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MSstats relies on a flexible family of linear mixed models.<\/jats:p>\n               <jats:p>Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2014) and used via graphical user interface.<\/jats:p>\n               <jats:p>Contact: \u00a0ovitek@purdue.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu305","type":"journal-article","created":{"date-parts":[[2014,5,4]],"date-time":"2014-05-04T00:24:55Z","timestamp":1399163095000},"page":"2524-2526","source":"Crossref","is-referenced-by-count":1039,"title":["MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Meena","family":"Choi","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching-Yun","family":"Chang","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Clough","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Broudy","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trevor","family":"Killeen","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brendan","family":"MacLean","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Vitek","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Statistics, Purdue University, West Lafayette, IN, 2Department of Genome Sciences, University of Washington, Seattle, WA 98195 and 3Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,2]]},"reference":[{"key":"2023012711530206000_btu305-B1","doi-asserted-by":"crossref","first-page":"2521","DOI":"10.1093\/bioinformatics\/btu148","article-title":"A framework for installable external tools in Skyline","volume":"30","author":"Broudy","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012711530206000_btu305-B2","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.014662","article-title":"Protein significance analysis in selected reaction monitoring (SRM) measurements","volume":"11","author":"Chang","year":"2012","journal-title":"Mol. 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