NSCPHD1225  Advanced Chromatography and Mass Spectrometry

Volume 2015/2016


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This course shares lectures, colloquia sessions, laboratory and theoretical exercises with the MSc course "Advanced Analytical Chemistry - Chromatography and Mass Spectrometry - NPLK13004U

Advanced course in chromatography and mass spectrometry for chemical analysis of organic compounds. This 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 organic compounds with special emphasize on the molecular mechanism and theory of analyte-column interactions for liquid and gas chromatography, and the theory of ionization, fragmentation, mass separation, detection and data-analysis for all kind of mass spectrometers and ionization techniques in common use coupled to gas chromatography, liquid chromatography and capillary electrophoresis. All common analytical instruments and techniques from GC-FID/MS to UPLC-UV/FLU/MSMS are addressed. The theory is supplemented with computer simulations and hands-on experiments and expert guest-lectures of selected topics.

Learning Outcome

Skills - the students should be able to:

  • Describe, compare and contrast, operate and optimise common mass spectrometric ionisation techniques and mass analysers
  • Describe, compare and contrast common detectors for chromatography other than mass spectrometers.
  • Describe, perform and evaluate fragmentation experiments and exact mass measurements using mass spectrometry.
  • Assess, quantify and compensate for matrix effects in ionization processes.
  • 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.
  • 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 analytes from complex matrices including selection and assessment of column, mobile phase and chromatographic parameters, ionisation source and mode, and mass analyser parameterisation.
  • Put the chromatographic and mass spectrometric theory and practice into the context of their own, or part of their own, PhD-project research area. 

Knowledge - the students should have:

  • A solid theoretical understanding of chromatography and mass spectrometry at an advanced level.


  • 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.

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.
For questions feel free to contact Nikoline Juul Nielsen.
Lectures, student presentations of curriculum, expert lectures, excursions, hands-on experiments, theoretical exercises, computer simulations, and individual project related to your PhD.
7,5 ECTS
Type of assessment
Oral examination, 30 min
The examination format is a 30 min oral exam with three sub-tasks:
1) An overall subject within e.g. ionization or mass analysers with app. 5 sub-questions for which the student has 1 week of preparation. At the exam the student gives a 5 min introduction and we discuss the subject for an additional 10 min.
2) An overall subject within e.g. chromatographic techniques or detectors for chromatography with app. 2 sub-questions for which the student has 30 min of preparation. At the exam the student gives a short (1-2 min) introduction and we discuss the subject for an additional 5 min.
3) A question within e.g. the linear solvent strength model, the hydrophobic subtraction model or general chromatographic optimization. No preparation and we discuss for 5 min.
Exam registration requirements

In 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 handing in approved laboratory reports (4 out of 5) is required, individually or group-wise. The PhD-students should also hand in a project-report in order to get their diploma. 4 ECTS is given if students follow the course in either Chromatography only or Mass Spectrometry only; if this is the case only the subject matter will be assessed at the exam.

Marking scale
passed/not passed
Censorship form
No external censorship
Exam period

Block 2 exam-week, module A exam-day (often Thursday) plus an additional day of the exam-week.

  • Category
  • Hours
  • Preparation
  • 120
  • Lectures
  • 48
  • Theory exercises
  • 16
  • Practical exercises
  • 16
  • Exam
  • 10
  • Total
  • 210