BMB205: Advanced methods in protein mass spectrometry and proteomics

Study Board of Science

Teaching language: English
EKA: N220005112, N220005102
Censorship: Second examiner, Second examiner: External
Grading: Pass/Fail
Offered in: Odense
Offered in: Autumn
Level: PhD

STADS ID (UVA): N220005101
ECTS value: 10

Date of Approval: 09-03-2020

Duration: 1 semester

Version: Approved - active


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

  1. PhD students after time of enrollment
  2. Students with the most ECTS from their master
  3. 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.

Entry requirements

Bachelor degree (biomedicine, molecular biology or similar).

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


  • 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.


The literature will be original articles. List will be handed out before course start.

Examination regulations

Prerequisites for participating in the exam a)




Exercises in the laboratory. Will be performed in smaller groups




Second examiner




Student Identification Card


Normally, the same as teaching language

Examination aids

To be announced during the course

ECTS value


Additional information

The prerequisite examination is a prerequisite for participation in exam element a)

Exam element a)




Type Prerequisite name Prerequisite course
Examination part Prerequisites for participating in the exam a) N220005101, BMB205: Advanced methods in protein mass spectrometry and proteomics






Second examiner: External




Full name and SDU username


Normally, the same as teaching language

Examination aids

To be announced during the course

ECTS value


Additional information

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.

The examination form for re-examination may be different from the exam form at the regular exam.

Indicative number of lessons

60 hours per semester

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

Teacher responsible

Name E-mail Department
Martin Røssel Larsen Institut for Biokemi og Molekylær Biologi, KI, BRIDGE, Brain Research - Inter-Disciplinary Guided Excellence

Additional teachers

Name E-mail Department City
Pia Jensen Institut for Biokemi og Molekylær Biologi


Administrative Unit

Biokemi og Molekylær Biologi

Team at Registration & Legality


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