SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods

被引：18

作者：

Chang, Cheng ^{[1
,2
]}

Zhang, Jiyang ^{[3
]}

Han, Mingfei ^{[1
,2
]}

Ma, Jie ^{[1
,2
]}

Zhang, Wei ^{[3
]}

Wu, Songfeng ^{[1
,2
]}

Liu, Kehui ^{[1
,2
]}

Xie, Hongwei ^{[3
]}

He, Fuchu ^{[1
,2
,4
]}

Zhu, Yunping ^{[1
,2
]}

机构：

[1] Inst Radiat Med, Natl Ctr Prot Sci Beijing, Beijing Proteome Res Ctr, Dept Bioinformat,State Key Lab Prote, Beijing 102206, Peoples R China

[2] Natl Engn Res Ctr Prot Drugs, Dept Bioinformat, Beijing 102206, Peoples R China

[3] Natl Univ Def Technol, Coll Mechatron & Automat, Dept Automat Control, Changsha 410073, Hunan, Peoples R China

[4] Fudan Univ, Inst Biomed Sci, Dept Chem, Shanghai 200032, Peoples R China

来源：

BIOINFORMATICS | 2014年 / 30卷 / 04期

基金：

中国国家自然科学基金;

关键词：

MASS-SPECTROMETRY; PEPTIDE IDENTIFICATIONS; PROTEIN QUANTIFICATION; SOFTWARE TOOL; CELL-CULTURE; AMINO-ACIDS; PROTEOMICS; ACCURACY; RANGE;

D O I：

10.1093/bioinformatics/btt726

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

With the advance of experimental technologies, different stable isotope labeling methods have been widely applied to quantitative proteomics. Here, we present an efficient tool named SILVER for processing the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein levels, respectively. Several new quantification confidence filters and indices are used to improve the accuracy of quantification results. The performance of SILVER was verified and compared with MaxQuant and Proteome Discoverer using a large-scale dataset and two standard datasets. The results suggest that SILVER shows high accuracy and robustness while consuming much less processing time. Additionally, SILVER provides user-friendly interfaces for parameter setting, result visualization, manual validation and some useful statistics analyses.

引用

页码：586 / 587

页数：2

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