Quality Control of Protemics Data

Documentation for package ‘MQmetrics’ version 1.10.0

generateReport	Generates a report including all the plots of MQmetrics.
make_MQCombined	Read MaxQuant Tables From Directory
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.
PlotiRT	Max intensities of the iRT peptides in each sample.
PlotiRTScore	Score vs retention time of the iRT peptides
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.
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.
PlotPTM	Post-Translational Modifications
PlotPTMAcrossSamples	Plot PTM across samples
PlotTotalIonCurrent	Total Ion Current
ReportTables	Report Tables with summary data