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EMBL-EBI-Wellcome Trust workshop on Proteomics Bioinformatics

10-14 November 2014

Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Application deadline: 4 July 2014


This joint EBI-Wellcome Trust workshop 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. The workshop 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 (including large datasets) when collected.

Topics and Resources covered include:

  • Mass Spectroscopy Basics
  • MS Search Engines and post-processing software
  • Quantitative proteomics
  • SRM/MRM approaches
  • Protein sequence databases and their use
  • Protein sequence data in UniProt
  • Proteomics data and services integration
  • Standardising proteomics data
  • MS proteomics repositories and the ProteomeXchange consortium
  • PRIDE and PRIDE related tools
  • Proteogenomics
  • Protein interaction data through IntAct and the IMEX consortium
  • Placing proteins in pathways using Reactome

The course will be taught by trainers from the European Bioinformatics Institute and will include seminars from distinguished guest speakers.

Scientific Organising Committee

Juan A. Vizcaíno (EMBL-EBI, UK)
Lennart Martens
(Ghent University and VIB, Belgium)

Feedback from previous courses

“I am very grateful for this opportunity and this certainly opens up a new avenue for my research and career. I am very happy and satisfied with this course.”

“Thank you for the opportunity. I had a great time there, and obtained a lot of new information that were applicable for my future research interest.”

“I recommend every PhD student especially international to attend these courses at least once during the period of the study.”

How to apply

Applicants should be 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 course tuition fees are subsidised by the Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course, without exception, and there is a fee of £500 for non-commercial applicants towards accommodation and food for the duration of the course. The fee for commercial applicants is £1500.

Limited bursaries are available for non-commercial applicants (up to 50% of the course fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Application forms for this course can now be completed online. If you have any problems with the online application process, please email us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.

Application deadline: 4 July 2014

Supported by:


European Bioinformatics Institute

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888