Objective and content

Objective and learning outcomes

The aim of the course is to give an understanding of the differences between untargeted and targeted metabolomics and the possibilities of combining both techniques in the research. 

The course will take place in a well-equipped laboratory at Aarhus University, Foulum. The following instruments will be available: LC-QTrap 5500 from ABsciex and LC-QTof from Bruker.

Also there will be an opportunity to analyze few of your own samples - please contact Natalja Nørskov for further information. 


After finalizing the course, the students will:

1)       Understand the differences in sample preparation between targeted and untargeted metabolomics

2)       Be able to prepare the samples for targeted and untargeted metabolomics

3)       Be able to optimize the instrument for targeted metabolomics

4)       Understand the use of QC samples, internal standards and blank samples

5)       Be able to validate the methods

6)       Be able to perform quantification of metabolites (targeted)

7)       Be able to perform data-processing and clean-up (untargeted)

8)       Be able to perform data interpretation using PCA (untargeted)


The course is mixture between lectures and hands-on laboratory work. The same samples will be used in both targeted and untargeted metabolomics.

The course covers the following topics:

·         Sample preparation

·         Method validation

·         Instrument optimization

·         Quantification with MRM

·         New quantification method MRM3

·         Data-processing and clean-up using DataAnalysis and ProfileAnalysis

·         Data interpretation using  Principal Component Analysis in LatentiX

·         Metabolite identification


Part of the practical exercises can take place in the evening, depending on the needs of participants. The purpose is that all the participants have plenty of hands-on time.

Participants are expected to deliver 160 working hours: 50-60 hours during the course week, including lectures and laboratory work and 100 hours preparation and written report.

Prerequisites and Course assesment

The course targets PhD students and researchers within the field of metabolomics and LC-MS.

For all participants the presence 90 % of the course is required to obtain the course diploma. For PhD students participation in the course plus written report (15-20 pages).

The report is assessed as “passed” or “not passed”.

Participants who are not PhD students and who do not need the ECTS points do not have to write the report.