Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database – Xindice

The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database.Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/ webcite.The completion of human and other model-organism genome projects has provided a sequence infrastructure to allow an improved understanding of the dynamic processes of cellular signaling, regulation, and metabolism. Although all cells contain the complete genome, only a fraction of the genes are expressed within a given cell. Under different conditions or within different tissues of the same organism, a specific set of proteins are expressed and/or post-translationally modified to carry out the special function of the cell [1-3]. The term 'proteome' is a hybrid of "PROTEin" and "genOME" and it refers to the entire protein components, along with all covalent protein modifications in a selected cell. With the arrival of the post-genomic era, functional genomics has become a new focus of biological research, and proteomics has emerged as a promising field for assessing global protein function [4].In order to understand the roles of different proteins played and to dissect protein-protein interaction networks, high-throughout methodologies are being applied in the emerging field of proteomics. As a result, large amounts of experimental data have been generated by high-throughout proteomics methodologies, such as large-scale two-hybrid systems, high-throughout ma