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. 

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
• UniProt for proteomics applications

Please read our support page before starting your application. 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 GMT on 15 March 2026. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 30 March 2026.  If you have any questions regarding the application process, please contact Anca Belu.

Posters
All participants are expected to present a poster, and successful applicants will be asked to submit their poster upon registration. We expect the posters to act as a talking point between you, other participants, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

Flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.

Registration fees 
The registration fee includes: 

• access to the full five-day course programme
• access to a bespoke online course handbook
• secure community space on Slack
• secure virtual machine to work on that is accessed via the internet
• dedicated online support team
• certificate on completion of the course

The registration fee includes:

• Catering as detailed on the course programme
• Accommodation for four nights (06-09 July) with a daily shuttle service if required. 
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Secure virtual machines for the practical sessions listed in the programme
• Shuttle bus on the final course day to Cambridge train station 

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your event organiser for more information.

Financial assistance
Financial assistance is available to a limited number of participants attending this course.

Registration fee waivers
A limited number of registration fee waivers are offered for this course.

• Application process:
  • Apply for the fee waiver alongside your course application.
  • Provide a brief explanation of why you require the waiver and how attending the course will benefit your career.
• Notification:
  • You will be informed of your waiver status at the same time as the outcome of your course application.
  • If awarded, the registration fee will be waived entirely.

Travel grants
A limited number of travel grants of up to £1,000.00 are available to support participants' travel expenses.

• Covered expenses:
  • Airfare, train, bus, taxi, and visa costs.
• Application process:
  • Apply for the travel grant when submitting your course application.
  • You will be informed of the grant decision, including the amount awarded, along with your course application outcome.
• Reimbursement process:
  • Participants must pay upfront for their travel costs.
  • A reimbursement form will be provided upon course completion.
  • Submit the completed form with receipts within one month of travel completion.
• Grant adjustment:
  • The organisers may adjust the grant amount to accommodate more participants.

Financial assistance terms and conditions

• Selection process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.

Travel information
Electronic Travel Authorisations (ETAs) are needed for visitors to the UK who do not currently need a visa for short stays, or who do not already have a UK immigration status. Full details and information on how to apply can be found at the UK Government website. 

Event terms and conditions

• Selection process: Recipients will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not affect your course application outcome.

Course materials
The materials for the 2025 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2026 course.