BMB210: Advanced methods in protein mass spectrometry and proteomics
Study Board of Science
Teaching language: English
EKA: N220016102
Assessment: Second examiner: None
Grading: Pass/Fail
Offered in: Odense
Offered in: Autumn
Level: PhD
STADS ID (UVA): N220016101
ECTS value: 5
Date of Approval: 10-03-2023
Duration: 1 semester
Version: Approved - active
Comment
For enrollment in this course please contact Pia Jensen pjensen@bmb.sdu.dk no later than May 30th.
The course has limited entry. The following criterias are taken into consideration when seats are assigned:
- PhD students after time of enrollment
- Students with the most ECTS from their master
- Students who follows master courses concurrent with their bachelor programme (dispensation to 30 ECTS Master courses)
If students are equal – seats are allocated based on random draw.
The academic envirometns at The faculty of science manages the prioritisation and at waiting list is established and will then be made aware from the faculty. The waiting list will not be transferred to the following year.
It is important to attend the first day of the course or inform the teacher, as there is a waiting list for the course.
It is important to attend the first day of the course or inform the teacher, as there is a waiting list for the course.
Entry requirements
Bachelor degree (biomedicine, molecular biology or similar).
The course cannot be chosen if you have passed, registered, or have followed BMB205.
The course cannot be chosen if you have passed, registered, or have followed BMB205.
Academic preconditions
The participants are expected to have a Master's degree or equivalent. Upon agreement, the course may be taken by master's students holding a Bachelor degree. Please notice that this is a PhD course and thus the level is very high.
Participant limit
Course introduction
In this course advanced methods for protein characterization and functional genomics/proteomics will be introduced, illustrated, discussed and the participants will have lab exercises with hands-on. Emphasis will be placed on separation technologies and mass spectrometry based methods, preparation of samples and analysis of the obtained results. The goal is to provide the students with the ability to apply the presented methods and strategies to their own research and provide them with a solid background within the field in order to understand and utilize the literature, with regards to both existing and new methods in mass spectrometry and functional proteomics. In addition, the course gives the students a unique chance to extent their network within the scientific field.
As the course is a Ph.d. course, the participants are expected to have an academic education within a relevant scientific area. They are expected to know the general terms within molecular biology and biochemistry and be able to use scientific methods for constructing and performing experimental analysis.
Active participation is expected from the students and teaching tools available on the e-learning platform used by SDU will be used during the course. The students are also expected to read articles listed by the teachers.
The students are expected to know about general laboratory safety and to be able to work in groups.
In order to reach the goal of the course, the students are expected to be able to demonstrate the ability to;
- Be capable of judging independently which of the experimental methods/strategies to use in different experimental setups.
- Make conclusions and reflections based on interpretation of data
- Write a scientific paper based on results obtained by experimental work
- Describe the theory behind relevant methods
Expected learning outcome
The learning objectives of the course are that the student demonstrates the ability to:
- Explain the principles behind Mass Spectrometry (MS), i.e. the construction, the principle of operation and the type of data expected from an MS instrument
- Describe the common ionization methods within the field of protein analysis, i.e. MALDI and ESI and clarify the difference between these
- Understand the basic principles for and the difference between different mass analyzers
- Describe fragmentation of peptides by CID, ECD and ETD, including the nomenclature
- Analyze and interpret peptide and protein spectra from MS and tandem MS instruments. This include understanding the principles behind manual interpretation of peptide fragment spectra
- Use simple bioinformatics tools for analysis of data sets and be able to critically evaluate the obtained results
- Understand and set up experimental strategies within the analysis of the proteome
- Describe the principles behind purification of specific post translational modifications (phosphorylation, glycosylation) and MS analysis of these. This include understanding the use of immonium ions and neutral loss
- Describe the principles for quantitative proteome analysis strategies like stable isotopic labeling and intensity profiling
- Read and understand scientific articles concerning protein mass spectrometry and proteome analysis
Content
- Principles of mass spectrometry based analytical methods for proteins, peptides and post translational modifications, including Matrix Assisted Laser Desorption/Ionization, electrospray ionization, mass analyzers and hybrid instruments.
- Methods for sample preparation prior to MS analysis
- Strategies for protein/peptide separation/purification prior to MS analysis, including electrophoretic and chromatographic techniques.
- Strategies for analysis of post translational modifications, with special emphasis on phosphorylation and glycosylation
- Strategies for quantitative analysis of peptide/proteins, e.g. with respect to research in disease markers
- Computational data analysis and database searching and other relevant bioinformatic analysis.
Literature
Examination regulations
Exam element a)
Timing
Autumn
Tests
Portfolio
EKA
N220016102
Assessment
Second examiner: None
Grading
Pass/Fail
Identification
Full name and SDU username
Language
Normally, the same as teaching language
Examination aids
To be announced during the course
ECTS value
5
Additional information
Portfolio exam consisting of:
- Participation in the laboratory part of the course
- E-tests during the course, as well as group presentations
Indicative number of lessons
Teaching Method
Activities during the study phase:
- E-tests
- Reading articles (approximately 30 scientific articles)
A list of literature containing 25-30 scientific articles and review (in total corresponding to approximately 200 pages with an expected study time on 25 hours) will be handed out. These are read and discussed in relation to the talks and laboratory exercises. As the course is an intense and consecutive course, the course days will consist of both intro- and training phase, whereas the study phase will take place both prior and after the course. E-tests will be used as study activities/student activation prior and during the course and the students will be encouraged to used blogs and discussionsboards to facilitate their learning and networking. The course is evaluated by E-test. In total the course will have a content corresponding to 5 ECTS.
Teacher responsible
Name | Department | |
---|---|---|
Martin Røssel Larsen | mrl@bmb.sdu.dk | Biomedicinsk Massespektrometri og systembiologi |
Additional teachers
Timetable
Administrative Unit
Team at Educational Law & Registration
Offered in
Recommended course of study
Transition rules
Transitional arrangements describe how a course replaces another course when changes are made to the course of study.
If a transitional arrangement has been made for a course, it will be stated in the list.
See transitional arrangements for all courses at the Faculty of Science.