Description Details Author(s) References
A set of tools for protein significance analysis in SRM, DDA and DIA experiments.
Package: | MSstats |
Version: | 3.7.3 |
Date: | 2017-01-16 |
License: | Artistic-2.0 |
LazyLoad: | yes |
The package includes four main sections: I. explanatory data analysis (data pre-processing and quality control of MS runs), II. model-based analysis (finding differentially abundant proteins), III. statistical design of future experiments (sample size calculations), and IV. protein quantification (estimation of protein abundance). Section I contains functions for (1) data pre-processing and quality control of MS runs (see dataProcess
) and (2) visualizing for explanatory data analysis (see dataProcessPlots
). Section II contains functions for (1) finding differentially abundant proteins (see groupComparison
) and (2) visualizing for the testing results (see groupComparisonPlots
) and for checking normality assumption (see modelBasedQCPlots
). Section III contains functions for (1) calculating sample size (see designSampleSize
) and (2) visualizing for the sample size calculations (see designSampleSizePlots
). Section IV contains functions for (1) per-protein group quantification and patient quantification (see quantification
)
Examples of data in MSstats are (1) example of required input data format from label-based SRM experiment SRMRawData
; (2) example of required input data format from DDA experiment DDARawData
; (3) example of required input data format from label-free SWATH experiment DIARawData
.
The functions for converting the output from spectral processing tools, (1) Skyline, SkylinetoMSstatsFormat
, (2) MaxQuant, MaxQtoMSstatsFormat
, (3) Progenesis, ProgenesistoMSstatsFormat
, (4) Spectronaut, SpectronauttoMSstatsFormat
, and (5) Proteome discovere, PDtoMSstatsFormat
are available.
Meena Choi, Cyril Galitzine, Tsung-Heng Tsai, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean and Olga Vitek. "MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments" Bioinformatics, 30(17):2524-2526, 2014.
Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek. "Protein significance analysis in selected reaction monitoring (SRM) measurements." Molecular & Cellular Proteomics, 11:M111.014662, 2012.
Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek. "Statistical protein quantification and significance analysis in label-free LC-M experiments with complex designs" BMC Bioinformatics, 13:S16, 2012.
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