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Hands-on Liquid Chromatography–Mass spectrometry course in the analysis of small molecules (phytochemicals, contaminants, primary metabolites) (Summer, 2015)

Name of course:

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

ECTS credits:


Course parameters:

Language: English

Level of course : PhD Course

Time of year: Monday 8 June – Friday 19 June 2015

No. of contact hours/hours in total incl. preparation, assignment(s) or the like:
Preparatory reading of textbook: Approx. 40 hours.

Monday 8 June – Friday 19 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

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.

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)

Name of lecturers:

  • Associate professor Inge S. Fomsgaard (course coordinator)  
  • Laboratory Technicians Bente Laursen, Kirsten Heinrichson, Claudia Jensen, Postdocs Thomas Etzerodt, Stine Krogh Steffensen, Hans A. Pedersen, Research assistants Khem B. Adhikari, Nanna Vidkjær, PhD students Fariha Tanwir, Weronika Graj, Fábio Schneider, Enock Dankyi
  • Mass spectrometry specialist, ABSciex; James Rudge, Phenomenex, Frants Roager Lauritsen, University South Denmark; Bo Svensmark, University of Copenhagen


Type of course/teaching methods:

Lectures, practical exercises


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

Course homepage:


Course assessment:

Elaboration of a 30-40 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.


Department of Agroecology

Special comments on this course:

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), e-mail:


Accommodation will be at Danhostel in Slagelse, Bjergbygade 78, DK-4200 Slagelse.


Comments from participants in our 2013 course:

"I felt like I was stuck and I couldn’t make a valid progress on my project, but during the course I have got my motivation back and I am excited to go back to apply what I have learnt here"

" The opportunity to handle the instrument and able to see the result from your own research work was very rewarding"

" The course has been really well organized and conducted. It is rare to experience such a comprehensive course."

"Perfect combination of theory and practice"


Monday 8 June – Friday 19 June 2015


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


Deadline for registration and payment:

Deadline for registration: 1 March, 2015. Maximum number of participants: 12. First come, first served.

Information regarding admission will be sent at registration.


For registration: Please register at 


If you have any questions, please contact contact Sonja Graugaard, e-mail:

Comments on content: 
Revised 05.11.2018