Package: MQmetrics 1.13.0

Alvaro Sanchez-Villalba

MQmetrics: Quality Control of Protemics Data

The package MQmetrics (MaxQuant metrics) provides a workflow to analyze the quality and reproducibility of your proteomics mass spectrometry analysis from MaxQuant.Input data are extracted from several MaxQuant output tables and produces a pdf report. It includes several visualization tools to check numerous parameters regarding the quality of the runs. It also includes two functions to visualize the iRT peptides from Biognosys in case they were spiked in the samples.

Authors:Alvaro Sanchez-Villalba [aut, cre], Thomas Stehrer [aut], Marek Vrbacky [aut]

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MQmetrics.pdf |MQmetrics.html✨
MQmetrics/json (API)
NEWS

# Install 'MQmetrics' in R:

install.packages('MQmetrics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:MQmetrics-1.13.0(bioc 3.20)MQmetrics-1.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

26 exports 0.49 score 105 dependencies

Last updated 2 months agofrom:97ce2bfb47

Exports:generateReport make_MQCombined MaxQuantAnalysisInfo PlotAcquisitionCycle PlotAllDynamicRange PlotAndromedaScore PlotCharge PlotCombinedDynamicRange PlotHydrophobicity PlotIntensity PlotiRT PlotiRTScore PlotIsotopePattern PlotMsMs PlotPCA PlotPeaks PlotPeptidesIdentified PlotProteaseSpecificity PlotProteinCoverage PlotProteinOverlap PlotProteinPeptideRatio PlotProteinsIdentified PlotPTM PlotPTMAcrossSamples PlotTotalIonCurrent ReportTables

Dependencies:abind backports base64enc bit bit64 boot broom bslib cachem car carData cli clipr colorspace corrplot cowplot cpp11 crayon Deriv digest doBy dplyr evaluate fansi farver fastmap fontawesome fs generics ggforce gghalves ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr hms htmltools isoband jquerylib jsonlite knitr labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plyr polyclip polynom prettyunits progress purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen readr reshape2 rlang rmarkdown rstatix sass scales SparseM stringi stringr survival systemfonts tibble tidyr tidyselect tinytex tweenr tzdb utf8 vctrs viridisLite vroom withr xfun yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: MQmetrics 1.13.0

MQmetrics: Quality Control of Protemics Data

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