Evidence for existence of thirty hypothetical proteins in rat brain

Background: The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms. Results: We constructed a two-dimensional protein map and searched for expression of hypothetical proteins in rat brain. Two-dimensional electrophoresis (2-DE) with subsequent in-gel digestion of spots and matrix-assisted laser desorption/ionization (MALDI) spectrometric identification were applied. In total about 3700 spots were analysed, which resulted in the identification of about 1700 polypeptides, that were the products of 190 different genes. A number of hypothetical gene products were detected (30 of 190, 15.8%) and are considered brain proteins. Conclusions: A major finding of this study is the demonstration of the existence of putative proteins that were so far only deduced from their nucleic acid structure by a protein chemical method independent of antibody availability and specificity and unambiguously identifying proteins.