Advanced Analytical Chemistry - Chromatography and Mass Spectrometry

Course content

Today, chromatography and mass spectometry are by far the most common used analytical techniques. A thorough understanding of the chromatographic theory, and operating mechanism of ionisation techniques and mass analysers is essential for method selection, development and optimisation. This is an advanced course in chromatography and mass spectrometry for chemical analysis of organic compounds. The course is a natural extension of any basic course in analytical chemistry for everybody who is going to use modern hyphenated techniques such as GC-MS, LC-MS(MS) for analysis of complex mixtures.

The course covers chromatographic separation of small molecule organic compounds with special emphasize on the molecular mechanism and theory of analyte-column interactions for gas, supercritical fluid and liquid chromatography, and the theory of ionization, fragmentation, mass-to-charge separation, ion detection and data interpretation for all common mass spectrometers and ionization techniques. The theory is taught using lectures, colloquia sessions, laboratory and theoretical exercises supplemented with guest-lectures of selected topics.


MSc Programme in Chemistry
MSc Programme in Environmental Science

Learning outcome

After completing the course the student should have acquired:

Knowledge - the student has:
-A solid theoretical understanding of chromatography and mass spectrometry at an advanced level.
-Some experience in adressing complex analytical problems, and acquaintance with tools to solve them.
- Hands-on experience with advanced and diverse chromatographic systems and mass spectrometers.

Skills - the student will be able to:
 -Describe, compare and contrast, operate and optimize common ionization techniques and mass analysers.
-Describe, perform and evaluate exact mass measurements and fragmentation experiments using mass spectrometers.
-Asses, quantify and compensate for matrix effects in ionization processes.
-Use mass spectrometry and fragmentation theory to annotate mass spectra.
-Describe and use the rate theory, the plate theory, the linear solvent strength model and the hydrophobic subtraction model to optimize chromatography, select and characterize columns and to explain experimental data.
-Use chromatographic theory to predict retention behavior.
-Describe, compare and contrast, operate common chromatographic techniques.
-Optimise in a time- and cost effective manner any chromatographic separation.
-Critically assess reported chromatographic and/or mass spectrometric research.
-Select suitable analytical platform for the separation, detection and quantification of analytes from complex matrices including selection and assessment of column, mobile phase and chromatographic parameter; ionisation mode, source and mass analyser parameterisation.

Competences - enables the student to:
- Plan and perform analysis of complex mixtures using modern chromatographic techniques and high-end detectors, including the selection of method, columns and mode of detection, as well as optimization of chromatographic and mass spectrometric conditions for all common instrumental analytical separation methods.

Lectures, student presentations of curriculum (colloquia), guest lectures, hands-on experiments, theoretical exercises, computer simulations.

Specific literature is given on Absalon. Previous years we used:

Recent editions of:

"Introduction to Modern Liquid Chromatography", by Lloyd R. Snyder; Joseph J. Kirkland and John W. Dolan, Wiley 2009.

"Mass Spectrometry. Principles and Applications", by Edmond de Hoffmann and Vincent Stroobant, Wiley 2007.

“High-Performance Gradient Elution: The Practical Application of the Linear-Solvent-Strength Model”, by Lloyd Snyder and John Dolan, Wiley-Blackwell 2007.

“Interpretation of Mass Spectra”, by Fred McLafferty and Frantisek Turecek, University Science Books, 1993.

Furthermore, selected articles will be used.

The course NPLB14027U Analytical Chemistry or equivalent is recommended, since all basic theory of separation and mass spectrometry is assumed to be known. If you did not already pass this course, then you should contact the course responsible before signing up ( Recommended reading prior to or concurrent with the course: An analytical chemistry curriculum corresponding to a recent edition of Quantitative Chemical Analysis by Daniel C. Harris.

Academic qualifications equivalent to a BSc degree is recommended.

Continuous feedback during the course of the semester
Peer feedback (Students give each other feedback)
7,5 ECTS
Type of assessment
Oral examination, 20 min
25 min. preparation
All aids allowed

All aids allowed.

Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examiner
Criteria for exam assessment

The student should be able to explain, contrast and compare the operating mechanism of a range of chromatographic techniques, ionisation sources and mass spectrometers, preferably with examples from the laboratory exercises. The student should be able to explain and use the theoretical models for chromatography, which we used during the course.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 26
  • Class Instruction
  • 10
  • Preparation
  • 120
  • Theory exercises
  • 5
  • Laboratory
  • 20
  • Excursions
  • 4
  • Project work
  • 20
  • Exam
  • 1
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 2
A maximum of 30 participants
Study Board of Physics, Chemistry and Nanoscience
Contracting department
  • Department of Plant and Environmental Sciences
Contracting faculty
  • Faculty of Science
Course Coordinator
  • Nikoline Juul Nielsen   (3-7e7a7e50807c757e3e7b853e747b)

Ass. prof. Nikoline Juul Nielsen and others

Saved on the 01-03-2021

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