topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

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.

Package overview Data Generation for topdownr Fragmentation Analysis with topdownr

Vignettes Man pages API and functions Files

Package details
Author	Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Pavel Shliaha [aut] (<https://orcid.org/0000-0003-3092-0724>), Ole Nørregaard Jensen [aut] (<https://orcid.org/0000-0003-1862-8528>)
Bioconductor views	Coverage ImmunoOncology Infrastructure MassSpectrometry Proteomics
Maintainer	Sebastian Gibb <mail@sebastiangibb.de>
License	GPL (>= 3)
Version	1.12.0
URL	https://github.com/sgibb/topdownr/
Package repository	View on Bioconductor
Installation	Install the latest version of this package by entering the following in R: `if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("topdownr")`