Course at EMBL-EBI
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.
Who is this course for?
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.
What will I learn?
Learning 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
Course content
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
Trainers
EMBL-EBI, UK
EMBL-EBI, UK
Ghent University & VIB, Belgium
Programme
Day 1 - Sunday 21 July 2019 |
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17:00-17:30 | Arrival, check-in and registration | |
17:30-18:30 | Introductions, networking and expectations | Anna Swan |
18:30-19:00 | Course introduction and a proteomics history | Juan Antonio Vizcaíno |
19:00 | Welcome drinks | Hinxton Hall Lounges |
19:30 | Evening BBQ | Hinxton Hall Restaurant |
Day 2 - Monday 22 July 2019 |
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08:15 | Arrival | EMBL-EBI South Building |
08:30-08:45 | Training Room orientation | Anna Swan |
08:45-10:00 | Mass spectrometry search engines | Lennart Martens |
10:00-10:30 | Break | |
10:30-11:30 | Mass spectrometry search engines | 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 | 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 23 July 2019 |
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08:15 | Arrival | |
08:30-10:45 | Identification recap | Lennart Martens & Harald Barsnes |
10:45-11:15 | Break | |
11:15-12:30 | Keynote talk | Evangelia Petsalaki |
12:30-13:30 | Lunch and posters | |
13:30-14:45 | Introduction to quantitative proteomics | Kathryn Lilley |
14:45-16:00 | Quantitative proteomics and experimental design | Kathryn Lilley & Oliver Crook |
16:00-16:30 | Break | |
16:30-17:15 | Quantitative proteomics and experimental design | Kathryn Lilley & Oliver Crook |
17:15-19:00 | Basics of peptide/protein quantification | Lieven Clement |
19:30 | Evening meal | Hinxton Hall Restaurant |
Day 4 – Wednesday 24 July 2019 |
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08:15 | Arrival | |
08:30-09:30 | Overview of tools for quantitative proteomics | Yasset Perez-Riverol |
09:30-10:30 | Introduction to MaxQuant | Tami Geiger |
10:30-11:00 | Break | |
11:00-12:30 | MaxQuant practical | Tami Geiger |
12:30-13:30 | Lunch | |
13:30-15:00 | MaxQuant practical | Tami Geiger |
15:00-15:30 | Proteomics data standards | Juan Antonio Vizcaino |
15:30-16:00 | Break | |
16:00-19:00 | Introduction to data-independent acquisition approaches | Simon Hubbard, David Lee & Paul Brack |
19:30 | Evening meal | Hinxton Hall Restaurant |
Day 5 – Thurasday 25 July 2019 |
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08:15 | Arrival | |
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 and posters | |
13:30-14:45 | ProteoGenomics | Theo Roumelitis |
14:45-15:30 | Integration of proteomics data in Ensembl | Yasset Perez-Riverol |
15:30-16:00 | Break | |
16:00-18:45 | IntAct, PSIMEX and PSICQUIC | Sandra Orchard & Pablo Porras |
19:30 | Evening meal | Hinxton Hall Restaurant |
Day 6 – Friday 26 July |
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08:00 | Checkout of accommodation | |
08:15 | Arrival | |
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 | Bijay Jassal |
15:15-15:30 | Course Survey | Anna Swan |
15:30 | End of course |
Registration is handled through the Wellcome Trust Advanced Courses website.