Proteomics Bioinformatics

Date:

 Sunday 16 Friday 21 July 2017

Venue: 

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

Application opens: 

Tuesday January 03 2017

Application deadline: 

Friday March 31 2017

Participation: 

Open application with selection

Registration fee: 

£680

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. 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

Time Topic Trainer
Day 1 - Sunday 16 July
16:30 - 17:30 Registration  Conference Centre
17:30 - 18:15 Introduction and expectations Tom Hancocks
18:15 - 19:00 Proteomics history   Juan Antonio Vizcaíno
19:00 - 19:30

Welcome drinks

Conference Centre

19:30 - 20:30

Dinner

Hinxton Hall Restaurant

Day 2 - Monday 17 July
08:15 Arrival EBI South Building
08:30 - 08:45 Training room orientation Tom Hancocks
08:45 - 10:30 Mass spectrometry basics Lennart Martens
10:30 - 11:00 Break 
11:00 - 13:30 Mass spectrometry basics and MS search engines Lennart Martens
12:30 - 13:30 Lunch and posters
13:30 - 14:30 Introduction to UniProt and other protein sequence databases

To be confirmed

14:30 - 15:15 Practical databases and raw data conversion

Harald Barsnes & Lennart Martens

15:15 - 16:00 MS search engines

Harald Barsnes

16:00 - 16:30 Break
16:30 - 18:00 Practical on identification

Harald Barsnes & Lennart Martens

18:00 - 19:30

Posters and drinks

All
20:00  Dinner

Hinxton Hall Restaurant

Day 3 - Tuesday 18 July
08:15 Arrival  
08:30 - 09:00 Protein inference

Harald Barsnes

08:30 - 10:30 Practical on identification

Harald Barsnes & Lennart Martens

10:30 - 11:00 Break
11:00 - 11:30 Identification validation and FDR

Harald Barsnes

11:00 - 12:30 Practical on identification

Harald Barsnes & Lennart Martens 

12:30 - 13:30 Lunch
13:30 - 14:45 Keynote: Analysing post-translational modifications   Rene Zahedi
14:45 - 16:00 Introduction to quantitative proteomics  Kathryn Lilley
16:00 - 16:30 Break
16:30-19:00  Quantitative proteomics practical

Kathryn Lilley

19:30 Dinner 

Hinxton Hall Restaurant

Day 4 - Wednesday 19 July
08:30 - 10:30 Quantitative proteomics: Introduction to MaxQuant Jurgen Cox
10:30 - 11:00 Break
11:00 - 12:30 MaxQuant practical Jurgen Cox
12:30 - 13:30 Lunch 
13:30 - 15:30 Introduction to the Open MS framework  Yasset Perez-Riverol
15:30 - 16:00 Break
16:00 - 16:30 Proteomics data standards Juan Antonio Vizcaino
16:30 - 19:00 Galaxy framework for proteomics analysis Conrad Bessant
19:30 Dinner 

Hinxton Hall Restaurant

Day 5 - Thursday 20 July
08:30 - 09:00

Proteomics repositories, PRIDE and ProteomeXchange

 

Juan Antonio Vizcaíno
09:00 - 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 - 15:45 Representation of proteomics data in Ensembl

To be confirmed

15:45 - 16:15 Break
16:15-19:00  IntAct, PSIMEX and PSICQUIC 

Sandra Orchard & Pablo Porras

19:30 Dinner

Hinxton Hall Restaurant

Day 5 - Friday 21 July
08:30-10:30 Functional analysis I  Steve Jupe
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  Pablo Porras
15:15-15:30 Course Survey Tom Hancocks
15:30 End of course