Chapter 1 Prerequisites

  1. Download OpenMS for converting the format of MS2-files

  2. (optional) Download WinSCP for transferring local files to the server of GNPS

  3. Export MS2-files as .mzML from \(dataanalysis\)

  4. In order to install all essential packages, please run script set_up_enviroment.R under the folder of J:\CBMR\SUN-CBMR-Metabolomics\Workflow\Scripts\utils\utils_MS2_set_up before doing any step

  5. If you would like to use tools on GNPS, please register for your personal username and password

  6. You should replace values of variables with yours under the section ends with 🕵️

  7. You could select whether run the section ends with ✈️