BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics

Study Board of Science

Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N200012112, N200012102
Censorship: Second examiner: None
Grading: Pass/Fail
Offered in: Odense
Offered in: Summer school (autumn)
Level: Bachelor

STADS ID (UVA): N200012101
ECTS value: 5

Date of Approval: 29-04-2019

Duration: 1 semester

Version: Approved - active


01011501 (former UVA) is identical with this course description. 

The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration. 

Entry requirements


Academic preconditions

Students taking the course are expected to:

  • Have knowledge of fundamental molecular biology terms and biochemistry processes (the content of BMB533 and BMB508 is assumed known)

  • Be able to use traditional it-tools, including excel

  • Active participation is expected, including an oral presentation from the students in groups

  • Knowledge regarding general laboratory safety is expected

Participant limit


Course introduction

The course aims to give students an insight into the planning, implementation and evaluation of a molecular biology experiment in which various molecular biology techniques will be combined with proteome analysis, phosphoproteomics and bioinformatics (pathway analysis). During the course, students will characterize phosphorylation-dependent signaling pathways in eukaryotic cells (e.g. stem cells or human neurons) after knock-down of essential genes (e.g. kinases) or by extracellular stimulation (e.g. cellular differentiation).

The course builds on the knowledge acquired in the courses at the second year and combines elements from several courses into one molecular biology problem which is explored experimentally and related to information extracted from relevant literature.

In relation to the competence profile of the degree it is the explicit focus of the course to:

  • Ability to independently plan and perform studies with the methods used

  • Present and pass on knowledge obtained in the course

  • Critically evaluate the results obtained with the methods used in the course

  • The course includes laboratory-based projects, providing personal competence in organizing the laboratory work.

  • The laboratory projects will be made in teams in order to strengthen their ability to cooperate in all phases of the work.

Expected learning outcome

The learning objectives of the course are that the student demonstrates the ability to:

  • Describe the basic principles behind tandem mass spectrometry

  • Understand and interpret data generated by tandem mass spectrometry

  • Describe different methods used for quantitative proteomics

  • Understand the role of post-translational modifications in cellular signaling in eukaryotic cells

  • Understand the principle of the characterization of phosphorylated proteins by tandem mass spectrometry, including enrichment of phosphorylated peptides

  • Understand the principles of working with cell cultures and protein knock-down

  • Explain and perform methods for validation of knock-down experiments, incl. Western blotting, PCR and Selected/Parallel Reaction Monitoring (SRM/PRM)

  • Use the bioinformatics programs utilized in the course


The following main topics are contained in the course:

  • Theory:

    • Introduction to proteomics and tandem mass spectrometry

    • Introduction to phosphorylation and characterization of cellular signaling pathways

    • Introduction to protein knock-down techniques, and validation of knock-down efficiency using Western blotting, PCR or SRM / PRM

    • Introduction to neural differentiation

  • Methods/Techniques:

    • Quantitative proteomics/phosphoproteomics (including purification and characterization of phosphorylated peptides)

    • Electrospray tandem mass spectrometry

    • Bioinformatics (incl. protein/peptide identification and quantitation and pathway analysis programs)

    • Western blotting

    • SRM/PRM

    • Cell culture

    • RNAi knock-down

    • (others)

NB: This training course is conducted according to legal safety instructions, but using experimental protocols and chemicals that are suspected to be potentially harmful to pregnant / lactating. Pregnant / nursing students should therefore contact the course coordinator in good time before course registration or as soon as possible.


See itslearning for syllabus lists and additional literature references.

Examination regulations

Prerequisites for participating in the exam a)




Active participation in the exercises




Second examiner: None




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) N200012101, BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics


Test in itslearning, group presentation and laboratory work




Second examiner: None




Student Identification Card


Normally, the same as teaching language

Examination aids

To be announced during the course

ECTS value


Additional information

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

Indicative number of lessons

70 hours per semester

Teaching Method

At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.

Intro phase: 15 hours

Skills training phase: 55 hours, hereof:

  • Tutorials: 15 hours
  • Laboratory exercises: 40 hours

Activities during the study phase:

  • Read the compendium 
  • Read a few articles
  • Watch a few videos
  • Preparation for laboratory work

As the course is an intense summer course, the course days will consist of element both from the intro- and training phase, whereas the study phase will take place both prior and during the course.

Teacher responsible

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


08 - 09
09 - 10
10 - 11
11 - 12
12 - 13
13 - 14
14 - 15
15 - 16
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Administrative Unit

Biokemi og Molekylær Biologi

Team at Registration & Legality


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