Proteomics Bioinformatics

Date:

 Sunday 4 - Friday 9 December 2016

Venue: 

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

Application deadline: 

Friday 23 September 2016

Participation: 

Open application with selection

Contact: 

Yvonne Thornton

Registration fee: 

£590

Registration closed

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 (including large datasets) when collected.

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

Programme

Time Topic Trainer
Day 1 - Sunday 4 December 2016
16:30 - 17:30 Registration 
17:30 - 18:30 Introduction and expectations Tom Hancocks
18:30 - 19:00 Proteomics history   Juan Antonio Vizcaíno
19:30

Dinner and drinks
Day 2 - Monday 5 December 2016
08:30 - 10:30 Mass Spectrometry basics   Lennart Martens
10:30 - 11:00 Break 
11:00 - 13:30 Mass Spectrometry basics, MS search engines session 2  Lennart Martens
12:30 - 13:30 Lunch 
13:30 - 14:30 Introduction to UniProt and other protein sequence databases

Emmanuele Alpi
14:30 - 16:00 Mass Spectrometry basics, MS search engines session 2 

Harald Barsnes, Marc Vaudel & Lennart Martens
16:00 - 16:30 Break
16:30 - 18:00 Mass Spectrometry basics, Quality Control / Practical Searching Mass Spectral Data Session 1 

Harald Barsnes, Marc Vaudel & Lennart Martens
18:00 - 19:45

Poster Session 

 All
20:00  Dinner 
Day 3 - Tuesday 6 December
08:30 - 10:30 Practical Searching Mass Spectral Data Session 2 

Harald Barsnes, Marc Vaudel & Lennart Martens
10:30 - 11:00 Break
11:00 - 12:30 Practical Searching Mass Spectral Data Session 3 

Harald Barsnes, Marc Vaudel & Lennart Martens 
12:30 - 13:30 Lunch
13:30 - 14:45 Talk: 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 continues including practical session on Experimental Design

Kathryn Lilley

Laurent Gatto 
19:30 Dinner 
Day 4 - Wednesday 7 December 2016
08:30 - 10:30 Quantitative Proteomics: Introduction to MaxQuant (including practical session)   Emmanuele Alpi
10:30 - 11:00 Break
11:00 - 12:30 Quantitative Proteomics: Introduction to MaxQuant (including practical session) 2   Emmanuele Alpi
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 - 18:30 Galaxy for Proteomics including Practical   Conrad Bessant
19:30 Dinner 
Day 5 - Thursday 8 December 2016
08:30 - 09:00 Introduction to PSI standard data formats   Juan Antonio Vizcaíno
09:00 - 10:30 Proteomics repositories and ProteomeXchange Juan Antonio Vizcaíno
10:30 - 11:00 Break
11:00 - 12:30 Practical on PRIDE and ProteomeXchange 

Juan Antonio Vizcaíno & Andrew Jarnuczak
12:30 - 13:30 Lunch 
13:30 - 14:45 Talk: ProteoGenomics Jyoti Choudhary
14:45 - 15:45 Practical on PRIDE and ProteomeXchange 2 - Reanalysis of PRIDE data using PeptideShake

Harald Barsnes, Marc Vaudel & Juan Antonio Vizcaíno
15:45 - 16:15 Break
16:15-19:00  IntAct, PSIMEX and PSICQUIC 

Sandra Orchard & Pablo Porras
19:30 Dinner

 
Day 5 - Friday 9 December 2016
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
15:30-16:00 Coffee break All
16:00-17:00 Q&A All
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

Details of the course (programme, trainers and the cost) are yet to be confirmed and are subject to funding arrangements. Please register your interest to stay informed about this course.

Previous versions of the course can be viewed here

Application deadline

23 September 2016

Number of places

30 places

Registration closed

Organisers

Tom Hancocks - EMBL-EBI, UK

Juan Antonio Vizcaino

Lennart Martens

Trainers

Tom Hancocks - EMBL-EBI, UK

Juan Antonio Vizcaino - EMBL-EBI, UK

Lennart Martens - Ghent University & VIB

Jyoti Choudhary - Wellcome Trust Sanger Institute, UK

Rene Zahedi - ISAS Dortmund