General comments about the use of CASCADE

This vignette describes the minimal requirements for Contextualization of untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts.

Pre-requisites

A file (.mzML) containing DDA MS data with an additional detector (PDA, ELSD, CAD)
A file (.csv) containing features, as obtained by mzmine
A file (.tsv) containing annotations, as obtained by TIMA

All coming steps admit you already installed cascade:

install.packages(
  "cascade",
  repos = c(
    "https://adafede.r-universe.dev",
    "https://bioc.r-universe.dev",
    "https://cloud.r-project.org"
  )
)

More details

More details are available in the related vignettes.

A note about parallelization

This package uses {furrr} from the futureverse. If you think you could benefit from parallelization, have a look at https://future.futureverse.org/reference/plan.html to see how to set it up.