Proteomics Bioinformatics

21–26 July 2019

Wellcome Genome Campus, UK

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, search engines and post-processing software, introduction to 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 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 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 basics
  • Standardisation of proteomics data
  • MS proteomics repositories, including PRIDE, PRIDE-related tools and ProteomeXchange
  • Introduction to proteogenomics
  • Protein interaction data through IntAct and IMEX resources
  • Functional analysis of proteins using Cytoscape and Reactome


Learning Outcomes
After completing the course, participants will be able to:

  • Use and understand 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

Instructors and speakers

Scientific Organising Committee

Juan A. Vizcaíno

Lennart Martens
Ghent University and VIB, Belgium

Tom Hancocks

Course Instructors

The course will be taught by trainers from EMBL-EBI.

Evangelia Petsalaki
Wellcome Sanger Institute, UK

Theo Roumeliotis
Institute of Cancer Research, UK

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.

How to Apply
Please complete the online application form. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager 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. Applications without a supporting statement cannot be considered.

Travel visas
Successful applicants will be provided with a support letter for their visa application, if required.

Please visit the following websites for further information on visiting the UK:


Cost Accommodation / meals
*Course fee £725 This is a residential course and the fee includes all accommodation and meals.

*The course fee is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and applies to non-commercial applicants. Please contact us for the commercial fee.

Limited bursaries are available (up to 50% reduction on the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Where there are many bursary applications, the selection committee may issue smaller amounts.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Additional funding opportunities
Visit our support page for additional financial support currently available.

Accommodation services phishing scam – please be vigilant. More information.


Feedback from the 2018 course:

“Thank you so much for a great week of proteomics, everything from the organisation to the teaching in this course was fantastic!”

“Fantastic and very inspiring course. Thanks to it I have discovered all the application and power that proteomics has. Good course, I definitely would recommend it.”

“A generally very high quality, well resourced, well run and comprehensive course. Thank you.”

“Overall I was really satisfied. I did not have an extensive background in proteomics, so I do think it provided me the tools to know where to start from. I really found really useful all the hands-on practicals.”

“The course was really good organized. Accommodation and food service was excellent and we participants really did not have to worry about anything like that. Also the schedule and program were arranged that everything worked out without bigger problems. The organizers were really friendly and super helpful.”

“Excellent handouts and training materials to take home. Lecturers very good at answering questions.”

“Great coverage of basics – very illustrative and also great mixture of attendants to change experience with and learn new fields. Also very skilful tutors!”

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