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


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Documentation for package ‘MSstats’ version 3.16.2

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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
designSampleSizeClassification Estimate the optimal size of training data for classification problem
designSampleSizeClassificationPlots Visualization for sample size calculation in classification problem
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