Overview
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.
Installation
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")Get started
See the Filter vignette to get started.
Getting help
If you encounter an issue, please file an issue on GitHub. Please include a minimal reproducible example with your issue.
Contributing
Is there a feature you’d like to see included, please let us know! Pull requests are welcome on GitHub.