Siepen, JA and Swainston, N and Jones, AR and Hart, SR and Hermjakob, H and Jones, P and Hubbard, SJ (2007) An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Sci, 5. 4 - ?. ISSN 1477-5956

[img]
Preview
Text
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ..pdf - Published Version
Available under License Creative Commons Attribution.

Download (328kB) | Preview

Abstract

BACKGROUND: Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed. RESULTS: We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ reported intensities from Mascot output, into a valid PRIDE XML entry. CONCLUSION: We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard.

Item Type: Article
Subjects: Q Science > QH Natural history
Divisions: Faculty of Medicine and Health Sciences > Institute for Science and Technology in Medicine
Related URLs:
Depositing User: Symplectic
Date Deposited: 10 Sep 2015 08:05
Last Modified: 20 May 2016 14:13
URI: http://eprints.keele.ac.uk/id/eprint/855

Actions (login required)

View Item View Item