| 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 | 1.42.1 | Morgan et al. (2025) |
| BiocVersion | 3.21.1 | Morgan (2024) |
| 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 | 2.34.1 | Gatto and Lilley (2012); Gatto, Gibb, and Rainer (2020) |
| mzR | 2.42.0 | 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) |
CASCADE 
Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts.
⚠️ This repository is not maintained and will not be except for extreme interest. It has just been opened for the sake of transparency.
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.
Requirements
Here is what you minimally need:
Installation
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.
Main Citations
CASCADE
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.
mzmine
SIRIUS
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
LOTUS
General: https://doi.org/10.7554/eLife.70780
⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5794106
ISDB
General: https://doi.org/10.1021/acs.analchem.5b04804
⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5607185
TIMA
General: https://doi.org/10.3389/fpls.2019.01329
⚠️ Do not forget to cite which version you used: https://doi.org/10.5281/zenodo.5797920
Others
- NPClassifier: https://doi.org/10.1021/acs.jnatprod.1c00399
Additional software credits
References
Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown.
Barrett, Tyson, Matt Dowle, Arun Srinivasan, Jan Gorecki, Michael Chirico, Toby Hocking, Benjamin Schwendinger, and Ivan Krylov. 2025. data.table: Extension of “data.frame”. https://r-datatable.com.
Bengtsson, Henrik. 2025. R.utils: Various Programming Utilities. https://henrikbengtsson.github.io/R.utils/.
Chambers, Matthew C., Maclean, Brendan, Burke, Robert, Amodei, et al. 2012. “A cross-platform toolkit for mass spectrometry and proteomics.” Nat Biotech 30 (10): 918–20. https://doi.org/10.1038/nbt.2377.
Cheng, Joe, Carson Sievert, Barret Schloerke, Winston Chang, Yihui Xie, and Jeff Allen. 2024. htmltools: Tools for HTML. https://github.com/rstudio/htmltools.
Fairbanks, Mark. 2024. tidytable: Tidy Interface to “data.table”. https://markfairbanks.github.io/tidytable/.
Gagolewski, Marek. 2022. “stringi: Fast and Portable Character String Processing in R.” Journal of Statistical Software 103 (2): 1–59. https://doi.org/10.18637/jss.v103.i02.
Gatto, Laurent, Sebastian Gibb, and Johannes Rainer. 2020. “MSnbase, Efficient and Elegant r-Based Processing and Visualisation of Raw Mass Spectrometry Data.” bioRxiv.
Gatto, Laurent, and Kathryn Lilley. 2012. “MSnbase - an r/Bioconductor Package for Isobaric Tagged Mass Spectrometry Data Visualization, Processing and Quantitation.” Bioinformatics 28: 288–89.
Iannone, Richard, Joe Cheng, Barret Schloerke, Ellis Hughes, Alexandra Lauer, JooYoung Seo, Ken Brevoort, and Olivier Roy. 2025. gt: Easily Create Presentation-Ready Display Tables. https://gt.rstudio.com.
Keller, Andrew, Jimmy Eng, Ning Zhang, Xiao-jun Li, and Ruedi Aebersold. 2005. “A Uniform Proteomics MS/MS Analysis Platform Utilizing Open XML File Formats.” Mol Syst Biol.
Kessner, Darren, Matt Chambers, Robert Burke, David Agus, and Parag Mallick. 2008. “ProteoWizard: Open Source Software for Rapid Proteomics Tools Development.” Bioinformatics 24 (21): 2534–36. https://doi.org/10.1093/bioinformatics/btn323.
Liland, Kristian Hovde, Trygve Almøy, and Bjørn-Helge Mevik. 2010. “Optimal Choice of Baseline Correction for Multivariate Calibration of Spectra.” Applied Spectroscopy 64: 1007–16. https://doi.org/10.1366/000370210792434350.
Liland, Kristian Hovde, and Bjørn-Helge Mevik. 2025. baseline: Baseline Correction of Spectra. https://github.com/khliland/baseline/.
Martens, Lennart, Matthew Chambers, Marc Sturm, Darren Kessner, Fredrik Levander, Jim Shofstahl, Wilfred H Tang, et al. 2010. “MzML - a Community Standard for Mass Spectrometry Data.” Mol Cell Proteomics. https://doi.org/10.1074/mcp.R110.000133.
Morgan, Martin. 2024. BiocVersion: Set the Appropriate Version of Bioconductor Packages. https://doi.org/10.18129/B9.bioc.BiocVersion.
Morgan, Martin, and Marcel Ramos. 2025. BiocManager: Access the Bioconductor Project Package Repository. https://bioconductor.github.io/BiocManager/.
Morgan, Martin, Jiefei Wang, Valerie Obenchain, Michel Lang, Ryan Thompson, and Nitesh Turaga. 2025. BiocParallel: Bioconductor Facilities for Parallel Evaluation. https://doi.org/10.18129/B9.bioc.BiocParallel.
Pedrioli, Patrick G A, Jimmy K Eng, Robert Hubley, Mathijs Vogelzang, Eric W Deutsch, Brian Raught, Brian Pratt, et al. 2004. “A Common Open Representation of Mass Spectrometry Data and Its Application to Proteomics Research.” Nat Biotechnol 22 (11): 1459–66. https://doi.org/10.1038/nbt1031.
Popov, Mikhail. 2020. WikidataQueryServiceR: API Client Library for “Wikidata Query Service”. https://github.com/bearloga/WikidataQueryServiceR.
R Core Team. 2025. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Rutz, Adriano. 2025. cascade: Contextualizing Untargeted Annotation with Semi-Quantitative Charged Aerosol Detection for Pertinent Characterization of Natural Extracts.
Rutz, Adriano, and Pierre-Marie Allard. 2025. tima: Taxonomically Informed Metabolite Annotation. https://doi.org/10.5281/zenodo.5797920.
Rutz, Adriano, Miwa Dounoue-Kubo, Simon Ollivier, Jonathan Bisson, Mohsen Bagheri, Tongchai Saesong, Samad Nejad Ebrahimi, Kornkanok Ingkaninan, Jean-Luc Wolfender, and Pierre-Marie Allard. 2019. “Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation.” Frontiers in Plant Science 10. https://doi.org/10.3389/FPLS.2019.01329.
Rutz, Adriano, and Jean-Luc Wolfender. 2023. “Automated Composition Assessment of Natural Extracts: Untargeted Mass Spectrometry-Based Metabolite Profiling Integrating Semiquantitative Detection.” Journal of Agricultural and Food Chemistry 71 (46). https://doi.org/10.1021/acs.jafc.3c03099.
Sievert, Carson. 2020. Interactive Web-Based Data Visualization with r, Plotly, and Shiny. Chapman; Hall/CRC. https://plotly-r.com.
Tuszynski, Jarek. 2024. caTools: Tools: Moving Window Statistics, GIF, Base64, ROC AUC, Etc.
Wickham, Hadley. 2011. “testthat: Get Started with Testing.” The R Journal 3: 5–10. https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.
Wickham, Hadley, Winston Chang, Jim Hester, and Lionel Henry. 2024. pkgload: Simulate Package Installation and Attach. https://github.com/r-lib/pkgload.
Xie, Yihui. 2014. “knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
———. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.
———. 2025. knitr: A General-Purpose Package for Dynamic Report Generation in R. https://yihui.org/knitr/.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.
Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.