Training

This course, run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, provides hands-on training in the basics of mass spectrometry and proteomics bioinformatics, search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists and incorporation of information from molecular interaction and pathway databases.

The course will include lecture and practical, computational sessions covering the following topics:

• Mass Spectrometry Basics
• MS Search Engines and post-processing software
• Quantitative proteomics
• Protein sequence databases and their use
• Protein sequence data in UniProt
• Post-translational modifications
• Standardisation of proteomics data
• MS proteomics repositories and the ProteomeXchange consortium
• PRIDE and PRIDE-related tools
• Proteogenomics
• Protein interaction data through IntAct and the IMEX consortium
• Functional analysis of proteins using Cytoscape
• Placing proteins in pathways using Reactome

After completing the course, participants should be able to:

• Use and understand bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
• Browse, search, submit and retrieve proteomics data from widely used public repositories
• Discuss standards in proteomics bioinformatics and recognise its importance
• Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
• Use tools to perform functional annotation of lists of proteins

Participants have the opportunity to display an A2 (420x594mm) poster for the duration of the course. Accommodated will be provided in the Wellcome Trust Conference Centre.The course includes breakfast and meals in Hinxton Hall, and breaks and lunches outside the EMBL-EBI training rooms.