Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts.
The initial work is available at https://doi.org/10.1021/acs.jafc.3c03099, with some improvements made since then. The workflow is illustrated below.
Here is what you minimally need:
- A file
(.mzML)
containing DDA
MS
data with an additional detector
(PDA,
ELSD,
CAD)
- In case you don’t know how to obtain it, see: wiki/How-to-create-a-compliant-mzML-file
- A file (.csv) containing features, as obtained by mzmine
- A file (.tsv) containing annotations, as obtained by TIMA
As the package is not (yet) available on CRAN, you will need to install with:
install.packages(
"cascade",
repos = c(
"https://adafede.r-universe.dev",
"https://bioc.r-universe.dev",
"https://cloud.r-project.org"
)
)Once installed, you are ready to go through our documentation, with the major steps detailed.
https://doi.org/10.1021/acs.jafc.3c03099
According to which steps you used, please give credit to the authors of the tools/resources used.
General: https://doi.org/10.1038/s41587-023-01690-2
General: https://doi.org/10.1038/s41592-019-0344-8
- CSI:FingerId: https://doi.org/10.1073/pnas.1509788112
- ZODIAC: https://doi.org/10.1038/s42256-020-00234-6
- CANOPUS: https://doi.org/10.1038/s41587-020-0740-8
- COSMIC: https://doi.org/10.1038/s41587-021-01045-9
General: https://doi.org/10.7554/eLife.70780
General: https://doi.org/10.1021/acs.analchem.5b04804
General: https://doi.org/10.3389/fpls.2019.01329
- NPClassifier: https://doi.org/10.1021/acs.jnatprod.1c00399
| Package | Version | Citation |
|---|---|---|
| base | 4.5.1 | R Core Team (2025) |
| baseline | 1.3.7 | Liland, Almøy, and Mevik (2010); Liland and Mevik (2025) |
| BiocManager | 1.30.26 | Morgan and Ramos (2025) |
| BiocParallel | 1.43.4 | Wang et al. (2025) |
| BiocVersion | 3.22.0 | Morgan (2025) |
| cascade | 0.0.0.9001 | Rutz and Wolfender (2023); Rutz (2025) |
| caTools | 1.18.3 | Tuszynski (2024) |
| data.table | 1.17.8 | Barrett et al. (2025) |
| gt | 1.0.0 | Iannone et al. (2025) |
| htmltools | 0.5.8.1 | Cheng et al. (2024) |
| knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) |
| MSnbase | 2.35.0 | Gatto and Lilley (2012); Gatto, Gibb, and Rainer (2020) |
| mzR | 2.43.1 | Pedrioli et al. (2004); Keller et al. (2005); Kessner et al. (2008); Martens et al. (2010); Chambers et al. (2012) |
| pkgload | 1.4.0 | Wickham et al. (2024) |
| plotly | 4.11.0 | Sievert (2020) |
| R.utils | 2.13.0 | Bengtsson (2025) |
| rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) |
| stringi | 1.8.7 | Gagolewski (2022) |
| testthat | 3.2.3 | Wickham (2011) |
| tidytable | 0.11.2 | Fairbanks (2024) |
| tidyverse | 2.0.0 | Wickham et al. (2019) |
| tima | 2.12.0 | Rutz et al. (2019); Rutz and Allard (2025) |
| WikidataQueryServiceR | 1.0.0 | Popov (2020) |
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