MaxQuantAnalysisInfo    Experiment Information
PlotAcquisitionCycle    Acquisition Cycle and MS/MS
PlotAllDynamicRange     Plots the dynamic range for all samples
PlotAndromedaScore      Andromeda score for the best associated MS/MS
                        spectrum.
PlotCharge              The charge-state of the precursor ion.
PlotCombinedDynamicRange
                        Dynamic range of all the samples combined
PlotHydrophobicity      Peptide hydrophobicity by GRAVY score
PlotIntensity           Intensity / LFQ intensity per sample.
PlotIsotopePattern      Plot Isotope Pattern and Isotope Pattern
                        Sequenced
PlotMsMs                Comparison of the MS/MS submitted and
                        identified in each sample.
PlotPCA                 Principal Component Analysis of the Intensity
                        values.
PlotPTM                 Post-Translational Modifications
PlotPTMAcrossSamples    Plot PTM across samples
PlotPeaks               Total number of peaks detected and sequenced
PlotPeptidesIdentified
                        Total number of peaks detected and sequenced
PlotProteaseSpecificity
                        Protease Specificity
PlotProteinCoverage     Protein coverage and degradation.
PlotProteinOverlap      Protein Overlap Between Samples
PlotProteinPeptideRatio
                        Identification Ratio Between Peptides and
                        Proteins
PlotProteinsIdentified
                        Proteins Identified per sample.
PlotTotalIonCurrent     Total Ion Current
PlotiRT                 Max intensities of the iRT peptides in each
                        sample.
PlotiRTScore            Score vs retention time of the iRT peptides
ReportTables            Report Tables with summary data
generateReport          Generates a report including all the plots of
                        MQmetrics.
make_MQCombined         Read MaxQuant Tables From Directory
