Pathway Analysis for Targeted and Untargeted Metabolomics

Methods Mol Biol. 2020;2104:387-400. doi: 10.1007/978-1-0716-0239-3_19.


Recent advances in analytical techniques, particularly LC-MS, generate increasingly large and complex metabolomics datasets. Pathway analysis tools help place the experimental observations into relevant biological or disease context. This chapter provides an overview of the general concepts and common tools for pathway analysis, including Mummichog for untargeted metabolomics. Examples of pathway mapping, MetScape, and Mummichog are explained. This serves as both a practical tutorial and a timely survey of pathway analysis for label-free metabolomics data.

Keywords: MetScape; Metabolic network; Metabolomics; Mummichog; Pathway analysis; Untargeted metabolomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Chromatography, Liquid
  • Computational Biology / methods*
  • Data Analysis
  • Databases, Factual
  • Humans
  • Metabolic Networks and Pathways*
  • Metabolomics* / statistics & numerical data
  • Software*
  • Tandem Mass Spectrometry
  • User-Computer Interface