PDA08 Proteomics Data Analysis

The course starts with a primer on Image Analysis, applied to 2D Gels. You will be working hands-on at computers with cutting-edge 2D gel image analysis software as well as learning the basic theory of 2D gel image analysis data quality. This class covers the same material as being tought exclusively at the prestigeous proteomics training courses at the National Institutes of Health in USA.
The afternoon lectures will (re)introduce you to such fundamental concepts of modern protein mass spectrometry as the type and amount of information available from accurate mass analysis and MS/MS fragmentation. We will discuss the needs for and the methods of performing protein quantification.

On the second and third days will then introduce the bioinformatics techniques, tools and methods that are available for analysing mass spectrometry based proteomics data.
We will focus on the challenges involved in peptide identification and spectrum comparison, inferring protein identification from identified peptides and performing clustering.
Then we will focus on the database tools and resources available at the European Bioinformatics institute, including sequence databases (UniProt and IPI), databases of protein annotation, domains, families and functions (UniProt and InterPro), and the PRIDE Proteomics Identifications Database. There will also be an introduction to the Reactome database of metabolic pathways, which is integrated into the PRIDE Proteomics Identifications Database.
The course will end with a demonstration of some of the available web service tools and infrastructure that allow the building of powerful and reusable data analysis workflows.

 Course website: http://gtpb.igc.gulbenkian.pt/bicourses/PDA08