mpactr: Correction of Preprocessed MS Data
An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
| Version: | 0.2.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | cli, data.table, ggplot2, R6, Rcpp, readr, stats, treemapify, viridis |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0), tidyverse, plotly, Hmisc, corrplot, ggdendro, ggtext |
| Published: | 2025-03-13 |
| DOI: | 10.32614/CRAN.package.mpactr |
| Author: | Allison Mason 
[aut],
Gregory Johnson
[aut],
Patrick Schloss
[aut, cre, cph] |
| Maintainer: | Patrick Schloss <pschloss at umich.edu> |
| BugReports: | https://github.com/mums2/mpactr/issues |
| License: | GPL (≥ 3) |
| URL: | https://www.mums2.org/mpactr/, https://github.com/mums2/mpactr |
| NeedsCompilation: | yes |
| Citation: | mpactr citation info |
| Materials: | README NEWS |
| CRAN checks: | mpactr results |
Documentation:
| Reference manual: | mpactr.pdf |
| Vignettes: |
downstream_analyses (source, R code) phylotypr (source, R code) reference_semantics (source, R code) |
Downloads:
| Package source: | mpactr_0.2.0.tar.gz |
| Windows binaries: | r-devel: mpactr_0.1.0.zip, r-release: mpactr_0.1.0.zip, r-oldrel: mpactr_0.1.0.zip |
| macOS binaries: | r-devel (arm64): mpactr_0.2.0.tgz, r-release (arm64): mpactr_0.2.0.tgz, r-oldrel (arm64): mpactr_0.1.0.tgz, r-devel (x86_64): mpactr_0.2.0.tgz, r-release (x86_64): mpactr_0.2.0.tgz, r-oldrel (x86_64): mpactr_0.1.0.tgz |
| Old sources: | mpactr archive |
Linking:
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