GPDE: A biological view on PRIDE

Abstract

Clinical proteomics are unthinkable without the extensive use of meta-analysis. By the development of the Proteomics Identification Database Engine (PRIDE) extensive markup language (XML) data format in 2005 a standardized data format for proteomics data publishing was created. Here we present the Griss Proteomics Database Engine (GPDE, http://www.griss.co.at/?GPDE): an open source web-based bioinformatic tool that uses the possibilities of this standardized data format to create biologically-based meta-analysis over an unlimited number of proteomics experiments. Its aims are (1) to be fully compatible with the PRIDE XML data schema, (2) to integrate the data of different experiments or projects based on specially defined "cell types" thus dissolving the "borders" between different experiments and (3) to provide an intuitive web interface to access data otherwise only accessible via complex queries. The GPDE is free software and available for download under the terms of the Affero General Public License (AGPL, http://www.fsf.org/licensing/licenses/agpl-3.0.html). The GPDE is currently used by the Clinical Proteomics Laboratories at the Medical University of Vienna (CPL/MUW) (available at http://www.meduniwien.ac.at/proteomics/database). There the GPDE is used in three different ways: 1) as an in silico alternative to multiple Western analyses; 2) to provide easy access to cellular proteome reference maps and 3) to reliably support the assessment of the specificity of biomarker candidates. © 2009 Griss J, et al.