MSstats (version 2.4.0)

MSstats-package: Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments

Description

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

Details

Package:

MSstats

Version:

2.1.3

Date:

2014-01-05

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 the model-based quality control (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 or results in MSstats are (1) example of required input data format RawData; (2) example of raw data after data pre-processing QuantData; (3) results of significance testing of a single comparison testResultOneComparison; (4) results of significance testing of multiple comparisons testResultMultiComparisons.

References

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.