Open Source System for Analyzing, Validating, and Storing Protein Identification Data

This paper describes an open-source system for analyzing, storing, and validating proteomics
information derived from tandem mass spectrometry. It is based on a combination of data analysis
servers, a user interface, and a relational database. The database was designed to store the minimum
amount of information necessary to search and retrieve data obtained from the publicly available data
analysis servers. Collectively, this system was referred to as the Global Proteome Machine (GPM). The
components of the system have been made available as open source development projects. A publicly
available system has been established, comprised of a group of data analysis servers and one main
database server.
Keywords: proteomics database • GPM • X Tandem • protein identification • XIAPE