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学科主题: 物理化学
题名: 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
作者: Wu, Qi1, 2;  Shan, Yichu1;  Qu, Yanyan1, 2;  Jiang, Hao1, 2;  Yuan, Huiming1;  Liu, Jianxi1, 2;  Zhang, Shen1, 2;  Liang, Zhen1;  Zhang, Lihua1;  Zhang, Yukui1
通讯作者: 张丽华
刊名: ANALYST
发表日期: 2014
DOI: 10.1039/c3an01738a
卷: 139, 期:1, 页:138-146
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Analytical
研究领域[WOS]: Chemistry
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.
关键词[WOS]: QUANTITATIVE PROTEOMICS ;  SHOTGUN PROTEOMICS ;  PEPTIDES ;  ABUNDANCE ;  INTENSITY ;  DATABASES ;  MS
语种: 英语
WOS记录号: WOS:000327548400018
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/144454
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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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

Recommended Citation:
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.
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