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
There is no timetable available for the chosen semester.

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
Advanced methods for protein characterisation and functional genomics/proteomics will be introduced, illustrated, discussed and the partipants 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 litterature, with regards to both existing and new methods in mass spectrometry and functional proteomics.

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


Subject overview

• Principles of mass spectrometry based analytical methods for proteins, peptides and post translational modifications, including Maldi 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
There isn't any litterature for the course at the moment.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
Exercises in the laboratory. Will be performed in smaller groups. Pass/fail, internal evaluation by teacher.

Assessment and marking:
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 censorship.

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

Forelæsninger: 25 timer
Eksaminatorietimer/opgaveregning: 5 timer
Laboratorieøvelser: 30 timer

Der udleveres en litteraturliste som indeholder 15-20 videnskabelige originalartikler og oversigtsartikler svarende til i alt ca. 175 sider med et forventet tidsforbrug på 20 timer. Artiklerne læses og drøftes i forbindelse med forelæsninger og laboratorieøvelser. Kurset evalueres ved skriftlig rapport som udarbejdes/opbygges som en videnskabelig artikel. Dette betyder at kurset får et omfang svarende til i alt 10 ECTS.
Educational activities

Language
This course is taught in English.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.