Proteomics Bioinformatics

Date:

 Sunday 15 Friday 20 July 2018

Venue: 

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

Application opens: 

Wednesday November 22 2017

Application deadline: 

Monday March 26 2018

Participation: 

Open application with selection

Registration fee: 

695

Registration closed

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Overview

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.

Audience

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

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

Additional information

Participants have the opportunity to display an A2 (420x594mm) poster for the duration of the course; we will ask you to submit these before the course for printing on site. Accommodated will be provided in the Wellcome Trust Conference Centre.The course includes breakfast and meals in Hinxton Hall, and breaks and lunches outside the EMBL-EBI training rooms. 

Programme

The programme below is from our 2017 Proteomics Bioinformatics course. It will be revised with the full agenda shortly. Whilst small changes to session titles and speakers may happen, the overall themes will be the same.

Time Topic Trainer
Day 1 - Sunday 15 July
17:00 - 17:30 Arrival and registration  Conference Centre
17:30 - 18:30 Introduction and expectations Tom Hancocks
18:30 - 19:00 Proteomics history   Juan Antonio Vizcaíno
19:00 - 19:30 Welcome drinks Hinxton Hall Lounges
19:30 Welcome BBQ Hinxton Hall Restaurant
Day 2 - Monday 16 July
08:15 Arrival  
08:30 - 08:45 Training room orientation Tom Hancocks
08:45 - 10:15 Mass spectrometry basics Lennart Martens
10:15 - 10:30 Break 
10:30 - 11:30 Introduction to UniProt and other protein sequence databases Sandra Orchard
11:30 - 12:30 MS search engines Lennart Martens
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 Protein interference Lennart Martens
17:00 - 18:00 Practical on identification 2 Harald Barsnes & Lennart Martens
18:00 - 19:30 Poster session and drinks All
20:00  Evening meal Hinxton Hall Restaurant
Day 3 - Tuesday 17 July
08:15 Arrival  
08:30 - 09:30 Identification validation and FDR Harald Barsnes
09:30 - 10:30 Practical on identification 3 Harald Barsnes & Lennart Martens
10:30 - 11:00 Break
11:00 - 12:30 Practical on identification 4 Harald Barsnes & Lennart Martens
12:30 - 13:30 Lunch
13:30 - 14:45 Keynote: The functional landscape of the human phosphoproteome Pedro Beltrao
14:45 - 16:00 Introduction to quantitative proteomics  Kathryn Lilley
16:00 - 16:30 Break
16:30 - 19:00 Quantitative proteomics practical Kathryn Lilley & Tom Smith
19:30 Evening meal  Hinxton Hall Restaurant
Day 4 - Wednesday 18 July
08:30 - 10:30 Quantitative proteomics: Introduction to MaxQuant Andrew Jarnuczak
10:30 - 11:00 Break
11:00 - 12:30 MaxQuant practical Andrew Jarnuczak
12:30 - 13:30 Lunch 
13:30 - 15:30 Introduction to the Open MS framework  Yasset Perez-Riverol & Mathias Walzer
15:30 - 16:00 Break
16:00 - 16:30 Proteomics data standards Juan Antonio Vizcaino
16:30 - 19:00 Introduction to Data Independent Acquisition approaches Simon Hubbard & David Lee
19:30 Evening meal  Hinxton Hall Restaurant
Day 5 - Thursday 19 July
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
13:30 - 14:45 Keynote: ProteoGenomics Jyoti Choudhary
14:45 - 16:00 Integration of proteomics data in Ensembl Yasset Perez-Riverol
16:00 - 16:30 Break
16:30 - 19:00 IntAct, PSIMEX and PSICQUIC  Sandra Orchard & Pablo Porras
19:30 Evening meal Hinxton Hall Restaurant
Day 5 - Friday 20 July
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 Thawfeek Varusai
15:15 - 15:30 Course Survey Tom Hancocks
15:30 End of course