BMB205: Advanced methods in protein mass spectrometry and proteomics (10 ECTS)

STADS: 01012301

Level
PhD course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: mrl@bmb.sdu.dk

Additional teachers
hjernoe@bmb.sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Comment:
Max deltagerantal: 18. kurset er et ph.d.-kursus som kan tages af både kandidat- og ph.d.-studerende

Prerequisites:
None

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.

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

Qualifications

• 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 instrumentes. 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 stabel isotopic labeling and intensity profiling 
• Read and understand scientific articles concerning protein mass spectrometry and proteome analysis

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

Subject overview

• 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

Litteraturen vil være originalartikler. Liste vil blive udleveret før kursusstart

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam

1. Exercises in the laboratory. Will be performed in smaller groups. Pass/fail, internal marking by teacher. (01012312).

Assessment and marking:

1. Based on the knowledge obtained during the lectures, computer exercises and litterature studies, the participants are expected to compose a report concerning the laboratory exercises. The obtained results are analysed and presented. The report is expected to including theory, methods, results, conclusion and perspectives. Grade by the Danish 7-point scale and external marking. (10 ECTS). (01012302).

Expected working hours
The teaching method is based on three phase model.
Intro phase: 25 hours
Skills training phase: 35 hours, hereof:
 - Tutorials: 5 hours
 - Laboratory exercises: 30 hours

Educational activities

Educational form
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 a written report made/formed as a scientific article. In total the course will have a content corresponding to 10 ECTS.

Language
This course is taught in English.

Remarks
The course has limited entry. The following 4 criterias are taken into consideration when seats are assigned.

1. Students with the most ECTS from their master
2. Students who are accepted conditionally on the master 
3. Students who follows master courses concurrent with their bachelor programme
4. Bachelor students

If the score is even lots are drawn.

The academic enviroments of 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.

In order to keep the assigned seat you need to attend the first course day or notify the teacher, otherwise the seat is given to the next student from the waiting list.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.