Johannes Griss and Christopher Gerner
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 sour ce 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 dissolv- ing 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 Af fer o General Public License (AGPL, http://www.fsf.org/licensing/licenses/agpl-3.0.html ). The GPDE is curr ently used by the Clinical Pr oteomics Laboratories at the Medical University of V ienna (CPL/MUW) (available at http://www .meduniwien.ac.at/pr oteomics/database ). Ther e the GPDE is used in thr ee dif fer ent ways: 1) as an in silico alternative to multiple W estern analyses; 2) to pr ovide easy access to cellular pr oteome r efer - ence maps and 3) to reliably support the assessment of the specificity of biomarker candidates.