MSstats-package: Tools for protein significance analysis in DDA,SRM and DIA...

Description Details Author(s) References


A set of tools for protein significance analysis in SRM, DDA and DIA experiments.


Package: MSstats
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, (5) Proteome discovere, PDtoMSstatsFormat, (6) OpenMS, OpenMStoMSstatsFormat, (7) OpenSWATH, OpenSWATHtoMSstatsFormat, and (8) DIAUmpire, DIAUmpiretoMSstatsFormatare available.


Meena Choi, Tsung-Heng Tsai, Ting Huang, Cyril Galitzine, Olga Vitek.

Maintainer: Meena Choi (


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.

MSstats documentation built on Feb. 28, 2021, 2:01 a.m.