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Pride Wizard: generation of standards compliant quantitative proteomics data

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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.

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Correspondence to Neil Swainston.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Keywords

  • System Biology
  • Protein Identification
  • Proteomics Data
  • Control Vocabulary
  • Peak List