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 Filter vignette.
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("SchlossLab/mpactr")See the Filter vignette 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.