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This is the development version of MQmetrics; for the stable release version, see MQmetrics.

Quality Control of Protemics Data

Bioconductor version: Development (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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


Reference Manual PDF


biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.13.0
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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