Course at EMBL-EBI

Introduction to metabolomics analysis

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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.

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 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.

What will I learn?

Learning outcomes

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
Course content

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.


Alexandra Holinski
Keeva Cochrane
Claire O’Donovan
Nicola Gray
University of Reading, UK
Ralf Weber
University of Birmingham, UK
Alyssa Imbert
CNRS, France
Steffen Neumann
IPB, Halle, Germany
MetaboLights team
Kim Kultima
Uppsala University, Sweden


Day 1 – Tuesday 5th February 2019
10:30 Registration & coffee  
11:00 - 11:30 Introduction to EMBL-EBI Alexandra Holinski
11:30 - 13:00

Part 1 Overview experimental design

Experimental design - ensuring data quaility

Nicola Gray
13:00 - 14:00 Lunch  
14:00 - 15:30 Part 1 Introduction to analytical platforms;
overview all options; Introduction to LC-MS
Hands on experimental design
Nicola Gray
15:30 - 16:00 Tea/coffee break  
16:00 - 17:00 Part 2 Basics of metabolomics analysis; What is
a workflow
Ralf Weber
18:30 Evening meal  
Day 2 – Wednesday 6th February 2019
09:30 - 10:30 Part 3 Processing data Ralf Weber
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Part 3 Processing data Ralf Weber
13:00 - 14:00 Lunch  
14:00 - 15:30 Part 4 Introduction to data interpretation & stats Alyssa Imbert
15:30 - 16:00 Tea/coffee break  
16:00 - 17:30 Part 4 Introduction to data interpretation & stats Alyssa Imbert
18:30 Evening meal  
Day 3 – Thursday 7th February 2019
09:30 - 10:30 Part 5 Metabolite Annotation Steffen Neumann
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Part 5 Metabolite Annotation Steffen Neumann
13:00 - 14:00 Lunch  
14:00 - 15:00 Hands-on session Steffen Neumann
15:00 - 15:30 Tea/coffee break  
15:30 - 16:30

Introduction to MetaboLights database

MetaboLights Labs - Workspace

MetaboLights Team
16:30 - 17:30 Posters  
18:30 Evening meal  
Day 4 – Friday 8th February 2019
09:30 - 10:30 MetaboLights study submission MetaboLights Team
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Clinical case study Kim Kultima
12:30 - 13:30 Lunch  
13:30 - 15:00 Clinical case study Kim Kultima
15:00 - 15:30 Wrap-up and course feedback Alexandra Holinski
15:30 Coach to Cambridge train station  

In order to be considered for a place on this course, applicants must do the following:

  1. Complete the online application form
  2. Submit a WORD document to containing 200 words for your biography and work history and a 100 words on your current research interests (300 words total).
  3. Provide a letter of support from a supervisor or a senior co-worker, explaining why you should be selected for this course

Further details will be provided in the confirmation email after completing the online form

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

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Course materials

05 - 08 February 2019
European Bioinformatics Institute United Kingdom
Johanna Langrish

  • Claire O’Donovan
  • Keeva Cochrane
  • Alexandra Holinski

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