Introduction to Metabolomics Analysis


 Monday 30 March Thursday 2 April 2020


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

Application opens: 

Monday 23 September 2019

Application deadline: 

Friday 06 December 2019


Open application with selection


Meredith Willmott

Registration fee: 

£590.00 - Including meals and accommodation

Registration closed

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This course will provide an introduction to metabolomics data analysis. It will focus on Liquid Chromatography – Mass Spectrometry techniques and will encompass a combination of lectures and practical sessions covering principles of experimental design, data standards and analysis. Participants will learn about data sharing of metabolomics data with the EMBL-EBI’s MetaboLights repository. Practicals will explore each stage of data analysis using training datasets and use freely-available metabolomics tools accessed through the Workflow4Metabolomics platform. The content will allow participants to create their own open-source analysis workflows to process LC-MS data based on the examples used during the course.


This course is aimed at scientists new to the field of metabolomics who want to gain insights into the data analysis process. The course assumes little prior knowledge of using bioinformatics tools and the workflow platform covered will allow a wide-range of backgrounds to access the practical content. Ideal applicants will be those wanting to include metabolite profiling in their current research, either as they move into the field or in addition to other -omics data work they are currently engaged in.

Syllabus, tools and resources

During this course you will learn about:

  • Fundamentals of metabolomics experimental design
  • Basic concepts of metabolomics data analysis
  • Availability of opensource tools available for metabolomics data analysis
  • How to combine tools to create an analysis workflow


After this course you should be able to:

  • Design experiments to generate high-quality metabolomics data
  • Generate standardised workflows to perform routine metabolomics analysis with publically-available software
  • Access and utilise metabolomics data resources
  • Recognise the importance of data standards and data sharing in the metabolomics field

Additional information

All participants are expected to present a poster that will be displayed during the course outside the training room. Please send your poster in PDF format to Meredith Willmott ( and we will print it on campus. 
All posters should:

  • be A2 in size - 420mm x 594 mm
  • be in a portrait orientation
  • include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.


W4M team Metabolomics team
Jean-François Martin Keeva Cochrane
Mélanie Pétéra Kenneth Haug
Franck Giacomoni Venkata Chandrasekhar Nainala
Estelle Pujos-Guillot  
Blandine Comte  


Day 1 – Monday 30 March 2020
11:00-12:00 Arrival and registration  
12:00-13:00 Lunch  
13:00-14:00 Welcome, introductions and networking Tom Hancocks & Keeva Cochrane
14:00-15:30 Introduction to metabolomics and experimental design Aniko Kende
15:30-16:00 Experimental design activity All
16:00-16:30 Break  
16:30-18:30 Untargeted LCMS metabolomics in nutrition and health Estelle Pujos-Guillot
18:30 End of day  
18:45 Check-in at accommodation  
19:30 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 31 March 2020
08:45-09:00 Arrival and registration  
09:00-10:00 Raw data formatting W4M team
10:00-10:30 Break  
10:30-11:30 Introduction to MetaboLights data EMBL-EBI Metabolomics team
11:30-12:30 Workflows using W4M platform W4M team
12:30-13:30 Lunch  
13:30-15:30 Data pre-processing W4M team
15:30-16:00 Break  
16:00-18:00 Data processing W4M team
18:00 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 3 – Wednesday 1 April 2020
08:45-09:00 Arrival and registration  
09:00-10:30 Statistics in metabolomics Julien Boccard
10:30-11:00 Break  
11:00-12:00 Statistics in metabolomics Julien Boccard
12:00-13:00 Statistics in workflows W4M team
13:00-14:00 Lunch  
14:00-15:30 Metabolite identification Elena Chekmeneva
15:30-16:00 Break  
16:00-17:00 Metabolite identification workflows W4M team
17:00-18:00 Submitting metabolomics data EMBL-EBI Metabolomics team
18:00 End of day  
19:00 Drinks on arrival Red Lion, Hinxton
19:30 Evening meal Red Lion, Hinxton
Day 4 – Thursday 2 April 2020
08:30 Check-out of accommodation  
08:45-09:00 Arrival and registration  
09:00-10:30 Using metabolic networks Nathalie Poupin 
10:30-11:00 Break  
11:00-12:00 Using metabolic networks Nathalie Poupin 
12:00-13:00 Lunch  
13:00-14:30 Getting to know metabolomics data Blandine Comte
14:30-14:45 Wrap-up & Feedback  
14:45 End of course  
15:00 Shuttle to Cambridge Station (Stop 5)