# Quality Control of Protemics Data

## Documentation for package ‘MQmetrics’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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