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 2016 course

“I really enjoyed the course. I feel that I learned a lot, and I feel
confident with practising on most of the tools were talked about”
“Best course I have been on. Heavy workload but lectures/tutorials were
mostly delivered at the right speed with a few exceptions. Very well
organised and wonderful surroundings.”
“Overall, this course was great! Each of the topics were good and the
speakers were phenomenal! The instructors were great! Well organized!”
“I found the course very valuable and well organised, and will utilise
much of the information provided here. I am looking forward to analysing
my own data with the tools provided.”
“I would highly recommend this course to anyone that wants to use
proteomics and bioinformatics in the future! I’m glad that I was able to
participate!”
“Excellent course and useful for anyone carrying out proteomics
bioinformatics. Also suitable for both biologists and
bioinformaticians”.

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

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

Guest speakers
Pedro Beltrao EMBL-EBI, UK
Jyoti Choudhary Wellcome Trust Sanger Institute, UK

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 £680 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

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

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

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 £680 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

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.