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.

Who is this course for?

The course 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 once it has been generated.

What will I learn?

Learning outcomes

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

Course content

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

Trainers

Registration is handled through the Wellcome Trust Advanced Courses website.