Volume 1 Supplement 1

BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology

Open Access

Pride Wizard: generation of standards compliant quantitative proteomics data

  • Neil Swainston1Email author,
  • Jennifer A Siepen2,
  • Andrew R Jones2, 3,
  • Sarah R Hart4,
  • Henning Hermjakob5,
  • Phil Jones5 and
  • Simon J Hubbard2
BMC Systems Biology20071(Suppl 1):P27

DOI: 10.1186/1752-0509-1-S1-P27

Published: 8 May 2007

The introduction of the Proteomics Identifications Database (PRIDE) provided the proteomics community with a standards compliant data repository for proteomics data. PRIDE implements standards put forward by the Proteome Standards Initiative (PSI) including mzData.

Many commonly used proteomics software packages do not currently support these standards. As such, formatting data to adhere to the PRIDE schema requires the writing of data parsers to perform the conversion. To address this, the Pride Wizard has been introduced to perform the transformation steps required to convert more commonly used file formats into documents that adhere to the PRIDE schema. Examples of these include .mgf files for peak lists and Mascot .dat files for peptide and protein identifications.

The existing PRIDE schema has no provision for quantitative proteomics data. A new controlled vocabulary is introduced here to allow storage of quantitative I-TRAQ data. It is envisaged that this can be extended to allow submission of quantitative data from other labelling techniques.

The tool has been used to populate a PRIDE database with mass spectra and associated protein identifications and quantifications from a comprehensive set of proteomics experiments from a systems biology study of growth-rate in the eukaryotic cell.

Authors’ Affiliations

(1)
Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester
(2)
Faculty of Life Sciences, Michael Smith Building, University of Manchester
(3)
School of Computer Science, Kilburn Building, University of Manchester
(4)
Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester
(5)
EMBL Outstation, European Bioinformatics Institute, Welcome Trust Genome Campus

Copyright

© Swainston et al; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd.

Advertisement