{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T03:01:35Z","timestamp":1761102095989},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>Availability and implementation: SILVER and its source codes are freely available under the GNU General Public License v3.0 at http:\/\/bioinfo.hupo.org.cn\/silver.<\/jats:p>\n               <jats:p>Contact: \u00a0zhuyunping@gmail.com, hefc@nic.bmi.ac.cn and xhwei65@163.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt726","type":"journal-article","created":{"date-parts":[[2013,12,17]],"date-time":"2013-12-17T02:04:39Z","timestamp":1387245879000},"page":"586-587","source":"Crossref","is-referenced-by-count":22,"title":["SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods"],"prefix":"10.1093","volume":"30","author":[{"given":"Cheng","family":"Chang","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingfei","family":"Han","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Ma","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songfeng","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kehui","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongwei","family":"Xie","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuchu","family":"He","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunping","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"},{"name":"1 Department of Bioinformatics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Institute of Radiation Medicine and 2Department of Bioinformatics, National Engineering Research Center for Protein Drugs, Beijing 102206, 3Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073 and 4Department of Chemistry, Institutes of Biomedical Sciences, 130 DongAn Road, Fudan University, Shanghai 200032, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,12,15]]},"reference":[{"key":"2023012710423995800_btt726-B1","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1074\/mcp.M112.017178","article-title":"Precision, proteome coverage, and dynamic range of Arabidopsis proteome profiling using (15)N metabolic labeling and label-free approaches","volume":"11","author":"Arsova","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012710423995800_btt726-B2","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1021\/pr050300l","article-title":"Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics","volume":"5","author":"Callister","year":"2006","journal-title":"J. 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Chem."},{"key":"2023012710423995800_btt726-B8","article-title":"Evaluation of empirical rule of linearly-correlated peptide selection (ERLPS) for proteotypic peptide-based quantitative proteomics","author":"Liu","year":"2013","journal-title":"Proteomics"},{"key":"2023012710423995800_btt726-B9","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1021\/pr900721e","article-title":"MSQuant, an open source platform for mass spectrometry-based quantitative proteomics","volume":"9","author":"Mortensen","year":"2010","journal-title":"J. Proteome Res."},{"key":"2023012710423995800_btt726-B10","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1038\/nmeth0910-681","article-title":"Mass spectrometry in high-throughput proteomics: ready for the big time","volume":"7","author":"Nilsson","year":"2010","journal-title":"Nat. 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