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
文献类型：期刊论文
| 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 |
| 刊名 | analyst
 |
| 出版日期 | 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. |
| WOS标题词 | science & technology ; physical sciences |
| 学科主题 | 物理化学 |
| 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 |
| 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. |
入库方式： OAI收割
来源：大连化学物理研究所
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