Course Syllabus for


KIM085F, 3 credits

Valid from: Autumn 2020
Decided by: Senior lecturer Åsa Håkansson
Date of establishment: 2020-05-28

General Information

Division: Immunotechnology
Course type: Third-cycle course
Teaching language: English


Mass spectrometry (MS)-based proteomics today enables the identification of over 1000 peptides per minute and is frequently used in basic protein-related research as well as for analysis of clinical samples, such as plasma in biomarker studies. The function of proteins is often dynamically regulated by so-called post translational modifications (PTMs) such as phosphorylation, glycosylation and methylation. This course gives an overview of the theory and practice for large-scale MS-based analysis of proteomes and PTMs. After completion of the course, participants are expected to be able to design and perform tailored MS-based workflows to address specific scientific questions.


Knowledge and Understanding

For a passing grade the doctoral student must

Competences and Skills

For a passing grade the doctoral student must

Judgement and Approach

For a passing grade the doctoral student must

Course Contents

The course gives an overview on how mass spectrometry (MS) can be used for large scale quantitative analysis of proteins and their post translation modifications (PTMs). Lectures cover the theory of mass spectrometry as well as key aspects of MS-based proteomic workflows, including enrichment of PTMs. Wet lab exercises give hands on experience with sample preparation, including PTM enrichment, for MS analysis as well as MS instrument operation. Dry lab exercises concern annotation and interpretation of MS fragment spectra for both unmodified and PTM-containing peptides.

Course Literature

Distributed handouts and scientific articles.

Instruction Details

Types of instruction: Lectures, laboratory exercises, exercises. The 1-week intense course comprises lectures as well as wet and dry lab exercises.

Examination Details

Examination formats: Written report, seminars given by participants. Pass or fail. To pass the course, student must have (1) attended > 95 % of lectures and exercises, (2) given a 15-minute oral presentation on how proteomics can be implemented in the student’s research and (3) written a 1-page report on the same topic.
Grading scale: Failed, pass

Admission Details

Admission requirements: On-going third cycle studies within life sciences and basic knowledge in protein biochemistry.

Further Information

The course is given each autumn through the Postgraduate Courses in the Life Sciences ( if at least 6 students are accepted.

Course Occasion Information

Contact and Other Information

Course coordinators:

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