Advanced Analytical Chemistry - Chromatography and Mass Spectrometry

Course content

Today, chromatography and mass spectometry are by far the most common used analytical techniques for separation and detection of molecules. 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 common mass spectrometers (quadrupole, TOF, Ion trap, Orbitrap, FT-ICR and their combinations) and ionization techniques (EI, CI, ESI, APCI, APPI, DESI etc).

The theory is taught using lectures, laboratory exercises and reports, theoretical exercises and colloquia sessions supplemented with guest-lectures of selected topics.

Currently softwares such as MassLynx and ChemStation are used for data acquisition, visualisation and inspection. Excel is used for simulations, data processing and for evaluating experimental designs. Electronic databases such as or NIST may also be used.


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 different types of chromatography (RP, NP, HILIC, SFC, IEC, IPC) and important stationary and mobile phases and molecular interactions associated with each type of chromatography.

-A solid theoretical understanding of different types of ionisation techniques (EI, CI, ESI, APCI, APPI, DESI), mass analysers (quadrupole, TOF, Ion trap, Orbitrap, FT-ICR and their combinations) and detectors as well as their mechanism of operation.

-Hands-on experience in separation and detection of small molecules from complex samples using diverse chromatographic systems and mass spectrometers.

- The ability to acquire raw data, and to critically asses instrumental raw data using digital tools i.e. instrument software for data acquisition and data interpretation.

Skills - the student will be able to:

-Describe and compare common chromatographic techniques, and select the most suitable technique for specific scientific problems. Operate and optimize chromatographic platforms.

-Describe and compare common ionization techniques, mass analysers and their mode of operation, and select the best set of ionization, mass analyser and mode of operation for specific scientific problems. Operate and optimize mass spectrometry platforms.

-Perform and evaluate exact mass measurements and fragmentation experiments using mass spectrometers.

-Asses and compensate for matrix effects in ionization processes.

-Use mass spectrometry- and fragmentation theory to annotate mass spectra.

-Describe and use chromatographic theory and mathematical models to optimize chromatographic separations, to select and characterize columns and to explain experimental data.

-Use chromatographic theory to understand and predict retention behavior.

-Optimise in a systematic manner chromatographic separations.

-Acquire, analyse and report chromatographic and mass spectrometric raw data.

-Critically assess information and research derived from chromatographic and/or mass spectrometric experiments.

-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; mass analyser as well as source and mass analyser parameterisation.

Competences - this course enables the student to:

- Plan and perform analysis of complex mixtures of small organic molecules using modern chromatographic techniques and mass spectrometers.

Lectures, student presentations of curriculum (colloquia), guest lectures, laboratory exercises and reports, theoretical exercises, computer simulations.

Specific literature is given on Absalon. Previous years we have 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
Type of assessment details
25 min. preparation
Exam registration requirements

Following are required for participation in the exam

  • Active participation in a minimum of 60% of colloquia activities is required to qualify for the exam. The 3 colloquia subjects are: 1) separation of polar compounds; 2) ionization; 3) recap on the laboratory exercises and
  • Active participation in a minimum of 80% of laboratory exercises and associated reporting activities is required to qualify for the exam. There are 5 laboratory exercises and associated reports embedded in the course.
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners.

The re-exam is as the ordinary exam.

Students who do not fulfill the requirements need to follow the course the following study year.

Criteria for exam assessment

The student should be able to describe, 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. The student should be able to predict chromatographic changes under specified conditions. The student should be able to describe fundamental principles used for compound identification from mass spectra.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 26
  • Class Instruction
  • 10
  • Preparation
  • 120
  • Theory exercises
  • 9
  • Excursions
  • 0
  • Laboratory
  • 20
  • 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
The number of seats may be reduced in the late registration period
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   (3-7470744676726b7434717b346a71)

Associate professor Nikoline Juul Nielsen and others

Saved on the 28-02-2023

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