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Quality Control of Protemics Data

Bioconductor version: Release (3.18)

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.

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

Maintainer: Alvaro Sanchez-Villalba <sanchezvillalba.alvaro at>

Citation (from within R, enter citation("MQmetrics")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MQmetrics HTML R Script
Reference Manual PDF


biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Imports ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra, utils, stringr, ggpubr, stats, cowplot, RColorBrewer, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown, ggrepel, gghalves, tools
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Follow Installation instructions to use this package in your R session.

Source Package MQmetrics_1.10.0.tar.gz
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macOS Binary (x86_64) MQmetrics_1.10.0.tgz
macOS Binary (arm64) MQmetrics_1.10.0.tgz
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