Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Documentation for package ‘MSstats’ version 3.20.3

Help Pages

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
dataProcess	Data pre-processing and quality control of MS runs of raw data
dataProcessPlots	Visualization for explanatory data analysis
DDARawData	Example dataset from a label-free DDA, a controlled spike-in experiment.
DDARawData.Skyline	Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
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
designSampleSizePlots	Visualization for sample size calculation
DIARawData	Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
DIAUmpiretoMSstatsFormat	Generate MSstats required input format for DIA-Umpire output
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
groupComparisonPlots	Visualization for model-based analysis and summarizing differentially abundant proteins
linear_quantlim	Calculation of the LOB and LOD with a linear fit
MaxQtoMSstatsFormat	Generate MSstats required input format for MaxQuant output
modelBasedQCPlots	Visualization for model-based quality control in fitting model
MSstats	Tools for protein significance analysis in DDA,SRM and DIA proteomic experiments for label-free workflows or workflows with stable isotope labeled reference
nonlinear_quantlim	Calculation of the LOB and LOD with a nonlinear fit
OpenMStoMSstatsFormat	Generate MSstats required input format for OpenMS output
OpenSWATHtoMSstatsFormat	Generate MSstats required input format for OpenSWATH output
PDtoMSstatsFormat	Generate MSstats required input format for Proteome discoverer output
plot_quantlim	Plot of the curve used to calculate LOB and LOD
ProgenesistoMSstatsFormat	Generate MSstats required input format for Progenesis output
quantification	Protein sample quantification or group quantification
SkylinetoMSstatsFormat	Generate MSstats required input format for Skyline output
SpectronauttoMSstatsFormat	Generate MSstats required input format for Spectronaut output
SpikeInDataLinear	Example dataset from an MRM spike-in experiment with a linear behavior
SpikeInDataNonLinear	Example dataset from an MRM spike-in experiment with a nonlinear behavior
SRMRawData	Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study