Introduction to Metabolomics Analysis


 Tuesday 5 Friday 8 February 2019


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom

Application opens: 

Friday 28 September 2018

Application deadline: 

Monday 26 November 2018


Open application with selection


Johanna Langrish

Registration fee: 

£600 (Including Accommodation)

Registration closed

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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, particularly through using the EMBL-EBI’s MetaboLights repository and PhenoMeNal infrastructure. There will be a practical component, where participants will learn through hands-on tutorials to use some of the tools available for data analysis and data submission. The course will be completed with an interactive session which will build on the weeks learning to discuss how to develop a metabolomics workflow with a clinical case study.

Syllabus, Tools and Resources

During this course you will learn about:

  • Basic metabolomics experimental design
  • Case study based on a clinical example
  • Metabolomics resources: MetaboLights, Phenomenal, MetaboFlow
  • Open source metabolomics tools made available through customisable workflows.



This course is aimed at researchers who are new to the field of metabolomics and wish to learn about the process of developing a metabolomics study. Attendees will gain an understanding of the workflow process and some of the analysis techniques and so should benefit those who are planning to include metabolite profiling in their work, either moving into the field or as an addition to other omics. 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.


After this course you should be able to:

  • Discuss basic analytical methods in metabolomics, and factors that contribute to designing a successful metabolomics study
  • Discuss the issues of data sharing and data standards in metabolomics
  • Access metabolomics resources
  • Be familiar with the principles of creating a standardized workflow to perform basic metabolomics analysis


Day 1: Introduction to metabolomics & analysis; preprocessing

Day 2: Analysis; data interpretation and statistics

Day 3: Analysis; Metabolite annotation

Day 4: Case study and data management