The Gulbenkian Training Programme in Bioinformatics

GTPB runs at the Instituto Gulbenkian de Ciência on a yearly basis since 1999.
More than 1000 course attendees in 9 years
Pedro Fernandes, GTPB organizer

Proteomics Data Analysis

PDA08 - course website

Deadline for applications: Sept 8th 2008
Course date: September 24th - September 26th 2008


Ola Forsstrom-Olsson has an academic background in Engineering Physics and Medicine from Lund University, Sweden. In 2001 he founded the proteomics software company Ludesi ( in Sweden, and is today operating as the company's CEO. He won Medicon Valley Entrepreneurship Award in 2001, was nominated for MIT's Technology Review's Top100 list of the World's Best Technology Innovators in 2004, won the Global Emerging Technology of the Year Award 2008 from Frost & Sullivan for Ludesi's products and services in the 2D Gel Electrophoresis field. Ola Forsstrom-Olsson is a member of the Industrial Advisory Board of the Human Proteome Organization (HUPO). He is a regular lecturer at all proteomics training courses at the National Institutes of Health in Washington DC, USA."
Ludesi Corp, Malmö, Sweden and Boston, MA (USA)

Roman Zubarev studied technical physics in the Moscow Engineering Physics Institute and received his PhD in Ion Physics from the Uppsala University, Sweden. After postdoc training in Fred W. McLafferty's group at the Cornell University in USA, he became associate professor at the Chemistry Department in Odense, Denmark. In 2002 Dr. Zubarev came back to the Uppsala University as full professor, and became engaged in proteomics work. Dr. Zubarev is a Director of HUPO, and an awardee of the prestigious Carl Brunnee award (ISMS, 2006) and Biemann medal (ASMS, 2007) for his work in mass spectrometry. Dr. Zubarev has published more than 130 peer-reviewed papers, and has several patents. He teaches courses related to mass spectrometry and proteomics analysis.
Molecular Biometry Group, Institute for Cell and Molecular Biology, Uppsala University, Sweden

Lennart Martens studied biotechnology at Ghent University in Belgium, where he did his Master's thesis on the computational interpretation of peptide mass spectra. He then worked as a software developer and framework architect for a software company for a few years, before returning to Ghent University to pursue a Ph.D. in Biotechnology. During this time, he focussed on the development of high-throughput peptide centric proteomics techniques and on bioinformatics tools to support these new approaches. In 2003 he started the PRIDE proteomics database at the EBI as a Marie Curie fellow of the European Commission. After obtaining his Ph.D., Dr. Martens rejoined the PRIDE group at EBI, which he now coordinates. He is Bioinformatics Section Editor for the Springer journal Amino Acids, is an author on more than 50 peer-reviewed papers, and has written a Wiley textbook on Computational Methods for Mass Spectrometry.
European Bioinformatics Institute, Hinxton, UK

Phillip Jones studied Genetics ad the University of Sheffield in the UK and Software Engineering with the Open University in the UK. He spent six years working as a secondary level science teacher before moving into Bioinformatics Software Engineering with the UK Medical Research Council, in 2001. In 2004 he started working at the EBI, where he developed the UniProt DAS Reference Server, the MyDas DAS server framework and has spent most of his time working as the technical lead developer on the PRIDE proteomics database and the PRIDE BioMart. Philip regularly delivers training on EBI resources at both roadshows around the world and also at EBI based hands-on workshops.
European Bioinformatics Institute, Hinxton, UK

Course Description

The course starts with a primer on Image Analysis, applied to 2D Gels. You will be working hands-on at computers with cutting-edge 2D gel image analysis software as well as learning the basic theory of 2D gel image analysis data quality. This class covers the same material as being tought exclusively at the prestigeous proteomics training courses at the National Institutes of Health in USA.
The afternoon lectures will (re)introduce you to such fundamental concepts of modern protein mass spectrometry as the type and amount of information available from accurate mass analysis and MS/MS fragmentation. We will discuss the needs for and the methods of performing protein quantification.

On the second and third days will then introduce the bioinformatics techniques, tools and methods that are available for analysing mass spectrometry based proteomics data.
We will focus on the challenges involved in peptide identification and spectrum comparison, inferring protein identification from identified peptides and performing clustering.
Then we will focus on the database tools and resources available at the European Bioinformatics institute, including sequence databases (UniProt and IPI), databases of protein annotation, domains, families and functions (UniProt and InterPro), and the PRIDE Proteomics Identifications Database. There will also be an introduction to the Reactome database of metabolic pathways, which is integrated into the PRIDE Proteomics Identifications Database.
The course will end with a demonstration of some of the available web service tools and infrastructure that allow the building of powerful and reusable data analysis workflows.


PDA08 Proteomics Data Analysis
Sept 24th
Obtaining data for Proteomics   -   Day 1
09:30 - 11:00 2D gel image analysis: from lab bench to analysis results
11:00 - 11:30 Coffee Break
11:30 - 12:30 2D gel image analysis: practice
12:30 - 14:00 Lunch Break
14:00 - 16:00 Information available from MS and MS/MS and the methods of its obtaining
16:00 - 16:30 Tea Break
16:30 - 18:00 Toward protein quantification and pathway analysis
Sept 25th
Analysis of Mass Spectrometry data   -   Day 2
09:30 - 11:00 Peptide Identification and Spectrum Comparison
11:00 - 11:30 Coffee Break
11:30 - 12:30 From Peptides to Proteins: Protein Inference Combining Results from Several Experiments in One
12:30 - 14:00 Lunch Break
14:00 - 16:00 Peptide Identification and Clustering (Practical)
16:00 - 16:30 Tea Break
16:30 - 18:00 Protein Inference and Experiment Comparison (Practical)
Sept 26th
Database usage and integration   -   Day 3
09:30 - 11:00 Protein Sequence Databases at the EBI: UniProt and IPI (w/ Practical)
11:00 - 11:30 Coffee Break
11:30 - 12:30 The InterPro database and using InterProScan (w/ Practical)
12:30 - 14:00 Lunch Break
14:00 - 16:00 Proteomics Data Standards and the PRIDE Proteomics Identifications Database (w/ Practical)
16:00 - 16:30 Tea Break
16:30 - 18:00 The Reactome Pathway Database and Integrating Data using Web Services (w/ Demonstration)

Pre-requisites: Basic Molecular Biology and Biochemistry. Elementary computing skills.
Application process: Please fill-in the form available in

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Last updated:August 1st 2008