Course at EMBL-EBI

Introduction to metabolomics analysis

This course will provide an introduction to metabolomics using publicly available data, software and tools. Participants will become familiar with the current state of experimental design, data acquisition (LC-MS, GC-MS, MS imaging), processing and modelling as well as community standards and sharing in metabolomics, particularly through using the EMBL-EBI’s MetaboLights repository and Galaxy infrastructure. There will be a practical component, where participants will learn through hands-on tutorials to use tools available for data analysis and data submission. The course will be completed with an interactive session which will build on the week’s learning to discuss how to employ a metabolomics workflow with a case study.

In-person course

We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Who is this course for?

This course is aimed at researchers who are new to the field of metabolomics and wish to learn about the process of conducting a metabolomics study. Attendees will gain an understanding of a standardised workflow, from experimental design to data acquisition and analysis, and will benefit those who are planning to integrate metabolomics into their work, either moving into the field or as an investigator from other omics. We will primarily focus on a basic introduction to metabolomics with worked examples using a predesigned LC-MS analysis workflow. The course assumes little prior knowledge of using bioinformatics tools.

What will I learn?

Learning outcomes

After this course you should be able to:

  • Discuss basic data acquisition, processing and modelling in metabolomics, and factors that contribute to designing a successful metabolomics study
  • Discuss the issues of data standards and sharing in metabolomics
  • Access and use public metabolomics resources 
  • Be familiar with the principles of creating a standardised workflow to perform basic metabolomics analysis

Course content

During this course you will learn about:

  • Basic metabolomics experimental design, acquisition and analysis
  • Case study based on a published/public example
  • Public metabolomics resources: MetaboLights, Galaxy 
  • Open source metabolomics tools made available through customisable workflows.



Thomas Payne
Pamela Pruski
Elena Chekmeneva
Imperial College London
Goncalo Correia
Imperial College London
Rossana Zaru
Warwick Dunn
Liverpool University
Melanie Föll
University of Freiburg
Yann Guitton
Lorraine Brennan
University College Dublin
Theodore Alexandrov
EMBL, Heidelberg
This course has ended

24 - 27 May 2022
European Bioinformatics Institute
United Kingdom
Meredith Willmott

  • Claire O'Donovan
  • Thomas Payne
  • Pamela Pruski
  • Ajay Mishra

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