Introduction to Metabolomics Analysis


This course will provide an introduction to metabolomics data analysis using publicly available software and tools. Participants will become familiar with the current state of experimental design, data standards, analysis and sharing in metabolomics, particuarly through using the EMBL-EBI’s MetaboLights repository. There will be a large practical component, where participants will learn through hands-on tutorials to use a workflow-based approach and compute infrastructure for data analysis and data submission, under the guidance of the lecturers and teaching assistants.


This course is aimed at researchers who are new to the field of metabolomics and wish to learn the basics. Perhaps you normally work in a different field and have had the opportunity to send off some samples for metabolite profiling but are unsure about how to process your results – this course is for you. We will primarily focus on a basic introduction to metabolomics with a worked example using a predesigned LC-MS analysis workflow. The course assumes little prior knowledge of using bioinformatics tools.

Syllabus, tools and resources

During this course you will learn about:

  • Basic metabolomics
  • Metabolomics resources: MetaboLights, Phenomenal, MetaboFlow
  • Metabolomics tools made available through standardized, customisable workflows


After this course you should be able to:

  • Discuss basic analytical methods in metabolomics, and factors that contribute to designing a successful metabolomics study
  • Use standardized workflows to perform basic metabolomics analysis
  • Access metabolomics databases
  • Discuss the issues of data sharing and data standards in metabolomics

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