Proteomics Bioinformatics

Run jointly with EMBL-EBI, this
course 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 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.

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

Feedback from the 2015 course

• “Thank you to all involved for making the course run so smoothly AND in such a logical progression. The course structure was very well conceived.”
• “Thanks for the helpful and informative experience and this major milestone in my educational record alongside my PhD studies! You are the best :)”
• “I think this course is very well organized, with top speakers! Every one of the speakers was available for Q&A, which is great. Overall, the course provides all the tools necessary for carrying your proteomics project and even gives you new ideas about all you could do. Thanks!”
• “This is the best course that I have attended. Well done to the organizers and lecturers!”

The programme 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

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

Scientific Organising Committee
Juan A.
Vizcaíno EMBL-EBI, UK
Lennart
Martens Ghent University and VIB, Belgium
Annalisa Mupo
EMBL-EBI, UK

The course will be taught by trainers from the
European Bioinformatics
Institute.

Guest speakers
Jyoti
Choudhary Wellcome Trust Sanger Institute, UK
René P.
Zahedi Leibniz – Institut für Analytische Wissenschaften – ISAS –
e.V.

Prerequisites
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.

Cost
The
course is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £590 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to 50% of the course fee) and are awarded on merit. If you
would like to apply for a
bursary, please complete the bursary section
of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.