BMB802: Proteomics: Technologies and applications in biochemistry and biomedicine (10 ECTS)

STADS: 01009001

Level
Master's level course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: mrl@bmb.sdu.dk

Additional teachers
f.kir@bmb.sdu.dk
jenseno@bmb.sdu.dk
tjdj@bmb.sdu.dk
bab@bmb.sdu.dk
jens.andersen@bmb.sdu.dk
php@bmb.sdu.dk
hjernoe@bmb.sdu.dk

Timetable
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Comment:
Max 18 på hvert labhold.

Prerequisites:
None

Academic preconditions:
Bachelors degree in Biochemistry/Molecular Biology, Biomedicine or Bioinformatics from SDU; equivalent bachelor degrees from other universities.
Additionally, basic knowledge of mass spectrometry, chromatography and electrophoresis is assumed.

Course introduction
Introduce students to proteomics technologies and their recent applications in biology and biomedicine. Mass spectrometry based strategies for functional proteomics are emphasized, as are applications in molecular cell biology, including protein expressions studies, protein interactions and post-translational modifications.

Expected learning outcome
When the course is completed, the student should be able to:

• Explain the concept of Matrix Assisted Laser Desorption/Ionisation and Electrospray Ionisation, and argue for the choice of ionisation method in a given life science application.
• Explain the principles in contemporary mass analysers that are used in proteomics, including the options for tandem mass spectrometry, and account for the advantages and disadvantages of these mass analysers.
• Describe the common techniques for quantitative analysis in proteomics.
• Assess and explain the common separation principles of liquid chromatography and their use in proteomics.
• Explain then principles of 1- and 2-dimensional electrophoresis and multidimensional chromatography and their use in proteomics.
• Explain the characteristics of MS and tandem MS of proteins/peptides, nucleic acids, carbohydrates and lipids.
• Interpret common mass spectra and tandem mass spectra of biomolecules.
• Perform protein identification from a mass spectrometry-based dataset.
• Outline concepts for characterisation of posttranslational modifications.
• Compare different techniques used in structure determination of proteins. 
• Use selected software to retrieve and interpret information from a proteomics dataset.
• Understand and assess the use of biomolecular mass spectrometry in original scientific literature.
• Outline experiments that can answer specific questions in the field of proteomics.

Subject overview

• Brush-up on protein chemistry, cell biology and basic mass spectrometry (MS).
• Advanced MS and tandem MS. Proteomics strategies (concept of protein ID by peptide mass mapping and tandem MS).
• Post-translational modifications (phosphorylation, glycosylation, acetylation, etc)
• Protein quantitation by MS (peptide intensity profiling, stable isotope labeling)
• Separation techniques (gelelectrophoresis, Liquid chromatography) in combination with MS.
• MS of non-protein biomolecules (Nucleic acids, lipids, carbohydrates).
• Structure and interactions studied by MS.
• Clinical proteomics/Biomedical proteomics/other contemporary applications.
• Computational proteomics/bioinformatics
• Alternative techniques (two-hybrid systems, phage display, protein arrays).

Literature
There isn't any litterature for the course at the moment.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
None

Assessment and marking:
(a) Lab. work. Pass/fail, internal evaluation by teacher. (01009022)
(b) Required assignments. Pass/fail, internal evaluation by teacher. Required assignments include approval of student presentations as well as a smaller theoretical project. (01009012)
(c) Project assignment. Danish 7 mark scale, internal examiner. (01009002)

Reexamination in same termin

Expected working hours
The teaching method is based on three phase model.

Forelæsninger, antal timer 24.
Eksaminatorietimer/opgaveregning, antal timer 36.
Laboratorieøvelser, antal timer 20.
Eksaminatorierne inkluderer obligatoriske studenterpræsentationer.
Educational activities

Language
This course is taught in English, if international students participate. Otherwise the course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.