---
title: General comments about the use of CASCADE
author: Adriano Rutz
creative_commons: CC BY-SA
date: "`r Sys.Date()`"
opengraph:
    image:
      src: https://github.com/adafede/cascade/blob/main/man/figures/logo.svg
      alt: Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts
    twitter:
      creator: "@adafede"
vignette: >
  %\VignetteIndexEntry{General comments about the use of CASCADE}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

This vignette describes the minimal requirements for **C**ontextualization of untargeted **A**nnotation with **S**emi-quantitative **C**harged **A**erosol **D**etection for pertinent characterization of natural **E**xtracts.

## Pre-requisites

- A file ([.mzML](https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzML)) containing [DDA MS](https://en.wikipedia.org/w/index.php?title=Data-dependent_acquisition) data with an additional detector ([PDA](https://en.wikipedia.org/wiki/UV_detectors), [ELSD](https://en.wikipedia.org/wiki/Evaporative_light_scattering_detector), [CAD](https://en.wikipedia.org/wiki/Charged_aerosol_detector))
- A file ([.csv](https://en.wikipedia.org/wiki/Comma-separated_values)) containing features, as obtained by [mzmine](https://mzio.io)
- A file ([.tsv](https://en.wikipedia.org/wiki/Tab-separated_values)) containing annotations, as obtained by [TIMA](https://taxonomicallyinformedannotation.github.io/tima)

All coming steps admit you already installed `cascade`:

```{r eval=FALSE, include=TRUE}
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](https://adafede.github.io/cascade/articles).

## A note about parallelization

This package uses `{furrr}` from the [futureverse](https://www.futureverse.org/).
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.