The large‐scale systematic quantitation of proteins is an important component of proteomics and has contributed to the emergence of the new fields of systems biology and molecular medicine. Quantitative proteomics provides new insights into biological function, facilitates the identification of diagnostic or prognostic disease markers, and contributes to the discovery of proteins as therapeutic targets. The field is growing rapidly and currently driven by technological innovations. Bioinformatics is a crucial component of any proteomics strategy, but none more than quantitative analysis. The general aim of this course is to bring a higher level of understanding in core bioinformatics procedures concerning protein identification strategies, methods for quantitation, and the translation of this information to ontology and pathway analysis. The course forms a basis to a series of training modules where the overall aim is to confidently measure differences in protein expression, from single proteins to proteomes.
In this course the following elements of computational proteome analysis are covered:
‣ Experimental design for quantitative proteomics: SILAC, iTRAQ and label‐free analyses
‣ Identification strategies using (Mascot, Sequest, X! Tandem, Protein Pilot) combined with quantitative analysis
‣ Strategies for determining confidence scores for protein identification via peptide and protein prophets, False discovery rate (FDRs) and decoy strategies
‣ Quantitative analysis for label free measurements using, SuperHIRN, Mayu, Progenesis, and other tools
‣ Quantitative analysis using labelling methods such as SILAC, iTRAQ & TMT.
‣ Additional tools for data handling and validation, including: Trans‐proteomics pipeline (and prophets), Mascot distiller, ProteinPilot, Scaffold, Protein Centre and Pathway Search Engine analysis.
Trainers
Garry Corthals
Anne Rokka
Robert Moulder
Anni Vehmas
Turku Centre for Biotechnology, Turku
Jimmy Ytterberg
Hye Jung
Uni of Southern Denmark,Odense
David Shteynberg
Institute for Systems Biology, Seattle
Manfred Claasen
Ludovic Gillet
ETH, Zurich
Roman Zubarev
Karolinska Institute, Sweden
The course is from Monday 9 November until Friday 13 November at the Turku Centre for Biotechnology, BioCity Turku, Finland. The course will incorporate lectures and extensive practical training. To ensure all participants get hands‐on training the number of places is limited. The course is in the first instance open to PhD participants from Nordic countries (Finland, Denmark, Iceland, Norway, Sweden). Transport and accommodation will be provided to PhD participants from the Nordic countries, and course fees will be waived. Several places will be made available to other European participants, however in this case transport and accommodation costs cannot be provided and must be met in full by the participant. A fee of 1000€ exists for other participants.
Register to the course by sending a short application to Katri Kaunismaa (katri.kaunismaa(a)btk.fi). In the application which is no longer than one A4 page you should provide the following information:
1. Your name
2. Graduate school
3. Short description of your project (0,5 page max.)
4. Institution
5. Your supervisor
6. How bioinformatics would benefit your project
