Статья

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

Meena Choi1 1Department 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, USAChing-Yun Chang1 1Department 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, USATimothy Clough1 1Department 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, USADaniel Broudy1 1Department 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, USATrevor Killeen1 1Department 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, USABrendan MacLean1 1Department 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, USAOlga Vitek1 1Department 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

2014en

ABI

Аннотация

UNLABELLED: 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.

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Идентификаторы

DOI: 10.1093/bioinformatics/btu305

Цитирования и источники

Цитирований: 3Использованных источников: 0

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