Training

This joint EBI-Wellcome Trust workshop provides hands-on training in the basics of mass spectrometry and proteomics bioinformatics, search engines, quantitative approaches including SRM/MRM, 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 workshop is aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff, as well as specialists in related fields. The practical elements of the course will take raw data from a proteomics experiment and analyse it. Participants will be able to go from MS spectra, to identifying peptides and finally to lists of protein identifiers that can be analysed further using a wide range of resources. The final aim is to provide attendees with the practical bioinformatics knowledge they need to go back to the lab and process their own data (including large datasets) when collected.

Topics and Resources covered include:

• Mass Spectroscopy Basics
• MS Search Engines
• Quantitative proteomics
• SRM/MRM approaches
• Protein sequence databases and their use
• Protein sequence data in UniProt
• Proteomics data and services integration
• Standardising proteomics data
• MS proteomics repositories and the ProteomeXchange consortium
• PRIDE - The Proteomics Identification Database, PRIDE Converter and PRIDE Inspector
• Protein interaction data through IntAct and the IMEX consortium
• Placing proteins in pathways using Reactome

The course will be taught by trainers from the European Bioinformatics Institute and will include seminars from distinguished guest speakers.

Prerequisites

Applicants should be research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff, as well as specialists in related fields.