BMB542: Biomedical mass spectrometry – principles and applications

Study Board of Science

Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N200029102
Censorship: Second examiner: External
Grading: 7-point grading scale
Offered in: Odense
Offered in: Spring
Level: Bachelor

STADS ID (UVA): N200029101
ECTS value: 5

Date of Approval: 23-10-2018

Duration: 1 semester

Version: Approved - active


The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration.

Entry requirements


Academic preconditions

Academic preconditions. Students taking the course are expected to:

  • Have knowledge of organic chemistry, biochemistry, cell biology, biomedicine, as well as basic skills within mathematics, physics and statistics, corresponding to the courses in the first five semesters of a science degree at SDU.
  • Have basic computer skills
  • Have knowledge of the chemical structure of biomolecules including metabolites, drugs, lipids, proteins and nucleic acids
  • Be able to use chemical and biochemical terminology and biomedical concepts.
  • Have an understanding of the structure of molecules and cells, metabolism and other biochemical processes and basic cell signalling mechanisms.

Participant limit


Course introduction

The aim of the course is to enable the student to understand the principles of mass spectrometry (MS) and to get an overview of applications of the method in Biochemistry and Biomedicine. Mass spectrometry plays a central role in these research areas, also including clinical biochemistry.

The course builds on the knowledge acquired in the courses in cell biology, chemistry and biochemistry in the first five semesters of the bachelor programme, and gives an academic basis for studying the topics protein chemistry and proteome analysis, that are part of the degree. In addition, the course gives the academic basis for carrying out research projects and master projects with biomedical mass spectrometry, e.g. the topics metabolomics, lipidomics, protein chemistry/proteomics and computational biomedicine.

In relation to the competence profile of the degree it is the explicit focus of the course to:
  • Give the competence to enter into scientific discussions about the choice of method within biomedical mass spectrometry
  • Give the competence to set up experimental strategies where biomedical mass spectrometry is a central method
  • Give skills to set up methods, design experiments, and interpret data within biomedical mass spectrometry.
  • Give knowledge and understanding of sample preparation, ionisations methods, mass analysers and data analysis and interpretation, including interpretation of mass spectra and computer based data analysis.
  • Give knowledge about mass spectrometry in relation to systems biology experiments, including metabolomics, lipidomics and proteomics, as well as drug development and analysis, clinical biochemistry and forensic medicine.

Expected learning outcome

The learning objective of the course is that the student demonstrates the ability to:

  • Understand and describe common ionisation methods (ESI, MALDI, EI/CI)
  • Understand the importance of correct sample preparation, including understanding the physico-chemical parameters that affect ionisation of biomolecules and matrix effects.
  • Outline the principles of gas phase separation of ions in electric and magnetic fields.
  • Describe the structure of mass spectrometers and tandem mass spectrometers including hybrid instruments
  • Interpret mass spectra both manually and using computational tools
  • Understand the principles of molecular structure determination using mass spectrometry
  • Understand the principles of quantitative determination of biomolecules using internal standards and stable isotopes.
  • Select the best mass spectrometry technique to study a given class of biomolecules e.g. drugs, proteins, peptides, lipids, metabolites, nucleic acids.
  • Evaluate and suggest how Mass spectrometry can be used as a central method in specific biological and biomedical research projects.


The following main topics are contained in the course:
  • Short introduction to mass spectrometry and its many uses
  • History and development of mass spectrometry
  • Chemical structures and stable isotopes
  • Sample preparation, biomolecules
  • Separation methods (LG, GC, electrophoresis) and mass spectrometry
  • Ionisation methods with main focus on ESI and MALDI
  • Mass analysors (TOF, quadropole, orbitrap etc.) and their specifications
  • Hybrid mass spectrometers
  • Tandem mass spectrometers
  • Interpretation of mass spectra of biomolecules
  • Biomolecular structure determination by tandem mass spectrometry
  • Data analysis, computational tools and statistics
  • Cutting edge mass spectrometry methods and development
Selected applications of mass spectrometry within:
  • Analysis of drugs and their secondary metabolites
  • Qualitative and quantitative analysis of metabolites and lipids
  • Protein chemistry and protein structure analysis by mass spectrometry including peptide sequencing by tandem mass spectrometry
  • Qualitative methods for stable isotope labelling
  • The post-translational and chemical modifications of proteins
  • Imaging mass spectrometry
  • Forensic science, drug abuse, poisoning etc.
  • Food analysis
The above topics will be introduced in lectures followed by review/discussion of papers and assignments, as well as lab demonstrations and simple experiments. Data analysis will be done with a computer and by manual interpretation of mass spectra. In addition, we expect to invite 1-2 guest lecturer from relevant companies and hospitals to give an insight into specific uses of mass spectrometry in research/development.


See itslearning for syllabus lists and additional literature references.

Examination regulations

Exam element a)




Written exam




Second examiner: External


7-point grading scale


Student Identification Card


Normally, the same as teaching language


4 hours

Examination aids

Book and selected articles as well as the students’ own handwritten notes.
A closer description of the exam rules will be posted in itslearning.

ECTS value


Additional information

Assignment in English. The exam can be answered in Danish or english.

The examination form for re-examination may be different from the exam form at the regular exam: Re-examination 25 minuttes oral examination. 

Indicative number of lessons

32 hours per semester

Teaching Method

At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.
  • Intro phase (lectures, class lessons) - 16 hours
  • Training phase: 16 hours, including 10 hours tutorials and 6 hours laboratory
The intro phase is based on lectures which will introduce the basic concepts and methods. The lectures will be followed up by three mandatory two-hour demonstrations in the laboratory, which are then followed by one tutorial with assignments and data interpretation. In addition, there will be another three tutorials focused on interpretation of mass spectra and training in the use of data analysis tools. Thus, both theoretical and practical knowledge is obtained, as well as skills within data analysis and interpretation.

Activities during the study phase: 
  • Reading of scientific material: book and selected review papers and research papers
  • Repetition of scientific material, in connection with tutorials and lab demonstrations
  • A limited number of home assignments

Teacher responsible

Name E-mail Department
Ole Nørregaard Jensen Institut for Biokemi og Molekylær Biologi


Administrative Unit

Biokemi og Molekylær Biologi

Team at Registration & Legality


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