CASCADE

Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts.

⚠️ This repository is not functional, not maintained and will not be except for extreme interest.

It has just been opened for the sake of transparency.

1. Run bash bash/create_batch_file.sh <PATH_TO_YOUR_FILE> <polarity>

2. Run mzmine -b <PATH_TO_BATCH_CREATED_IN_1>

3. Run Rscript inst/scripts/install.R

4. Run Rscript inst/scripts/1_process_compare_peaks.R

5. Run annotation (in tima-r)

6. Run Rscript inst/scripts/2_process_plot_pseudochromatgrams.R

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.

MZmine3

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