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:

• 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

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

General: https://doi.org/10.1038/s41587-023-01690-2

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

• The RforMassSpectrometry packages suite for MS2 matching: https://doi.org/10.3390/metabo12020173
• chromatographR: https://doi.org/10.5281/zenodo.6944334
• NPClassifier: https://doi.org/10.1021/acs.jnatprod.1c00399