Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current

	Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current
	Wu, Qi 1,2; Shan, Yichu 1; Qu, Yanyan 1,2; Jiang, Hao 1,2; Yuan, Huiming 1; Liu, Jianxi 1,2; Zhang, Shen 1,2; Liang, Zhen 1; Zhang, Lihua 1; Zhang, Yukui 1
刊名	analyst
	2014
卷号	139 期号:1 页码:138-146
通讯作者	张丽华
英文摘要	proteome scale absolute quantification is fundamental for the quantitative understanding of an organism. the unsatisfactory accuracy for protein abundance estimation of current algorithms has been partially improved by the absolute protein expression profiling (apex) algorithm, which implements the prior expectations of peptides' appearances in the calculation of protein abundances. however, the abundance feature (af) in apex is the spectral count (sc); an af suffers from a narrow dynamic range, thus, unsatisfactory accuracy. therefore, we adopted another tandem mass spectrometric (ms/ms) level af called summed ms/ms total ion current (smt), which cumulates the ms/ms fragment intensities rather than simply counting the ms/ms spectra, to surmount this particular deficiency. the combination of apex and smt (abbreviated as apex-smt) is capable of improving the accuracy of absolute quantification by reducing the average relative deviation by similar to 55-85% compared to that of apex, through a series of tests on the universal proteomics standard sample with a dynamic range of 5 orders of magnitude (ups2). the algorithm could also be used for relative quantification. when applied to the relative quantification of a publicly available benchmark dataset, apex-smt could provide comparable accuracy to apex. all these results suggest that apex-smt is a promising alternative to apex for proteome quantification.
学科主题	物理化学
WOS标题词	science & technology ; physical sciences
类目[WOS]	chemistry, analytical
研究领域[WOS]	chemistry
关键词[WOS]	quantitative proteomics ; shotgun proteomics ; peptides ; abundance ; intensity ; databases ; ms
收录类别	SCI
语种	英语
WOS记录号	WOS:000327548400018
公开日期	2016-05-09
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/144454]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
作者单位	1.Chinese Acad Sci, Dalian Inst Chem Phys, Key Lab Separat Sci Analyt Chem, Natl Chromatog Res & Anal Ctr, Dalian 116023, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Wu, Qi,Shan, Yichu,Qu, Yanyan,et al. Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current[J]. analyst,2014,139(1):138-146.
APA	Wu, Qi.,Shan, Yichu.,Qu, Yanyan.,Jiang, Hao.,Yuan, Huiming.,...&Zhang, Yukui.(2014).Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current.analyst,139(1),138-146.
MLA	Wu, Qi,et al."Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current".analyst 139.1(2014):138-146.