{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T02:09:34Z","timestamp":1772503774069,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: \u00a0MSnbase is an R\/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. It provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation. MSnbase allows direct integration of quantitative proteomics data with additional facilities for statistical analysis provided by the Bioconductor project.<\/jats:p>\n               <jats:p>Availability: \u00a0MSnbase is implemented in R (version \u22652.13.0) and available at the Bioconductor web site (http:\/\/www.bioconductor.org\/). Vignettes outlining typical workflows, input\/output capabilities and detailing underlying infrastructure are included in the package.<\/jats:p>\n               <jats:p>Contact: \u00a0lg390@cam.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available from Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr645","type":"journal-article","created":{"date-parts":[[2011,11,24]],"date-time":"2011-11-24T01:41:00Z","timestamp":1322098860000},"page":"288-289","source":"Crossref","is-referenced-by-count":369,"title":["MSnbase-an R\/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation"],"prefix":"10.1093","volume":"28","author":[{"given":"Laurent","family":"Gatto","sequence":"first","affiliation":[{"name":"Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK"}]},{"given":"Kathryn S.","family":"Lilley","sequence":"additional","affiliation":[{"name":"Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,11,22]]},"reference":[{"key":"2023012511493138000_B1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012511493138000_B2","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"issue":"Suppl. 1","key":"2023012511493138000_B3","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012511493138000_B4","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1074\/mcp.M900628-MCP200","article-title":"Addressing accuracy and precision issues in itraq quantitation","volume":"9","author":"Karp","year":"2010","journal-title":"Mol. 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