title: MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.
abstract: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.
  
  
  METHODS
  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.
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Meena
authors.initials: M
authors.lastname: Choi
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Ching-Yun
authors.initials: CY
authors.lastname: Chang
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Clough
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Broudy
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Killeen
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Brendan
authors.initials: B
authors.lastname: MacLean
authors.affiliation: Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA Department of Statistics, Purdue University, West Lafayette, IN, Department of Genome Sciences, University of Washington, Seattle, WA 98195 and Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
mesh_terms: D003627:Data Interpretation, Statistical; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins