Proteomics bioinformatics (Cancelled)


 Sunday 26 Friday 31 July 2020


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday 31 January 2020

Application deadline: 

Wednesday 08 April 2020


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This course provides hands-on training in the basics of mass spectrometry and 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.


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.

Syllabus, tools and resources

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


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


Day 1 - Sunday 26 July 2020
17:00-17:30 Arrival and registration  
17:30-18:30 Introductions and expectations Ajay Mishra
18:30-19:00 Introduction and a proteomics history Juan Antonio Vizcaíno
19:15 Evening BBQ Hinxton Hall Restaurant
Day 2 - Monday 27 July 2020
08:15 Arrival EMBL-EBI South Building
08:30-08:45 Training Room orientation Ajay Mishra
08:45-10:15 Mass spectrometry search engines part I Lennart Martens
10:15-10:30 Tea/Coffee Break  
10:30-11:30 Mass spectrometry search engines part II 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 Tea/Coffee 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 28 July 2020
08:15 Arrival  
08:30-10:45 Identification recap Lennart Martens & Harald Barsnes
10:45-11:15 Tea/Coffee Break  
11:15-12:30 Keynote talk Pedro Beltrao
12:30-13:30 Lunch  
13:30-14:45 Introduction to quantitative proteomics Kathryn Lilley
14:45-16:00 Quantitative proteomics practical session on experimental design 1 Kathryn Lilley 
16:00-16:30 Tea/Coffee Break  
16:30-17:15 Quantitative proteomics practical session on experimental design 2 Kathryn Lilley
17:15-19:00 Basics of peptide/protein quantification Lieven Clement
19:30 Evening meal  Hinxton Hall Restaurant
Day 4 – Wednesday 29 July 2020
08:15 Arrival  
08:30-09:30 Overview of tools for quantitative proteomics Yasset Perez-Riverol
09:30-10:30 Introduction to MaxQuant with practicals I

Christoph Wichmann & Petra Gutenbrunner

10:30-11:00 Tea/Coffee Break  
11:00-12:30 Introduction to MaxQuant with practicals II Christoph Wichmann & Petra Gutenbrunner
13:30-15:00 Introduction to MaxQuant with practicals III Christoph Wichmann & Petra Gutenbrunner
15:00-15:30 Proteomics data standards Juan Antonio Vizcaino
15:30-16:00 Tea/Coffee Break  
16:00-19:00 Introduction to data-independent acquisition approaches with practicals Simon Hubbard & Paul Brack
19:30 Evening meal Hinxton Hall Restaurant
Day 5 – Thurasday 30 July 2020
08:15 Arrival  
08:30-09:30 Proteomics repositories, PRIDE and ProteomeXchange  Juan Antonio Vizcaíno
09:30-10:30 PRIDE and ProteomeXchange practicals 1 Juan Antonio Vizcaíno
10:30-11:00 Tea/Coffee Break  
11:00-11:30 PRIDE and ProteomeXchange practicals 2 Juan Antonio Vizcaino
11:30-12:30 Reuse of public proteomics data Juan Antonio Vizcaíno
12:30-13:30 Lunch and posters  
13:30-14:45 Keynote talk Jyoti Choudhary
14:45-15:30 Integration of public proteomics data in Ensembl Yasset Perez-Riverol
15:30-16:00 Tea/Coffee Break  
16:00-18:45 IntAct, PSIMEX and PSICQUIC  Pablo Porras & Livia Perfetto
19:30 Evening meal Hinxton Hall Restaurant
Day 6 – Friday 31 July 2020
08:00 Checkout of accommodation  
08:15 Arrival  
08:30-10:30 Functional analysis I Pablo Porras & Livia Perfetto
10:30-11:00  Break  
11:00-12:30 Functional analysis II Pablo Porras & Livia Perfetto
12:30-13:30 Lunch  
13:30-15:15 Functional analysis III Thawfeek Varusai
15:15-15:30 Wrap up and feedback Ajay Mishra
15:30 End of course