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Investigation of Fragmentation Conditions in Top-Down Proteomics

Bioconductor version: Release (3.19)

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Author: Sebastian Gibb [aut, cre] , Pavel Shliaha [aut] , Ole Nørregaard Jensen [aut]

Maintainer: Sebastian Gibb <mail at>

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


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:

Data Generation for topdownr HTML R Script
Fragmentation Analysis with topdownr HTML R Script
Reference Manual PDF


biocViews Coverage, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, Software
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 3)
Depends R (>= 3.5), methods, BiocGenerics(>= 0.20.0), ProtGenerics(>= 1.10.0), Biostrings(>= 2.42.1), S4Vectors(>= 0.12.2)
Imports grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase(>= 2.3.10), PSMatch(>= 1.6.0), ggplot2 (>= 2.2.1), mzR(>= 2.27.5)
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Suggests topdownrdata(>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2
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Depends On Me topdownrdata
Imports Me
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Follow Installation instructions to use this package in your R session.

Source Package topdownr_1.26.0.tar.gz
Windows Binary
macOS Binary (x86_64) topdownr_1.26.0.tgz
macOS Binary (arm64) topdownr_1.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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