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Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Author information

1
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.
2
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.

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.

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.

PMID:
24794931
DOI:
10.1093/bioinformatics/btu305
[Indexed for MEDLINE]

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