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Hands-on Liquid Chromatography–Mass spectrometry course in the analysis of small molecules (phytochemicals, contaminants, primary metabolites) (2020)

ECTS credits:

Course parameters:
Language: English
Level of course: PhD course
Time of year: Monday 8 June – Friday 19 June 2020
No. of contact hours/hours in total incl. preparation, assignment(s) or the like: Total hours workload: 230 – Preparatory reading of textbook: Approx. 40 hours. Hours per week during two weeks on-site work: approx 45/per week. 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 is 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 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; PhD students Bina Bhattarai, Kourosh Hooshmand, Hamidreza Ardalani, Hossein Hazrati.

Visiting lecturers:
Mass spectrometry specialist, Sciex; Chromatography specialist, Phenomenex.

Type of course/teaching methods:
Lectures, practical exercises

Study material will be shipped to the participating students not later than 15 May 2020.

Course homepage:

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.

Department of Agroecology, Aarhus University

Special comments on this course:
Lab days will include Saturday 13 June 2020. Sunday will be off.

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

Comments from participants in our 2019 course:

  • “Possibility to go to the lab on day 1, prepare and run samples right away”
  • “A very dense schedule with efficient use of time”
  • “The most rewarding thing about this course is that it was so much more than I expected. The way of teaching, the hands-on and the teachers were all amazing”
  • “It was very nice that a second week was focused on our own projects, where we could run our own samples, optimize methods for own analytes. That was very exciting”
  • “It was very nice to combine the basic study with practical study”

Monday 8 June – Friday 19 June 2020

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

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

Research Centre Flakkebjerg
Department of Agroecology
Aarhus University
Forsøgsvej 1
DK-4200 Slagelse

Tel: +45 87 15 81 92

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


Deadline for registration and payment: 15 March 2020. Maximum number of participants: 12. First come, first served.  Please register at https://events.au.dk/Hands-on-2020.

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 2020. 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

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