In order to evaluate PepLine efficiency, a strategy of validation had been designed.
This strategy involved several steps:
In the context of one of its collaborative research projects on Arabidopsis thaliana, the "Laboratoire de Chimie des Protéines" supplied experimental MS/MS data and its human mass spectrometry expertise.
To test PepLine protein identification performances, we chose to confront it against Mascot, the most commonly used protein identification software.
A database of Arabidopsis thaliana proteins has been chosen to apply a consistent confrontation. The database presents a high level of consistency between genomic and protein data and offers valuable gene/protein and protein/gene information.
The database has been screened by both PepLine and Mascot softwares.
The specificity of the PepLine genomic localization features makes its confrontation with another software difficult. Several tests were realized and PepLine was proved to be fast and reliable. Those first results cannot be shown yet because of the confidentiality of the experimental data; they will be available soon in a publication to come.
The PST approach demonstrated its usefulness for genome annotation with the localization of intron/exon boundaries. For instance, we proved the presence of a gene corresponding to a protein included in the Swiss-Prot database but not included in the TAIR database.