The Pediatric Ependymoma Protein Database (PEPD)

Proteomics, through application of modern high-end mass spectrometric (MS) approaches, offers the advantage of in-depth analysis of cancer tissues regarding their protein composition. Pediatric brain tumor malignancies are scarcely approached by modern holistic technologies (e.g. genomics, proteomics) due to rarity of samples and most importantly difficulty in their collection. Ependymoma, is the third most common tumor in children and is thought to arise from ependymal cells in the wall of the cerebral ventricles or the spinal canal. Due to the heterogeneity of the disease its biological characteristics remain largely unknown and prognostic factors are basically based on clinical and histological criteria. Through application of a modified nanoLC-MS/MS analysis experimental approach we achieved, for the first time, the in-depth examination of the pediatric ependymoma tissue proteome. In the present article we report on the construction of a high-confidence database; the Pediatric Ependymoma Protein Database (PEPD), including 4,157 protein groups originating from the identification and analysis of more than 15,000 peptides. The PEPD offers a first step towards targeted protein validation of the protein content of this specific devastating disease affecting the young population.