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

TLDR

The paper presents an open‑source system for analyzing, storing, and validating proteomics data from tandem mass spectrometry. The system, called the Global Proteome Machine, integrates data‑analysis servers, a user interface, and a relational database that stores only the essential information needed to search and retrieve data from public analysis servers. The components have been released as open‑source projects, and a publicly available system comprising multiple data‑analysis servers and a central database has been established.

Abstract

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.