Short Courses

Course 1: Understanding protein sequence databases for a better mass spectrometry identification
Monday 3rd December, morning – Ecole Hotelière – at 10:30 am
by Marie-Claude Blatter
of the Swiss Institute of Bioinformatics (Geneva).

During this 2 hour course, Marie-Claude Blatter will briefly describe UniProtKB, NCBInr, RefSeq, IPI,
Ensemble, MSDB and their relation with mass spectrometry identification.

This course will answer questions such as:

• What are the differences between these protein sequence databases?
• How are they constructed and how do they handle redundancy?
• Are there tools to correlate what is identified in one database with the identical or homologous sequences in the others?

Course 2: Computational Mass Spectrometry
Monday 3rd December, afternoon – Ecole Hotelière – at 2 pm.
by Jacques Colinge
of the Research Center for Molecular Medicine (Austrian Academy of Science, Wien).

During this 2 to 3 hour course, Jacques Colinge proposes to first introduce the general principle of identifying MS/MS spectra via database searching or peptide de novo sequencing, then discuss with more details the scoring function intended to measure the correlation between experimental MS/MS spectra and peptide sequences.

Although the main focus will be how classical statistical modeling techniques can be applied to the design of the scoring function, such as implemented in Phenyx, he will also introduce SEQUEST (and its many rescorers such as Peptide Prophet) and Mascot scoring concepts. Additional problems related to peptide-based protein identification, i.e., bottom-up proteomics, will be presented briefly.
Finally, he will evoke special approaches to search unannotated eukaryotic genomes directly, in order to find peptides coded across two exons.