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Advanced Analytical Chemistry - Chromatography and Mass Spectrometry
Provider: Faculty of Science

Activity no.: 5707-21-09-31There are 29 available seats 
Enrollment deadline: 01/11/2021
PlaceDepartment of Plant and Environmental Sciences
Date and time15.11.2021, at: 08:00 - 30.01.2022, at: 16:00
Regular seats30
ECTS credits7.50
Contact personNikoline Juul Nielsen    E-mail address: njn@plen.ku.dk
Enrolment Handling/Course OrganiserNikoline Juul Nielsen    E-mail address: njn@plen.ku.dk
Written languageEnglish
Teaching languageEnglish
Semester/BlockBlock 2
Scheme groupA (Tues 8-12 + Thurs 8-17)
Scheme group noteExam period: Block 2 exam-week, module A exam-day (Thursday) plus an additional day of the exam-week (often Friday)
Exam requirementsIn order to be allowed at the exam 75% of active participation in student colloquia (3 out of 4); laboratory exercises (4 out of 5) and approved of laboratory reports (4 out of 5) is required, individually or group-wise
Exam formOral examination
Exam detailsInternal censor. The examination format is a 20 min oral exam with 20 min of preparation time. Text aids and calculator allowed during the preparation, but no devices which enables communication. The first two questions are known prior to the 20 min preparation: The first question will be on ionization techniques or mass analysers; the second question will be on chromatographic techniques; and the final question, which will be given to the student during the examination, will be on chromatographic optimization or theoretical models.
Grading scalePassed / Not passed
Course workload
Course workload categoryHours
Theory exercises25.00
Practical exercises20.00



Today, chromatography and mass spectometry are by far the most commonly 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 supplemented with laboratory exercises, computer simulations and visiting lectures on selected topics.

This course shares lectures, colloquia sessions, laboratory and theoretical exercises with the MSc course "Advanced Analytical Chemistry - Chromatography and Mass Spectrometry

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 addressing 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 a suitable analytical platform for the separation, detection and quantification of small molecule organic analytes from complex matrices including selection and assessment of column, mobile phase and chromatographic parameters, ionisation source and mode, and mass analyser parameterisation.

This course 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.


"Introduction to Modern Liquid Chromatography", by Lloyd R. Snyder, Douglas Kirkland and John W. Dolan, Wiley 2009, and "Mass Spectrometry. Principles and Applications", by Edmond de Hoffmann and Vincent Stroobant, 3rd Ed., Wiley 2007. "High-Performance Gradient Elution. The Practical Application of the Linear-Solvent-Strength Model", by Lloyd R. Snyder and John W. Dolan, Wiley 2007 and “Interpretation of Mass Spectra”, by Fred W. McLafferty and Frantisek Turecek, University Science Books 1993 will be used to some extend. Furthermore, selected articles will be included.

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


Nikoline Juul Nielsen is responsible for the primary part of the teaching; occasionally we also have PhD-students, post docs or senior scientists affiliated in some sense to the Analytical Chemistry Group teach their area of expertise.


Academic qualifications
As prerequisite a course in instrumental analysis, like the course "Analytical Chemistry", is strongly recommended, since all basic theory of separation, chromatographic instruments and mass spectrometry is assumed to be known.

Please contact Nikoline Juul Nielsen on njn@plen.ku.dk directly before registering online and if you have any questions.

Course fee:
For participants from Danish Universities teaching is free of charge. External students are charged 5.000 DKK for the teaching in addition to the running costs of 9.000 DKK

All PhD students (including those from Danish Universities) are charged for instrument-time, laboratory expenses and expenses related to excursions amounting to a total of 9.000 DKK for the full course (7.5 ECTS), and 5.000 DKK for each of the separate parts: Chromatography alone (4 ECTS) or Mass Spectrometry alone (4 ECTS).


UCPH discloses non-sensitive personal data to course leader/speakers, if any. In addition, we will disclose non-sensitive personal data to the other participants in the course. Non-sensitive personal data includes names, job positions, institution names & addresses, telephone numbers and e-mail addresses

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