addSummaryChart         Add PRIDE summary charts
calcMSQCMetrics         Calculate the MS1 and MS2 level QC metrics
chargeStat              Charge distribution
cntStat                 contaminants stat
combineRun              Combine multiple results
createTargetDecoyDB     Create target-decoy database
getEnzyme               Get the enzymes list
getMods                 Get the modification list
labelRatio              Calculate the labeling efficiency of isobaric
                        labeling data
loadmsQCres             Load the result of 'msQCpipe'
msQCpipe                The main function of msQC pipeline
plotBioRepVenn          Venn plot in biological replicate level
plotFractionIDResult    Barplot in different level for each fraction
plotMS1Error            plot MS1 mass error
plotMS2Error            plot MS2 mass error
plotMS2Error_obsolete   plot MS2 mass error
plotSampleIDResultErrorBar
                        Error barplot in different level for each
                        fraction
plotSampleVenn          Venn plot in sample level
plotTechRepVenn         Venn plot in technical replicate level
print.msQCres           Print the information of msQCres object
proteinGroup            Protein inference
reportHTML              HTML format report generator
runTandem               Run X!Tandem
showEnzyme              Shown all enzymes
showMods                Shown all modifications
