From the use of MS/MS analysis data, the software has to : 1) confirm genes predictions ; 2) annotate new CDS; 3) correct intron-exon junctions. First, Peptide Sequence Tags (PST) are generated from MS/MS spectra analysis using the software Pepnovotag 3.1 beta . A PST is defined as a short peptide sequence (3 to 5 amino acids) flanked by two masses corresponding to the two adjacent polypeptides. We align and clusterize PSTs in the six reading frames using two modules of PepLine  (PMmatch and PMclust) adapted and optimized for the project. So the clusters obtained are evaluated and compared with the genes predictions produced by the conventional genome annotation.