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MsQuality - Quality metric calculation from Spectra and MsExperiment objects

Bioconductor version: Release (3.19)

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

Author: Thomas Naake [aut, cre] , Johannes Rainer [aut]

Maintainer: Thomas Naake <thomasnaake at>

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


To install this package, start R (version "4.4") 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:

QC for metabolomics and proteomics data HTML R Script
Reference Manual PDF


biocViews MassSpectrometry, Metabolomics, Proteomics, QualityControl, Software
Version 1.4.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports BiocParallel(>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata(>= 0.32.0), MsExperiment(>= 0.99.0), plotly (>=, ProtGenerics(>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra(>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0)
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Suggests BiocGenerics(>= 0.24.0), BiocStyle(>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR(>= 2.32.0), rmarkdown (>= 2.7), S4Vectors(>= 0.29.17), testthat (>= 2.2.1)
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Follow Installation instructions to use this package in your R session.

Source Package MsQuality_1.4.0.tar.gz
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macOS Binary (x86_64) MsQuality_1.4.0.tgz
macOS Binary (arm64) MsQuality_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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