PLEASE NOTE: This course was cancelled in 2020 due to the Covid-19 pandemic. Applications for the 2020 course have been carried over to 2021. The course is now open to new applicants.
We hope to resume our face-to-face courses in 2021. However, should the status of the pandemic not allow us to do this safely, the course may switch to a virtual format.
Hands-on training in the basics of mass spectrometry, proteomics bioinformatics, and related methods and resources
Run jointly with EMBL-EBI, this popular course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics approaches, search engines and post-processing software, quantitative proteomics approaches and related statistical concepts, MS proteomics data repositories and public data re-use, how to employ existing databases for protein analysis, perform the annotation of subsequent protein lists and the incorporation of information from molecular interaction and pathway databases.
The popular 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 and quantify peptides and finally to obtain 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 when collected.
The programme will include lecture and practical, computational sessions covering the following topics:
- Mass Spectrometry Basics
- Proteomics Bioinformatics Basics
- Quantitative proteomics
- Introduction to data independent acquisition approaches
- Standardisation of proteomics data
- MS proteomics repositories, including PRIDE and PRIDE-related tools and ProteomeXchange
- Introduction to Proteogenomics
- Protein interaction data through IntAct and IMEX resources
- Functional analysis of proteins using Cytoscape and Reactome
After completing the course, participants will be able to:
- Use and understand bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
- Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
- Browse, search, submit, retrieve and re-use proteomics data from widely used public proteomics data repositories
- Use tools to perform functional annotation of lists of proteins
Jyoti Choudhary, The Institute of Cancer Research, UK
Pedro Beltrao, EMBL-EBI, UK