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Summer school for PhD students and Early career researchers

September 15-22, 2021.

Name of course: Introduction to Environmental Metabolomics  

Course parameters: 

Language: English 

Level of course: PhD and early career researcher course 

Time of year: Q3, 2021. The course will take place as a 6-day summer school during September 15-22, 2021. 

No. of contact hours/hours in total incl. preparation, assignment(s) or the like:  

6 days of lectures, exercises and workshops (48 h) 

Preparation by reading book chapters, articles and preparing data for analysis (50 h) 

Capacity limits: max. 25, min. 10 participants. PhD students and early career researchers have highest priority.  

Course fee: €400 (3,000 DKK). 

ECTS credits: 5

Objectives of the course: 

Untargeted metabolomics is the comprehensive characterization of metabolites present in organisms and it is the closest measure of the phenotype at the molecular level. Application of metabolomics within the environmental sciences is known as environmental metabolomics and allows for studying interactions between organisms and the surrounding environment.
Moreover, it involves the study of (secondary) metabolites and interaction between host organisms and microbiomes, the exo- and endometabolomes, and it includes exposome characterization and non-targeted chemical screening to study the environmental occurrence, fate and impact of chemicals released from anthropogenic activities.   

The aim of the summer school is to introduce state-of-the-art environmental metabolomics based on high-resolution mass spectrometry including its possibilities and shortcomings.
The course will introduce analytical hardware (e.g. Orbitrap mass spectrometry) and acquisition strategies, study design and sample preparation in an environmental context.
The course will place its main focus (day 2-6) on working with state-of-the-art informatic tools for data (pre-)processing and statistical analysis, e.g. MZmine, XCMS, GNPS, Compound Discoverer, MatLab and R.
Participants can bring own untargeted metabolomic data for use in the workshops.  


The participants need to have a background in natural science at MSc level. Experience in Matlab, R,  Compound Discoverer, MZmine, XCMS or GNPS is an advantage. 

Name of lecturer[s]:

Martin Hansen (Aarhus University), Xiaomin Zhou (Aarhus University), Rikke Poulsen (Aarhus University) and several guest researchers, experts and companies. 

Type of course/teaching methods: 

Lecture, seminars, conference talks, exercises, workshops, and participant presentations. 


Department of Environmental Science, Aarhus University 

Time: September 15 to 22, 2021 

Place: Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde,         Denmark. https://envs.au.dk/en/ominstituttet/directions-map/ 


Send e-mail to Associate Professor Martin Hansen (martin.hansen@envs.au.dk), include your CV with a publication list, and in the message clearly stating your current experience within untargeted metabolomics (e.g. data acquisition, data analysis and informatic tools) and if you will bring your own study data for the workshops. 

Deadline for registration is September 5, 2021. Information regarding admission will be sent out no later than September 7, 2021.  

If you have any questions, please contact 

Associate Professor Martin Hansen  (martin.hansen@envs.au.dk)

Link to course description at Graduate School is pending.


Martin Hansen

Associate Professor Department of Environmental Science - Environmental chemistry & toxicology