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| Title | Proteomics by mass spectrometry: When and how. |
|---|---|
| Course number | 2522 |
| Programme | Tumörbiologi och onkologi (FoTO) |
| Language | English |
| Credits | 3.0 |
| Date | 2011-10-31 -- 2011-11-11 | Responsible KI department | Institutionen för onkologi-patologi |
| Specific entry requirements | |
| Intended learning outcomes | After completed course, the student will: Be able to use commonly used proteomics terminology and explain the principles of the most common proteomics methods. Acquire general understanding of the components of the proteomics research process such as study design, sample preparation, and selection of technologies. Be able to understand proteomics to such an extent that he/she will be able to take advantage of the proteomics core facilities or collaborate with proteomics researchers. Be aware of the false discovery rate of protein and peptide identification of the protein identities based on the peptide confidence levels. Be able to give examples of how modern proteomics is applied to clinical research and to evaluate when proteomics research could be beneficial to incorporate in a research projects. |
| Contents of the course | * Introduction to proteomics * Experimental design in clinical proteomics * The proteomics workflow * Analytical protein and peptide chemistry * Introduction to mass spectrometry * Advanced mass spectrometry; different instrumental techniques * Human protein Atlas * Cancer biomarkers * Clinical applications * Qualitative and quantitative proteomics by mass spectrometry, * Current state of art in clinical proteomics is highlighted through case studies, literature studies and demonstrations. * The course is a natural introduction to the course ""Omics data analysis: From raw data to biological information"". |
| Teaching and learning activities | The course contains lectures, literature studies, seminars, and laboratory demonstration of proteomics methods. The students will plan lab work as a case study as well as write a laboratory report. |
| Compulsory elements | * Attendance on lectures and lab demonstrations * Attendance to examination seminar and hand in the written examination assignment. * Extra written literature study can be used to compensate absence. |
| Examination | * A written laboratory demonstration report 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. Discussion questions is reported and presented for the group. * The 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 | Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006 Apr 14 312(5771), 212-7 (Review) Omenn GS. Strategies for plasma proteomic profiling of cancers. Proteomics. 2006 Oct 6(20), 5662-73 (Review) Matthias Gstaiger and Ruedi Aebersold, Applying mass spectrometry-based proteomics to genetics, genomics and network biology. NATURE REVIEWS | Genetics. 2009 September 10, 617-627 (Review) Hartmut Schlüter, Rolf Apweiler, Hermann-Georg Holzhütter and Peter R Jungblut. Finding one's way in proteomics: a protein species nomenclature. Chemistry Central Journal. 2009 3:11, 1-10 (Commentary) Bruno Domon & Ruedi Aebersold. Options and considerations when selecting a quantitative proteomics strategy. Nature biotechnology. 2010 JULY 28(7), 710-721. (Perspective) Christian H. Ahrens, Erich Brunner, Ermir Qeli, Konrad Basler and Ruedi Aebersold. Generating and navigating proteome maps using mass spectrometry. Nature Reviews | Molecular cell Biology. 2010 NOV 11, 789-801. (Review) |
| Number of students | 12 - 24 |
| Selection of students | Students will be selected based on their written motivation for participation in this course. |
| More information | Fulll time Monday to Friday during two weeks. The course will be given in the lecture hall Sievertrummet at the Karolinska Hospital area. |
| Additional course leader | |
| Latest course evaluation | Not available |
| Course responsible |
Jenny Forshed Institutionen för onkologi-patologi jenny.forshed@ki.se |
| Contact person |
Helena Bäckvall Institutionen för onkologi-patologi 0851770363 helena.backvall@ki.se Janne Lehtiö Institutionen för onkologi-patologi 0851776391 Janne.Lehtio@ki.se |
