Third-Cycle Courses

Faculty of Engineering | Lund University

Details for the Course Syllabus for Course KIM085F valid from Autumn 2020

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  • English
  • Every autumn semester
  • 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.
  • 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.
Knowledge and Understanding
  • For a passing grade the doctoral student must
  • be able to describe the basic principles of frequently used mass spectrometers for proteomics.
    be able to describe commonly used MS operation modes and quantitative approaches.
    be able to describe MS sample preparation workflows for both proteome and PTM analysis.
Competences and Skills
  • For a passing grade the doctoral student must
  • be able to perform and evaluate protein extraction and proteolytic digestion of proteins from cells, enrich PTMs (phosphorylation) and prepare samples for MS analysis.
    be able to operate the mass spectrometer for analysis of prepared samples.
    be able to perform a preliminary evaluation of obtained PTM-proteomic data.
Judgement and Approach
  • For a passing grade the doctoral student must
  • be able to demonstrate an holistic understanding of MS-based workflows for proteome and PTM analysis.
    be able to evaluate, choose and design well suited MS-based workflows to address specific scientific questions through proteomics.
Types of Instruction
  • Lectures
  • Laboratory exercises
  • Exercises
  • The 1-week intense course comprises lectures as well as wet and dry lab exercises.
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.
  • Failed, pass
Admission Requirements
  • On-going third cycle studies within life sciences and basic knowledge in protein biochemistry.
Assumed Prior Knowledge
Selection Criteria
  • Distributed handouts and scientific articles.
Further Information
  • The course is given each autumn through the Postgraduate Courses in the Life Sciences ( if at least 6 students are accepted.
Course code
  • KIM085F
Administrative Information
  • 2020-05-28
  • Senior lecturer Åsa Håkansson

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