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This article is part of the supplement: Proceedings of the 6th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-meeting 2010)

Open Access Proceedings

PRODIS: a proteomics data management system with support to experiment tracking

Alessandra Faria-Campos1*, Herbert Fernandes-Rausch1, Celina Val1, Peter Thorun1, Vinicius Abreu1, Paulo Henrique Batista1, Paulo Henrique Mendonça1, Vinicius Alves1, Maíra Ribeiro Rodrigues3, Adriano Pimenta2, Glória Franco2 and Sérgio Vale Aguiar Campos1

Author Affiliations

1 Departamento de Ciência da Computação, Universidade Federal de Minas Gerais, Brazil

2 Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal Minas Gerais, Brazil

3 Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal Minas Gerais, Brazil

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BMC Genomics 2011, 12(Suppl 4):S15  doi:10.1186/1471-2164-12-S4-S15

Published: 22 December 2011

Abstract

Background

A research area that has greatly benefited from the development of new and improved analysis technologies is Proteomics and large amounts of data have been generated by proteomic analysis as a consequence. Previously, the storage, management and analysis of these data have been done manually. This is, however, incompatible with the volume of data generated by modern proteomic analysis. Several attempts have been made to automate the tasks of data analysis and management. In this work we propose PRODIS (Proteomics Database Integrated System), a system for proteomic experimental data management. The proposed system enables an efficient management of the proteomic experimentation workflow, simplifies controlling experiments and associated data and establishes links between similar experiments through the experiment tracking function.

Results

PRODIS is fully web based which simplifies data upload and gives the system the flexibility necessary for use in complex projects. Data from Liquid Chromatography, 2D-PAGE and Mass Spectrometry experiments can be stored in the system. Moreover, it is simple to use, researchers can insert experimental data directly as experiments are performed, without the need to configure the system or change their experiment routine. PRODIS has a number of important features, including a password protected system in which each screen for data upload and retrieval is validated; users have different levels of clearance, which allow the execution of tasks according to the user clearance level. The system allows the upload, parsing of files, storage and display of experiment results and images in the main formats used in proteomics laboratories: for chromatographies the chromatograms and lists of peaks resulting from separation are stored; For 2D-PAGE images of gels and the files resulting from the analysis are stored, containing information on positions of spots as well as its values of intensity, volume, etc; For Mass Spectrometry, PRODIS presents a function for completion of the mapping plate that allows the user to correlate the positions in plates to the samples separated by 2D-PAGE. Furthermore PRODIS allows the tracking of experiments from the first stage until the final step of identification, enabling an efficient management of the complete experimental process.

Conclusions

The construction of data management systems for Proteomics data importing and storing is a relevant subject. PRODIS is a system complementary to other proteomics tools that combines a powerful storage engine (the relational database) and a friendly access interface, aiming to assist Proteomics research directly at data handling and storage.