instructions.Rmd

---
title: "Instructions"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Steps
  
  1. Convert `.raw` files to `.mzML` format using the MSConvert software (Proteowizard) adding the filter `Peak Picking`      
  2. Search if the compound is in the [list](CompoundDb.html)  
  3. Check the RT and which is the main ion and annotate it in the csv file  
  4. Search if there are MS2 and MSn:  
    - if yes & if there is already and html file and new MS/MS to add:  
      - delete html  
      - remove previous MS/MS  
  5. Run:  
    - [compoundDB](CompoundDb.Rmd)  
    - [molecules](molecules.Rmd)  
    - [stats](stats.Rmd)  
    - [compoundDB](CompoundDb.Rmd)  
  
<br>
  
# Folders to check   
  
`WATERS/experiments/`  
  
  * `Marynka Raw Files ORBITRAP`  
    - `BARCELONA_MAR`  
      - `standards`  
        - `legumes`  
          - <span style="color: red;">``peptides``</span>  
          - <span style="color: red;">``reinnections_dedicated_method``</span>  
          - <span style="color: blue;">``stds_varis``</span>
        - <span style="color: red;">`...`</span>
      - <span style="color: red;">`...`</span>
    - `STD_LIBRARY` <span style="color: red;">`...`</span>  
    - <span style="color: red;">`...`</span>
  * `orbitrap_raw_files` <span style="color: red;">`...`</span>
  * <span style="color: red;">`...`</span>
  
<span style="color: red;">`...`</span> Indicates that the other folders contained in that one still have to be checked.  
<span style="color: blue;">`abcdef`</span> Indicates that what it is inside that folder (and subfolders) is already checked.  
  
<br>
  
**Last update:** `r format(Sys.time(), "%d %b %Y")`