Untargeted metabolomics processing pipeline

This documentation describes the process of going from open-source mzML mass spectrometry files to aligned feature table(s). This is orchestrated by the script raw2feats.py. Each dataset folder must contain a machine-readable text file called a summary file which gives instructions to raw2feats.py. The format of this summary file, and all files required for MS processing, are described in this documentation.

Contents:

• Preparing your dataset for processing
• Data processing code
• Processing your data
• Common confusing errors

Indices and tables

• Index
• Module Index
• Search Page