This is an online handout for mass spectrometry based metabolomics data analysis. It would cover a full reproducible metabolomics workflow for data analysis and important topics related to metabolomics. Here is a list of topics:

  • Sample collection
  • Sample pretreatment
  • Principles of metabolomics data analysis
  • Software selection
  • Batch correction
  • Annotation
  • Omics analysis
  • Exposome

This is a book written in Bookdown. You could contribute it by a pull request in Github. A workshop based on this book could be found here. Meanwhile, a docker image xcmsrocker is available for metabolomics reproducible research.

R and Rstudio are the software needed in this workflow.