Course at EMBL-EBI

Proteomics bioinformatics

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

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

In-person course

We plan to deliver this course in an in-person manner 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 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 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 attendees 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 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
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
  • Standardisation of proteomics data
  • MS proteomics repositories, including PRIDE and PRIDE-related tools and ProteomeXchange
  • Introduction to proteogenomics
  • Protein interaction data through IntAct and IMEX resources
  • Functional analysis of proteins using Cytoscape and Reactome


Pedro Beltrao
Jyoti Choudhary
The Institute of Cancer Research, UK
Tine Clays
Ghent University and VIB, Belgium
Lieven Clement
Ghent University and VIB, Belgium
Daniela Ferretti
Max Planck Institute of Biochemistry, Germany
Deepti Jaiswal Kundu
Peli Kyriakidou
Max Planck Institute of Biochemistry, Germany
Kathryn Lilley
University of Cambridge, UK
Lennart Martens
Ghent University and VIB, Belgium
Kalpana Panneerselvam
Yasset Perez-Riverol
Ananth Prakash Surappa-Narayanappa
Eliot Ragueneau
Krishna Kumar Tiwari
Juan Antonio Vizcaino
Shengbo Wang
James Wright
The Institute of Cancer Research, UK


Note: Please note that the programme is still subject to minor changes.

All times are given in BST.

Time (BST)  Topic Trainer
Monday 18 July 2022    
10:00 - 10:30 Registration  
10:30 - 11:30 Introduction and expectations Daniel Thomas López
11:30 - 12:30 Mass spectrometry search engines Lennart Martens
12:30 - 13:30 Lunch  
13:30 - 14:30 Practical on sequence databases Lennart Martens and Tine Clays
14:30 - 15:30 Practical on identification, part one Lennart Martens and Tine Clays
15:30 - 16:00 Coffee break  
16:00 - 17:30 Practical on identification, part two Lennart Martens and Tine Clays
17:30 - 18:00 Practical on false discovery rate and protein inference Lennart Martens and Tine Clays
18:00 - 19:15 Poster session (including drinks)  
20:00 Dinner  
Tuesday 19 July 2022    
08:30 - 11:00 ID practicals - continued Lennart Martens and Tine Clays
11:00 - 11:30 Coffee break  
11:30 -12:30 ID practicals - continued Lennart Martens and Tine Clays
12:30 - 13:30 Lunch  
13:30 - 14:30 Keynote: Title TBC Pedro Beltrao
14:45 - 16:00 Introduction to quantitative proteomics Kathryn Lilley
16:00 - 16:30 Coffee break  
16:30 - 18:30 Quantitative proteomics practical session on experimental design Kathryn Lilley
19:00 Dinner  
Wednesday 20 July 2022    
08:30 - 09:30 Overview of tools for quantitative proteomics (pre-recorded) Yasset Perez-Riverol
09:30 - 10:30 Introduction to MaxQuant (including practical), part one Daniela Ferretti and Peli Kyriakidou
10:30 - 11:00 Coffee break  
11:00 - 12:30 Introduction to MaxQuant (including practical), part two Daniela Ferretti and Peli Kyriakidou
12:30 - 13:30 Lunch  
13:30 - 15:30 Introduction to MaxQuant (including practical), part three Daniela Ferretti and Peli Kyriakidou
15:30 - 16:00 Coffee break  

16:00 - 18:30

IntAct, PSIMEX and PSICQUIC Kalpana Panneerselvam and Eliot Ragueneau
19:00 Dinner  
Thursday 21 July 2022    
08:30 - 10:30 Functional analysis, part one Kalpana Panneerselvam
10:30 - 11:00 Coffee break  
11:00 - 12:30 Functional analysis, part two Kalpana Panneerselvam
13:00 - 14:00 Lunch  
14:00 - 15:30 ProteoGenomics Jyoti Choudhary and James Wright
15:30 - 16:00 Coffee Break  
16:00 - 19:00 Basics of peptide/protein quantification Lieven Clement
19:30 Dinner  
Friday 22 July 2022    
08:30 - 09:00 Proteomics data standards Juan A. Vizcaíno
09:00 - 10:00 Proteomics repositories, PRIDE and ProteomeXchange Juan A. Vizcaíno
10:00 - 10:30 Coffee Break  
10:30 - 12:00 Practical on PRIDE/ProteomeXchange Deepti J. Kundu, Ananth Prakash and Shengbo Wang
12:00 - 13:00 Reuse of public proteomics data (including example) Juan A. Vizcaíno
13:00 - 14:00 Lunch  
14:00 - 15:45 Functional analysis, part three: Reactome Eliot Ragueneau and Krishna Tiwari
15:45 - 16:15 Course wrap up and feedback Daniel Thomas López
16:30 Bus to Cambridge Train station  

The deadline for this course has now been extended to 08 April 2022. If you have any questions please contact Juanita Riveros.

Please read our page on application advice 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 providing answers as directed
  • 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 
    • current research 
  • Upload a 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 complete all sections and upload your letter of support by Friday 08 April 2022, BST. We will not consider incomplete applications. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 22 April 2022. If you have any questions regarding the application process please contact Juanita Riveros.

All participants are expected to present a poster that will be displayed during the course outside the training room. If you are successful you will be asked to send a poster in PDF format to Juanita Riveros which will be printed and displayed.  

All posters should:

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

We cannot display posters of a different size or orientation.

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.

The registration fee includes:

  • All meals (breakfast, lunch, dinner, and refreshment breaks for the course days)
  • Accommodation
  • Course materials
  • Use of a computer in the EMBL-EBI training room throughout the course
This course has ended

18 - 22 July 2022
European Bioinformatics Institute United Kingdom
Juanita Riveros

  • Lennart Martens
    Ghent University and VIB, Belgium
  • Daniel Vincent Thomas Lopez
  • Juan Antonio Vizcaino

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