mpactr is a collection of filters for the purpose of identifying high quality MS1 features by correcting peak selection errors introduced during the pre-processing of tandem mass spectrometry data.
Filters in this package address the following issues:
filter_mispicked_ions(): removal of mispicked peaks, or those
isotopic patterns that are incorrectly split during preprocessing.filter_group(): removal of features overrepresented in a specific
group of samples; for example removal of features present in solvent
blanks due to carryover between samples.filter_cv(): removal of non-reproducible features, or those that are
inconsistent between technical replicates.filter_insource_ions(): removal of fragment ions created during the
first ionization in the tandem MS/MS workflow.All filters are independent, meaning they can be used to create a project-specific workflow, or you can learn more in the Getting Started page.
You can install the CRAN version with:
install.packages("mpactr")
You can install the development version of mpactr from GitHub with:
# install.packages("devtools")
# devtools::install_github("mums2/mpactr")
install.packages("mpactr", repos = c('https://mums2.r-universe.dev', 'https://cloud.r-project.org'))
See the Getting Started page to get started.
If you encounter an issue, please file an issue on GitHub. Please include a minimal reproducible example with your issue.
Is there a feature you’d like to see included, please let us know! Pull requests are welcome on GitHub.