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MSstats

MSstats is an R-based/Bioconductor package for statistical relative quantification of peptides and proteins in mass spectrometry-based proteomic experiments. It is applicable to multiple types of sample preparation, including label-free workflows, workflows that use stable isotope labeled reference proteins and peptides, and work-flows that use fractionation. It is applicable to targeted Selected Reactin Monitoring(SRM), Data-Dependent Acquisiton(DDA or shotgun), and Data-Independent Acquisition(DIA or SWATH-MS). This github page is for sharing source and testing. The official webpage is msstats.org

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Version

Version

3.4.0

License

Artistic-2.0

Maintainer

Meena Choi

Last Published

February 15th, 2017

Functions in MSstats (3.4.0)

designSampleSizePlots

Visualization for sample size calculation
DDARawData

Example dataset from a label-free DDA, a controlled spike-in experiment.
plot_quantlim

Plot of the curve used to calculate LOD and LOQ
DIARawData

Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
designSampleSize

Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation
SpikeInDataNonLinear

Example dataset from an MRM spike-in experiment with a nonlinear behavior
nonlinear_quantlim

Calculation of the LOD and LOQ with a nonlinear fit
quantification

Protein sample quantification or group quantification
DDARawData.Skyline

Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
groupComparison

Finding differentially abundant proteins across conditions in targeted Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiment
MSstats-package

Tools for protein significance analysis in DDA,SRM and DIA proteomic experiments for label-free workflows or workflows with stable isotope labeled reference
dataProcessPlots

Visualization for explanatory data analysis
MaxQtoMSstatsFormat

Generate MSstats required input format for MaxQuant output
transformMSstatsToMSnSet

Transformation input format for MSstats to MSnSet class
dataProcess

Data pre-processing and quality control of MS runs of raw data
groupComparisonPlots

Visualization for model-based analysis and summarizing differentially abundant proteins
SpikeInDataLinear

Example dataset from an MRM spike-in experiment with a linear behavior
modelBasedQCPlots

Visualization for model-based quality control in fitting model
linear_quantlim

Calculation of the LOD and LOQ with a linear fit
transformMSnSetToMSstats

Transforms a MSnSet class dataset into a required input for MSstats
SRMRawData

Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study