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NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification
Wu, Qi1,2; Zhao, Qun1,2; Liang, Zhen1; Qu, Yanyan1,2; Zhang, Lihua1; Zhang, Yukui1
刊名ANALYST
2012
DOI10.1039/c2an35173k
137期:13页:3146-3153
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
关键词[WOS]TANDEM MASS-SPECTROMETRY ; SHOTGUN PROTEOMICS ; SACCHAROMYCES-CEREVISIAE ; ABSOLUTE PROTEIN ; IDENTIFICATION ; PEPTIDE ; LUNG ; ABUNDANCE ; DATABASE ; SURFACE
英文摘要Although widely applied in the label-free quantification of proteomics, spectral count (SC)-based abundance measurements suffer from the narrow dynamic range of attainable ratios, leading to the serious underestimation of true protein abundance fold changes, especially when studying biological samples that exhibit very large fold changes in protein expression. MS/MS fragment ion intensity, as an alternative to SC, has recently gained acceptance as the abundance feature of protein in label-free proteomic studies. Herein, we implemented two formats of MS/MS fragment ion intensity, Spectral Index (SI) and Summed MS/MS TIC (SMT), to alleviate this particular deficiency arising from SC. Both were in forms of replacing SC in the Normalized Spectral Abundance Factor (NSAF) formula, resulting in two algorithms, abbreviated as NSI and NSMT, respectively. The necessity of the normalization process was validated using a publicly available dataset. Furthermore, when applied to another well characterized benchmark dataset, both NSI and NSMT showed improved overall accuracy over NSAF for the relative quantification of proteomes. Hereinto, NSI enabled the sensitive detection of differentially expressed proteins, while NSMT ensured accurate calculation for protein abundance fold change. Therefore, the selective use of both algorithms might facilitate the screening and quantification of potential biomarkers on the proteome scale.
语种英语
WOS记录号WOS:000304913100033
引用统计
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/143105
专题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.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
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GB/T 7714
Wu, Qi,Zhao, Qun,Liang, Zhen,et al. NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification[J]. ANALYST,2012,137(13):3146-3153.
APA Wu, Qi,Zhao, Qun,Liang, Zhen,Qu, Yanyan,Zhang, Lihua,&Zhang, Yukui.(2012).NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification.ANALYST,137(13),3146-3153.
MLA Wu, Qi,et al."NSI and NSMT: usages of MS/MS fragment ion intensity for sensitive differential proteome detection and accurate protein fold change calculation in relative label-free proteome quantification".ANALYST 137.13(2012):3146-3153.
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