Joint EMBL-EBI/Wellcome Trust Course: Proteomics Bioinformatics

Date:

 Monday 10 - Friday 14 November 2014

Venue: 

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

Application deadline: 

Friday 04 July 2014

Participation: 

Open application with selection

Contact: 

Yvonne Thornton

Registration fee: 

£500

Registration closed

Overview

This joint EBI-Wellcome Trust workshop 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 workshop 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 (including large datasets) when collected.

Audience

The workshop is aimed at research scientists including laboratory and clinical staff, with some previous experience of proteomics.

Applicants without previous experience of bioinformatics are encouraged to apply, and if this applied to you then we strongly recommend that you familiarise yourself the R statistics package.

Syllabus, tools and resources

During this course you will learn about:

  • Mass Spectroscopy Basics
  • MS Search Engines and post-processing software
  • Quantitative proteomics
  • SRM/MRM approaches
  • Protein sequence databases and their use
  • Protein sequence data in UniProt
  • Proteomics data and services integration
  • Standardising proteomics data
  • MS proteomics repositories and the ProteomeXchange consortium
  • PRIDE and PRIDE related tools
  • Proteogenomics
  • Protein interaction data through IntAct and the IMEX consortium
  • Placing proteins in pathways using Reactome

Outcomes

After this course you should be able to:

  • Use bioinformatics tools to analyse SRM/MRM and quantitative proteomics data
  • Browse, search 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 approaches

Additional information

Feedback from previous courses

“I am very grateful for this opportunity and this certainly opens up a new avenue for my research and career. I am very happy and satisfied with this course.”

“Thank you for the opportunity. I had a great time there, and obtained a lot of new information that were applicable for my future research interest.”

“I recommend every PhD student especially international to attend these courses at least once during the period of the study.”

Programme

Time Topic Trainer
Day 1
10:30 Registration  
11:00 An introduction to the EBI and course expectations  Laura Emery
12:00 Lunch  
13:00 Proteomics history  Juan Antonio Vizcaíno
13:30 Mass spectrometry basics, MS search engines session 1  Lennart Martens (Ghent University)
15:30 Break  
16:00 Mass Spectrometry basics, MS search engines session 2  Lennart Martens (Ghent University)
18:15 Poster session (including drinks)  
20:00 Dinner  
     
Day 2
08:30 Protein sequences databases: UniProt and others  Sandra Orchard
10:30 Break  
11:00 Practical searching mass spectral data I  Harald Barsnes, Marc Vaudel, Lennart Martens
13:00 Lunch  
14:00 Practical searching mass spectral data II  Harald Barsnes, Marc Vaudel, Lennart Martens
15:30 Break  
16:00 Practical searching mass spectral data III  Harald Barsnes, Marc Vaudel, Lennart Martens
17:30 Keynote lecture  Rene Zahedi (ISAS Dortmund)
19:30 Dinner  
     
Day 3
08:30 Introduction to quantitative proteomics  Kathryn Lilley (University of Cambridge)
10:30 Break  
11:00 Quantitative proteomics group activity session  Laurent Gatto and Kathryn Lilley (University of Cambridge)
13:00 Lunch  
14:00 Quantitative Proteomics: Introduction to MaxQuant (including practical session)  Emanuele Alpi
15:30 Break  
16:00 Quantitative Proteomics: Introduction to MaxQuant (including practical session)  Emanuele Alpi
17:00 General introduction to targeted approaches in proteomics  Conrad Bessant (Queen Mary University of London)
 18:00 Galaxy framework for proteomics analysis Conrad Bessant (Queen Mary University of London)
 19:30 Dinner  
  Close  
     
Day 4
08:30 Introduction to PSI standard data formats  Juan Antonio Vizcaíno
09:00 Proteomics repositories and ProteomeXchange  Juan Antonio Vizcaíno
10:30 Break  
11:00 Practical on PRIDE and ProteomeXchange I  Juan Antonio Vizcaíno and TBD
13:00 Lunch  
14:00 Practical on PRIDE and ProteomeXchange II; Reanalysis of PRIDE data using PeptideShaker  (H. Barsnes/ M. Vaudel/ Juan Antonio Vizcaíno)
15:00 Break  
15:30 IntAct, PSIMEX and PSICQUIC  Sandra Orchard and Pablo Porras
18:15 Talk  James Wright (Wellcome Trust Sanger Institute)
19:45 Dinner  
     
Day 5
08:30 Functional Analysis  I  Pablo Porras
11:00 Break  
11:30 Functional Analysis II  Steve Jupe
13:30 Lunch  
14:30 Q&A and Course Feedback  
15:00 Close  

 

 

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

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

Application deadline

04 July 2014

Number of places

30 places

Registration closed

Organisers

Juan Antonio Vizcaino

Laura Emery

Lennart Martens

Trainers

Juan Antonio Vizcaino - EMBL-EBI, UK

Lennart Martens - EMBL-EBI, UK

Sandra Orchard - EMBL-EBI, UK

Harald Barsnes - University of Bergen, Norway

Marc Vaudel - Computational Omics and Systems Biology Group, VIB-UGent

Rene Zahedi - ISAS Dortmund

Kathryn Lilley - University of Cambridge, UK

Laurent Gatto - EMBL-EBI, UK

Emanuele Alpi - EMBL-EBI, UK

Conrad Bessant - Queen Mary University of London

Pablo Porras Millan - EMBL-EBI, UK

James Wright - Wellcome Trust Sanger Institute, UK

Steve Jupe - EMBL-EBI, UK

Materials & attachments

Joint EMBL-EBI-Wellcome Trust Course Proteomics Bioinformatics