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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
Source PublicationANALYST
2012
DOI10.1039/c2an35173k
Volume137Issue:13Pages:3146-3153
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
WOS SubjectChemistry, Analytical
WOS Research AreaChemistry
WOS KeywordTANDEM MASS-SPECTROMETRY ; SHOTGUN PROTEOMICS ; SACCHAROMYCES-CEREVISIAE ; ABSOLUTE PROTEIN ; IDENTIFICATION ; PEPTIDE ; LUNG ; ABUNDANCE ; DATABASE ; SURFACE
AbstractAlthough 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.
Language英语
WOS IDWOS:000304913100033
Citation statistics
Cited Times:10[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/143105
Collection中国科学院大连化学物理研究所
Affiliation1.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
Recommended Citation
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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