Proteomics

Aim

The purpose of the course is to provide a broad knowledge of methods and applications within proteomics. Many of the basic methodological principles have been introduced in earlier courses, but here the student learns how these principles are used within a very expansive research area: Global characterisation of the proteome with regard to protein abundance, function, interactions and localisation in different cell types. Transcriptomics is also discussed. To pass the course, the student should be able to

• describe and evaluate methods and strategies to analyse the transcriptome and the proteome
• identify proteins and peptides using mass spectra and genome databases
• in English, summarise the contents and interpret the message of original literature within the subject area of the course

Content

Quantitative mRNA-analysis with DNA microarrays, qPCR and methods based on Next Generation Sequencing. One- and multi-dimensional gel- and chromatography-based separation methods for proteins and peptides. Identification of cellular protein contents using enzymatic cleavage, MS- and MS/MS analysis and genome databases. Label-based and label-free protein quantification based on MS and MS/MS. Analysis of post-translational modifications. Analysis of protein-protein interactions using Y2H methodology, affinity chromatography, and protein microarrays. Immunoassays in proteomics. Characterization of disease-dependent proteome changes for biomarker-based diagnostics, including some basic principles of data analysis. Single-cell analysis. Human Proteome Atlas.