Course syllabus for Computational proteomics

Datoranalys av proteomikdata

Specific entry requirements

A Bachelor´s degree or a professional degree worth at least 180 credits in biomedicine, biotechnology, cellular and molecular biology, medicine, or the equivalent. Proficiency in English equivalent to the Swedish upper secondary school course English 6/English B.

Outcomes

Proteomics platforms are broadly used in biomedical research to measure entire proteomes and to characterize their post-translational modifications. Similar to data from other omics platforms, the resulting data needs to be correctly processed in order to obtain high-quality results and interpretations. This course provides basic knowledge of the most popular proteomics approach, peptide mass spectrometry, and the different steps in the data analysis. Furthermore, common concepts of quality control and quantitative analysis are introduced.
On completion of the course, the student should be able to:

1. explain the basic concepts of peptide mass spectrometry,
2. discuss different experimental approaches to quantify proteins,
3. describe the data analysis steps from raw spectra to interpretation,
4. apply quality control of proteomics data,
5. use tools for quantitative analysis.

Content

This course covers the following topics:

1. Basics of proteomics and mass spectrometry
2. Experimental design and statistics
3. Identification of proteins and post-translational modifications
4. Differential and functional analysis
5. Visualization and quality control
6. Proteomics databases

Teaching methods

The course is at Master's level, where students are assumed to be familiar with the most common study methods in higher education. The fundamental pedagogical view is based on learning as an active research process. Learning activities include:

1. On-line videos
2. Structured learning activities (Open EdX platform)
3. On-line assignments

Examination

On-line assignments and final written report. Graded Fail or Pass.

Compulsory participation
This is an online course run from the University of Southern Denmark. To complete the course the student must participate in and perform all teaching and learning activities.

The examiner assesses if and, in that case, how absence from compulsory components can be compensated. The student must participate in all compulsory parts or compensate for absence in accordance with the examiner's instructions, in order to pass the course. Absence from a compulsory activity may result in the student not being able to compensate the absence until the next time the course is given.

Limitations of the number of examinations or practical training sessions
A student who does not pass an examination at their first attempt is entitled to participate in five additional examination sessions. If the student does not pass after four examinations, he/she is recommended to retake the course at the next regular course occasion, and may, after that, participate in two more examination sessions. If the student has failed six examinations, no additional examination sessions are provided.

Physically attending or otherwise commencing an examination is regarded as an examination session. Handing in a blank exam is considered taking part in an examination session. An examination, for which the student registered but did not participate, is not counted as an examination session.

Adaption of examination
If there are special grounds, or a need for adaptation for a student with a disability, the examiner may decide to deviate from the syllabus's regulations on the examination form, the number of examination opportunities, the possibility of supplementation or exemptions from the compulsory section/s of the course etc. Content and learning outcomes as well as the level of expected skills, knowledge and abilities may not be changed, removed or reduced.

Other directives

This course is run by the Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense in an online mode.

The course language is English and examination is performed in English.

Course evaluation will be carried out in accordance with the guidelines established by the Committee for Higher Education.

This course replaces the course Computational proteomics, 4.5 credits (4BI111) and cannot be included in a degree together with the latter course.

Literature and other teaching aids

Online material in Open EdX with links to further literature, training material and software.