title: SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  SILVER and its source codes are freely available under the GNU General Public License v3.0 at http://bioinfo.hupo.org.cn/silver.
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Chang
authors.forename: Jiyang
authors.initials: J
authors.lastname: Zhang
authors.forename: Mingfei
authors.initials: M
authors.lastname: Han
authors.forename: Jie
authors.initials: J
authors.lastname: Ma
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Songfeng
authors.initials: S
authors.lastname: Wu
authors.forename: Kehui
authors.initials: K
authors.lastname: Liu
authors.forename: Hongwei
authors.initials: H
authors.lastname: Xie
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D007553:Isotope Labeling; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D012984:Software
chemical_list: D010455:Peptides; D020543:Proteome