Proteomics Bioinformatics

Run jointly with EMBL-EBI, this popular 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 and
quantify 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.

Feedback from the 2017 course
“The course is quite impressive, I will highly recommend this course.”
“The course was excellent and I have learned a lot and happy to
recommend.”
“I am very satisfied with this course, thank you for all of your
efforts!”
“Thank you for an excellent experience!”
“Many thanks! I really enjoyed the course, a great team job :)”
“Now I know so much more about proteomics than a week ago. And I know how
to build on this knowledge. The social aspect was also brilliant. Thanks
a lot for a fantastic week.”

The programme will include lecture and practical, computational sessions
covering the following topics:

• Mass Spectrometry Basics
• Proteomics Bioinformatics Basics
• Quantitative proteomics
• Protein sequence data in UniProt
• Standardisation of proteomics data
• MS proteomics repositories, including PRIDE and PRIDE-related tools and ProteomeXchange
• Introduction to Proteogenomics
• Protein interaction data through IntAct and resources from the IMEX consortium (e.g. IntAct)
• Functional analysis of proteins using Cytoscape

Learning Outcomes
After completing the course, participants will 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
• 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 Institute of Cancer Research, UK

Prerequisites
Applicants should be research scientists with a minimum of a degree in a
biological discipline, including laboratory and clinical staff, as well
as specialists in related fields.

Applications
Applications
can be submitted online. Places are limited and will be awarded on
merit. 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,
line manager, 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 to the UK. Note that letters will only 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
the fee is £695, including all accommodation and meals.
This subsidised fee is available to all 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 a 50% reduction 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.

Additional funding opportunities
Visit
our Funding webpage for additional funding opportunities currently
available.

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.