This course provides hands-on training in the basics of mass spectrometry (MS) and proteomics bioinformatics. Participants 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.

This course is organised in association with the Vlaams Instituut voor Biotechnologie (VIB).

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.

Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than six weeks. For more information please visit the UK Government website.

Who is this course for?

The course is aimed at research scientists with a minimum of an undergraduate degree in a biological discipline, including laboratory and clinical staff, as well as specialists in related fields. In place of a relevant biology-related degree, you may have some experience and/or knowledge in the field MS and proteomics. Some basic knowledge of MS and proteomics experiments is ideal.

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 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 participants with the practical bioinformatics knowledge they need to go back to the lab and process their own data when collected.

What will I learn?

Learning outcomes

After completing the course, participants 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 be advised that the application review process will take longer than planned. All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 2 May 2023.

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.

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.

Please submit all documents during the application process by 23:59 BST on Monday 3 April 2023. 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 Tuesday 25 April 2023. If you have any questions regarding the application process please contact Shereen Pethania.

The registration fee of £825.00 includes:

• Catering 
• Accommodation for four nights (3, 4, 5 and 6 July) with a daily shuttle service
• 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 

Accommodation 

Hotel rooms (including breakfast) will be provided at Holiday Inn Express, Duxford. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size – 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. 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.