The MsBackendTimsTof R package provides a backend for
Spectra objects enabling direct
import of MS data from Bruker TimsTOF .d data files. The package relies on the
opentimsr R package for some functionality. The opentimsr is an R wrapper
for the OpenTIMS C++ library.
The opentimsr package is no longer available on CRAN and hence needs to be installed from GitHub using:
remotes::install_github("michalsta/opentims/src/opentimsr")
The MsBackendTimsTof package can then be installed from GitHub using
# remotes::install_github("RforMassSpectrometry/MsBackendTimsTof")
install.packages("MsBackendTimsTof", repos = c('https://rformassspectrometry.r-universe.dev', 'https://cloud.r-project.org'))
For extraction of all spectra and peaks variables from the TimsTOF file format a
converter library is needed. This can be either the open-source library
shipped with opentimsr, or the shared C++ library from Bruker. By default,
MsBackendTimsTof uses, and loads the open-source library during the
library(MsBackendTimsTof) call. The setup_converter_library() function
can be used to download and select the Bruker library instead.
Please help us improving and completing the package! Any type of contribution welcome :open_hands: - including discussions, suggestions or actual code. Don't be afraid - we're friendly :relaxed:! :point_right: get involved by opening an issue.
Please also check out the RforMassSpectrometry Contributions Guide.
We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.