---
title: General comments about the use of CASCADE
author:
  name: Adriano Rutz
  orcid: 0000-0003-0443-9902
citation:
  url: https://adafede.github.io/cascade/vignettes/cascade.html
comments:
  giscus:
    repo: adafede/cascade
  hypothesis:
    showHighlights: always
creative_commons: CC BY
date: today
format:
  html:
    smooth-scroll: true
google-scholar: true
knitr:
  opts_chunk:
    collapse: true
    comment: "#>"
lang: en
license: CC BY
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
vignette: >
  %\VignetteIndexEntry{General comments about the use of CASCADE}
  %\VignetteEngine{quarto::html}
  %\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 install, eval=FALSE, include=TRUE}
install.packages(
  "cascade",
  repos = c(
    "https://adafede.r-universe.dev",
    "https://taxonomicallyinformedannotation.r-universe.dev",
    "https://bioconductor.org/packages/release/bioc",
    "https://cloud.r-project.org"
  )
)
```

## More details

More details are available in the following vignettes:

- <https://adafede.github.io/cascade/vignettes/articles/I-basics.html>
- <https://adafede.github.io/cascade/vignettes/articles/II-processing.html>
- <https://adafede.github.io/cascade/vignettes/articles/III-bonus.html>
- <https://adafede.github.io/cascade/vignettes/articles/IV-tima.html>
