Course catalogue doctoral education - HT23

  • Ansökan kan ske mellan 2023-04-17 och 2023-05-15
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Title Mass spectrometry-based proteomics: When and How.
Course number 2522
Programme 1-Ingår i flera program
Language English
Credits 3.0
Date 2014-10-13 -- 2014-10-24
Responsible KI department Institutionen för onkologi-patologi
Specific entry requirements
Intended learning outcomes After completed the course, the student will be able to

-Define and apply common proteomics terminology
-Recognize the principles of the most common proteomics techniques
-Understand the mass spectrometry based proteomics workflow: Experimental design, sample preparation and selection of techniques
-Understand proteomics to such an extent that he/she will be able to utilize proteomics core facilities or collaborate with proteomics researchers.
-Evaluate the quality of protein and peptide identifications.
-Demonstrate how modern proteomics is applied to clinical research and to evaluate when proteomics research could be beneficial to incorporate in research projects.
-Design their own research project by mass spectrometry based proteomics.
Contents of the course The aim of this course is to give an overview of mass spectrometry based proteomics for researchers that will apply these techniques in their own research.

Lectures and workshops on
-Overview of proteomics
-The proteomics workflow
-Basic of separation sciences: Protein and peptides
-Introduction to Mass spectrometry
-Experimental design
-Sample preparation, immunoprecipitation and enrichment strategy
-Quantitative and qualitative proteomics by mass spectrometry
-Global and targeted proteomics
-Human protein atlas and Biological validation
-Clinical applications

A practical laboratory exercise using mass spectrometry based proteomics

This course is focusing on proteomics technologies and applications, for proteomics data analysis we recommend our KI doctoral course ""Omics data analysis: From quantitative data to biological information""
Teaching and learning activities The course contains lectures, seminars, and a practical laboratory exercise using proteomics techniques. The students will plan their own project as a case study as well make an oral laboratory report.
Compulsory elements -Attendance at lectures and the practical laboratory exercise.
-Attendance at examination seminar and hand in the written examination assignment.
-Extra written assignments can be used to compensate absence.

The students are recommended to read literatures listed below in advance of the course.
Examination -Students shall describe a proteomics project (beneficially related to their research) including different aspects from the proteomics workflow. This is handed in as a written exam.
-The students shall perform an oral laboratory report
Literature and other teaching material The students are recommended to read in advance of the course. (Will be listed on Course website: PingPong)

* Matthias Mann, Nils A. Kulak, Nagarjuna Nagaraj, and Jurgen Cox. The Coming Age of Complete, Accurate,
and Ubiquitous Proteomes. Molecular Cell 2013 49; 583-590.

* F. Maarten Altelaar, Javier Munoz and Albert J. R. Heck. Next-generation proteomics: towards an integrative
view of proteome dynamics. Nat Rev Genetics. 2013. 14; 35-48

* Cox J. and Mann M. Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology. Annu. Rev.
Biochem. 2011. 80; 273-99

* Domon B. and Aebersold R. Options and considerations when selecting a quantitative proteomics strategy.
Nat Biotechnol. 2010 28(7); 710-721.

* Gstaiger M. and Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and
network biology. Nat Rev Genetics. 2009. 10; 617-627

Supplementary literatures will help to understand lectures and design of your project: Will be listed on PingPong.

Number of students 15 - 20
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given to earlier registration date)
More information Please note that this is a full-time course and that both lectures and the practical part are compulsory. Please refer to the course site in ping pong for additional information

This course is included in the doctoral programmes Allergy, immunology and inflammation (Aii) and Infection biology. See

Additional course leader
Latest course evaluation Course evaluation report
Course responsible Maria Pernemalm
Institutionen för onkologi-patologi
Contact person Maria Pernemalm
Institutionen för onkologi-patologi

Hanna Kjellin
Institutionen för molekylär medicin och kirurgi