Course at EMBL-EBI

Proteomics bioinformatics

This course, run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, 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.

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 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 once it has been generated.

What will I learn?

Learning outcomes

After completing the course, participants should be able to:

  • Use and understand bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
  • Browse, search, submit and retrieve proteomics data from widely used public repositories
  • Discuss standards in proteomics bioinformatics and recognise its importance
  • 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 course will include lecture and practical, computational sessions covering the following topics:

  • Mass Spectrometry Basics
  • MS Search Engines and post-processing software
  • Quantitative proteomics
  • Protein sequence databases and their use
  • Protein sequence data in UniProt
  • Post-translational modifications
  • Standardisation of proteomics data
  • MS proteomics repositories and the ProteomeXchange consortium
  • PRIDE and PRIDE-related tools
  • Proteogenomics
  • Protein interaction data through IntAct and the IMEX consortium
  • Functional analysis of proteins using Cytoscape
  • Placing proteins in pathways using Reactome


Tom Hancocks
Juan Antonio Vizcaino
Lennart Martens
Ghent University & VIB, Belgium


Day 1 - Sunday 21 July 2019
17:00-17:30 Arrival, check-in and registration  
17:30-18:30 Introductions, networking and expectations Anna Swan
18:30-19:00 Course introduction and a proteomics history Juan Antonio Vizcaíno
19:00 Welcome drinks Hinxton Hall Lounges
19:30 Evening BBQ Hinxton Hall Restaurant
Day 2 - Monday 22 July 2019
08:15 Arrival EMBL-EBI South Building
08:30-08:45 Training Room orientation Anna Swan
08:45-10:00 Mass spectrometry search engines Lennart Martens
10:00-10:30 Break  
10:30-11:30 Mass spectrometry search engines Lennart Martens
11:30-12:30 Practical on sequence databases Lennart Martens & Harald Barsnes
12:30-13:30 Lunch and posters  
13:30-15:30 Practical on identification 1 Harald Barsnes & Lennart Martens
15:30-16:00 Break  
16:00-17:00 Practical on identification 2 Harald Barsnes & Lennart Martens
17:00-18:00 Practical on FDR and protein inference Harald Barsnes & Lennart Martens
18:00-19:30 Poster session and drinks All
20:00 Evening meal Hinxton Hall Restaurant
Day 3 – Tuesday 23 July 2019
08:15 Arrival  
08:30-10:45 Identification recap Lennart Martens & Harald Barsnes
10:45-11:15 Break  
11:15-12:30 Keynote talk Evangelia Petsalaki
12:30-13:30 Lunch and posters  
13:30-14:45 Introduction to quantitative proteomics Kathryn Lilley
14:45-16:00 Quantitative proteomics and experimental design Kathryn Lilley & Oliver Crook
16:00-16:30 Break  
16:30-17:15 Quantitative proteomics and experimental design Kathryn Lilley & Oliver Crook
17:15-19:00 Basics of peptide/protein quantification Lieven Clement
19:30 Evening meal  Hinxton Hall Restaurant
Day 4 – Wednesday 24 July 2019
08:15 Arrival  
08:30-09:30 Overview of tools for quantitative proteomics Yasset Perez-Riverol
09:30-10:30 Introduction to MaxQuant Tami Geiger
10:30-11:00 Break  
11:00-12:30 MaxQuant practical Tami Geiger
12:30-13:30 Lunch  
13:30-15:00 MaxQuant practical Tami Geiger
15:00-15:30 Proteomics data standards Juan Antonio Vizcaino
15:30-16:00 Break  
16:00-19:00 Introduction to data-independent acquisition approaches Simon Hubbard, David Lee & Paul Brack
19:30 Evening meal Hinxton Hall Restaurant
Day 5 – Thurasday 25 July 2019
08:15 Arrival  
08:30-09:30 Proteomics repositories, PRIDE and ProteomeXchange  Juan Antonio Vizcaíno
09:30-10:30 PRIDE and ProteomeXchange practical Juan Antonio Vizcaíno & Andrew Jarnuczak
10:30-11:00 Break  
11:00-11:30 PRIDE and ProteomeXchange practical Juan Antonio Vizcaino & Andrew Jarnuczak
11:30-12:30 Reuse of public proteomics data Juan Antonio Vizcaíno
12:30-13:30 Lunch and posters  
13:30-14:45 ProteoGenomics Theo Roumelitis
14:45-15:30 Integration of proteomics data in Ensembl Yasset Perez-Riverol
15:30-16:00 Break  
16:00-18:45 IntAct, PSIMEX and PSICQUIC  Sandra Orchard & Pablo Porras
19:30 Evening meal Hinxton Hall Restaurant
Day 6 – Friday 26 July
08:00 Checkout of accommodation  
08:15 Arrival  
08:30-10:30 Functional analysis I Pablo Porras
10:30-11:00  Break  
11:00-12:30 Functional analysis II Pablo Porras
12:30-13:30 Lunch  
13:30-15:15 Functional analysis III Bijay Jassal
15:15-15:30 Course Survey Anna Swan
15:30 End of course  

Registration is handled through the Wellcome Trust Advanced Courses website.

This course has ended

21 - 26 July 2019
European Bioinformatics Institute United Kingdom
Advanced courses

  • Tom Hancocks
  • Juan Antonio Vizcaino
  • Lennart Martens
    Ghent University & VIB, Belgium
  • Anna Swan

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