wang, Rui-Min.,Zeng, Wen-Feng.,...&He, Si-Min.(2016).pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification.ANALYTICAL CHEMISTRY,88(6),3082-3090.
MLA	Sun, Rui-Xiang,et al."pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification".ANALYTICAL CHEMISTRY 88.6(2016):3082-3090.