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

Analytical R tools for Mass Spectrometry

Bioconductor version: Development (3.20)

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check []( for details.

Author: David Jimenez-Morales [aut, cre] , Alexandre Rosa Campos [aut, ctb] , John Von Dollen [aut], Nevan Krogan [aut] , Danielle Swaney [aut, ctb]

Maintainer: David Jimenez-Morales <biodavidjm at>

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


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:

Learn to use artMS HTML R Script
Reference Manual PDF


biocViews Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>= 3) + file LICENSE
Depends R (>= 4.1.0)
Imports AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx,, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml
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Suggests BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics,, rmarkdown, testthat
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Follow Installation instructions to use this package in your R session.

Source Package artMS_1.23.0.tar.gz
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macOS Binary (x86_64) artMS_1.23.0.tgz
macOS Binary (arm64) artMS_1.23.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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