Thank you to those of you who have applied, we have now selected our participants and wait list. There are no more spaces available. You can however register your interest for the 2025 course here. 

This course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics. You will receive training on how to use 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 practical elements of the course will take raw data from a proteomics experiment and analyse it. You will be able to go from MS spectra to identifying and quantifying peptides, and finally to obtaining lists of protein identifiers that can be analysed further using a wide range of resources. The final aim is to provide you with the practical bioinformatics knowledge you need to go back to the lab and process your own data when collected.

This course is organised in association with the Vlaams Instituut voor Biotechnologie (VIB, the Flemish Institute for Biotechnology).

Pre-recorded material may be provided before the course starts that you will need to watch, read, or work through to gain the most out of the actual training event. 

In-person course

The course fee is inclusive of four nights of accommodation and catering, including dinner.

We plan to deliver this course in-person onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Who is this course for?

The course is aimed at research scientists with a minimum of a degree in a scientific discipline, including industrial, laboratory and clinical staff, as well as specialists in related fields. Basic knowledge of mass spectrometry experiments for proteomics would be an advantage.

What will I learn?

Learning outcomes

After completing the course, you will be able to:

• Use and summarise bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
• Browse, search, submit, retrieve, and re-use proteomics data from widely used public proteomics data repositories
• 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 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
• MS proteomics repositories, including PRIDE and PRIDE-related tools and ProteomeXchange.
• Data re-use of public proteomics datasets.
• Introduction to proteogenomics
• Protein interaction data through IntAct and IMEX resources

Functional analysis of proteins using Cytoscape and Reactome

Trainers

Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 BST on Sunday 7 April 2024. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Monday 22 April 2024. If you have any questions regarding the application process please contact Barbara Etzi.

The registration fee of £850.00  includes:

• Catering as detailed on the course programme
• Accommodation for four nights (15, 16, 17, and 18 July)
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Shuttle bus on the final course day to Cambridge train station 

Fee bursaries

We have a limited number of fee bursaries available for this course, which will cover up to 50% of the course fee. Priority for allocation of these bursaries will be given to those from under-resourced regions. Recipients will be informed about their bursary application together with the outcome of their course application.

You may apply for financial assistance when submitting your application. During the application, you will be asked to justify your need to receive a fee bursary and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your application.

The scientific organisers will select the recipients of all financial assistance during the participant selection process. Bursary selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.