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

Quantitative features for mass spectrometry data

Bioconductor version: Development (3.20)

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Author: Laurent Gatto [aut, cre] , Christophe Vanderaa [aut]

Maintainer: Laurent Gatto <laurent.gatto at>

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


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.


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

Data visualization from a QFeatures object HTML R Script
Processing quantitative proteomics data with QFeatures HTML R Script
Quantitative features for mass spectrometry data HTML R Script
Reference Manual PDF


biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.15.2
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0), MultiAssayExperiment
Imports methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics, ProtGenerics(>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils(>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2
System Requirements
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Suggests SingleCellExperiment, MsDataHub(>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
Linking To
Depends On Me hdxmsqc, msqrob2, scp, scpdata
Imports Me MetaboAnnotation, MsExperiment, PSMatch
Suggests Me MsDataHub
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package QFeatures_1.15.2.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) QFeatures_1.15.2.tgz
macOS Binary (arm64) QFeatures_1.15.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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