Assumptions

We assume that you have:

  • a basic understanding of R and RStudio, and of metabolomics in general
  • access to the internet and remote access to your raw data
  • used Waters mass spectrometers and MassLynx software to obtain your data (although many steps in the workflow will be applicable to other instruments)
  • you have a sample list from MassLynx and that you can provide your own treatment information (metadata, though our code can help format this)
  • your files will be names with unique “Filename"s, ideally in the format of the following example:

  • experiment-identifier_001.raw
  • experiment-identifier_002.raw
  • experiment-identifier_003.raw

(you may have technical replicates, each with their own .raw file. This is dealt with in the documentation)

Extra assumptions for specific mass spectrometry approaches

  • If you wish to analyse LC-MS data, you will need to sign up for an XCMSonline/ METLIN account and have a working password (this can take a few days to activate so sign up ASAP)
  • We assume that if you have direct injection MS data, it has been run using an autoinjection system (and this is dealt with in the documentation)