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

dataProcessData pre-processing and quality control of MS runs of raw...
dataProcessPlotsVisualization for explanatory data analysis
DDARawDataExample dataset from a label-free DDA, a controlled spike-in...
DDARawData.SkylineExample dataset from a label-free DDA, a controlled spike-in...
designSampleSizePlanning future experimental designs of Selected Reaction...
designSampleSizeClassificationEstimate the optimal size of training data for classification...
designSampleSizeClassificationPlotsVisualization for sample size calculation in classification...
designSampleSizePlotsVisualization for sample size calculation
DIARawDataExample dataset from a label-free DIA, a group comparison...
DIAUmpiretoMSstatsFormatGenerate MSstats required input format for DIA-Umpire output
groupComparisonFinding differentially abundant proteins across conditions in...
groupComparisonPlotsVisualization for model-based analysis and summarizing...
linear_quantlimCalculation of the LOB and LOD with a linear fit
MaxQtoMSstatsFormatGenerate MSstats required input format for MaxQuant output
modelBasedQCPlotsVisualization for model-based quality control in fitting...
MSstats-packageTools for protein significance analysis in DDA,SRM and DIA...
nonlinear_quantlimCalculation of the LOB and LOD with a nonlinear fit
OpenMStoMSstatsFormatGenerate MSstats required input format for OpenMS output
OpenSWATHtoMSstatsFormatGenerate MSstats required input format for OpenSWATH output
PDtoMSstatsFormatGenerate MSstats required input format for Proteome...
plot_quantlimPlot of the curve used to calculate LOB and LOD
ProgenesistoMSstatsFormatGenerate MSstats required input format for Progenesis output
quantificationProtein sample quantification or group quantification
SkylinetoMSstatsFormatGenerate MSstats required input format for Skyline output
SpectronauttoMSstatsFormatGenerate MSstats required input format for Spectronaut output
SpikeInDataLinearExample dataset from an MRM spike-in experiment with a linear...
SpikeInDataNonLinearExample dataset from an MRM spike-in experiment with a...
SRMRawDataExample dataset from a SRM experiment with stable isotope...
MSstats documentation built on July 4, 2018, 10 a.m.