Proteomics aims to understand gene function and molecular processes of the living cell through a large-scale study of the expressed proteins. Although proteomics approach is largely applied on experimental models such as rodents, other animal models such as medaka fish (Oryzias latipes) also attracts considerable interest in proteomics field. Medaka is one of the most studied animal model in reproductive or developmental biology. Although, its genome has been sequenced, only a few proteins are available in the databases.

We present the procedure used in one experiment as a model of identification of proteins, in this case from liver of medaka treated by a hepatotoxic cyanotoxin, the microcystin.

Because O. latipes is not listed in mascot search engine, the identification of proteins (selected because modified by the treatment) was done on closed related species. First, 15 spots were analyzed using peptide mass fingerprinting (PMF). However none could be reliably identified using mascot engine. The reason for low sequence coverage is due to the fact that the outcome of the research depends on the completness of the protein database obtained from NCBInr and the availability of cross-species for protein identification. In order to improve the identification, the PMF search was combined with a search in a medaka nucleotide specific database and confirmed by MS/MS ion searches which revealed successful. This identification procedure has been successfully applied in different experiments with the medaka model.