Hands-on Liquid Chromatography–Mass spectrometry course in the analysis of small molecules (phytochemicals, contaminants, primary metabolites) 2017

ECTS credits: 8


Course parameters:

Language: English

Level of course: PhD course

Semester/quarter: Monday, 12 June – Friday, 23 June 2017

Preparatory reading of textbook: Approx. 40 hours.

Monday, 12 June – Friday, 23 June: Long and intensive days, - part of the exercises will take place in the evening to assure that all participants have plenty of hands-on time.

Report writing: Approx. 100 hours

Capacity limits: 12 participants


Objectives of the course: Advanced tools such as liquid or gas chromatography coupled to mass spectrometry are necessary tool in the research into small molecules, either phytochemicals with defense or health properties, environmental contaminants such as pesticides or primary metabolites that can be affected by the presence of other bioactive compounds. The objective of the course is to teach the participant the theoretical background as well as the practical use of these tools for quantitative analysis as well as for identification. The course will take place in a well-equipped laboratory at Aarhus University, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark. LC-MSMS, LCMS-QTRAP,  LC-TOF, GC-TOF instruments will be available for the students during the course and our experienced staff will provide instruction on the use of the equipment as well as practical techniques for the preparation of samples.

For more information look here

Learning outcomes and competences:

At the end of the course the student should be able to:

  • Use LCMSMS or GCMS equipment for quantitative and qualitative analysis of small molecules
  • Give an account for the principles behind development of chromatographic methods for separation of small molecules
  • Perform a basic method validation for quantitative analysis in LCMSMS
  • Optimize the parameters for analysis of selected compounds
  • Use LCMS-QTRAP or LC-QTOF in the identification of small molecules or their metabolization products


Compulsory programme:

Entire course.


Course contents:

The course is constructed as follows:

  • Preparatory reading of selected chapters in an LC-MSMS textbook
  • Approximately three days of practical exercises on basic LC-MSMS, quantitation methods, optimization of parameters for selected small molecules, preparation of samples, matrix effects, validation of the quantitative method
  • Approximately three days of practical exercises chosen on the basis of each student’s on-going PhD project
  • Theoretical lessons on
  • Optimization of extraction methods
  • Method validation: LOD, LOQ, recovery, matrix interferences
  • ESI and APCI inlet systems
  • Use of an ion trap for analysis of small molecules
  • HPLC method development and optimization
  • Interpretation of mass spectra
  • Metabolomics
  • Representative sampling: plants, soil and water
  • Good Laboratory Practice
  • New developments in mass spectrometry
  • Subsequent elaboration of a 30- to 40-page report on the practical exercises.



The course is for PhD students (in special individual cases master students with already planned PhD projects can be given access)


Lectures from Aarhus University

Associate professor Inge S. Fomsgaard (course coordinator) http://pure.au.dk/portal/en/persons/id(286ea173-7565-4768-86a7-c97182c4081f).html

Laboratory Technicians Bente Laursen, Kirsten Heinrichson, Claudia Jensen, Postdocs Thomas Etzerodt, Stine Krogh Steffensen, Hans A. Pedersen, Khem B. Adhikari, Nanna Vidkjær, PhD students  Weronika Graj, Antje Reiss, Maheswor Dev Gautam.


Visiting lecturers

Mass spectrometry specialist, Sciex; Chromatography specialist, Phenomenex, Frants Roager Lauritsen, University South Denmark; Bo Svensmark, University of Copenhagen.


Type of course/teaching methods: Lectures, practical exercises


Literature: Study material will be shipped to the participating students not later than May 15.


Course assessment:

Elaboration of a 30- to 40-page report on the practical exercises. The report is assessed as "passed" or "not passed". Presence at a minimum of 90% of theoretical and practical lessons is required to obtain the course diploma.


Provider: Department of Agroecology, Aarhus University


Course venue:

The course venue is Research Centre Flakkebjerg, situated in Southwest Zealand, 10 km south of Slagelse (100 km west of Copenhagen). Complete address:

Department of Agroecology, Research Centre Flakkebjerg, Forsøgsvej 1,

DK-4200 Slagelse, Denmark, Tel: +45 87 15 81 92

Direct telephone number to Inge S. Fomsgaard (+45 87 15 82 12 or +45 22 28 33 99).




Accommodation will be at Hotel Antvorskov, Trafikcenter Alle 2-4, DK-4200 Slagelse.


Comments from participants in our 2015 course

  •  “I got new ideas for working with my samples at my own university”
  •  “In-depth working on the LC-MS –you really get to know the process of working with chromatography”
  • “I really liked that the schedule for the course was announced on the first day and everything went according to the plan. That was really professional”
  • “I liked a lot that we had a red line from sample preparation over optimization to sample analysis”

Time: Monday, 12 June – Friday, 23 June 2017


Place: Aarhus University, Department of Agroecology, Forsøgsvej 1, DK-4200 Slagelse, Denmark



Deadline for registration and payment:  15 March, 2017. Maximum number of participants: 12. First come, first served.  Please register at https://auws.au.dk/Hands-on_Liquid.


Registration is binding, but you may cancel your registration by sending an e-email to sonja.graugaard@agro.au.dk no later than 1 May 2017. If you cancel your registration later than 1 May, your registration fee will be forfeit, and your seat may be transferred to another person.

If you have any questions, please contact Sonja Graugaard, e-mail: sonja.graugaard@agro.au.dk