Syllabus database for doctoral courses
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Syllabus database for doctoral courses
SYLLABI FOR DOCTORAL COURSES
| Swedish title | Proteomik med användning av mass spektrometri: När och Hur. |
|---|---|
| English title | Mass spectrometry-based proteomics: When and How. |
| Course number | 2522 |
| Credits | 3.0 |
| Responsible KI department | Institutionen för onkologi-patologi |
| Specific entry requirements | |
| Grading | Passed /Not passed |
| Established by | The Board of Doctoral Education |
| Established | 2013-03-13 |
| Purpose of the course | |
| Intended learning outcomes | After completed the course, the student will be able to * Define and apply common proteomics terminology * Illustrate the overview of proteomics * Recognize the principles of the most common proteomics techniques * Describe proteomics workflow: Experimental design, sample preparation and selection of techniques * Illustrate proteomics to such an extent that he/she will be able to utilize the proteomics core facilities or collaborate with proteomics researchers. * Define the false discovery rate of protein and peptide identification of the protein identities based on the peptide confidence levels. * 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 | * 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 * Comprehensive and targeted proteomics * Human protein atlas and Biological validation * Clinical applications * Current state of art in clinical proteomics is highlighted through case studies, literature studies and demonstrations. |
| Teaching and learning activities | The course contains lectures, literature studies with debate, seminars, and laboratory demonstration of proteomics techniques. The students will plan their own project as a case study as well as write a laboratory report. |
| Compulsory elements | * Attendance at lectures and lab demonstrations. * Attendance at examination seminar and hand in the written examination assignment. * Attendance at debate on the literatures regarding mass spectrometry-based proteomics. * Extra written literature study can be used to compensate absence. The students are recommended to read literatures listed below in advance of the course. |
| Examination | * A written assignment of laboratory demonstration shall be handed in. * A literature study with a critical view on a mass spectrometry based proteomics subject shall be discussed in a literature/expert group. The literature group will debate and present their conclusions during the course. * 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. |
| 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. |
Course responsible |
Maria Pernemalm Institutionen för onkologi-patologi Maria.Pernemalm@ki.se |
| Contact person |
Helena Bäckvall Institutionen för onkologi-patologi 0851770363 helena.backvall@ki.se Hanna Kjellin Institutionen för molekylär medicin och kirurgi Hanna.Kjellin@ki.se |
