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Briefings in Bioinformatics Advance Access published online on February 15, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn004
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Information quality in proteomics

David A. Stead, Norman W. Paton, Paolo Missier, Suzanne M. Embury, Cornelia Hedeler, Binling Jin, Alistair J. P. Brown and Alun Preece

Corresponding author. David A. Stead, School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK. Tel: +44 (0) 1224 555804; Fax: +44 (0) 1224 555844; E-mail: d.stead{at}abdn.ac.uk

Proteomics, the study of the protein complement of a biological system, is generating increasing quantities of data from rapidly developing technologies employed in a variety of different experimental workflows. Experimental processes, e.g. for comparative 2D gel studies or LC-MS/MS analyses of complex protein mixtures, involve a number of steps: from experimental design, through wet and dry lab operations, to publication of data in repositories and finally to data annotation and maintenance. The presence of inaccuracies throughout the processing pipeline, however, results in data that can be untrustworthy, thus offsetting the benefits of high-throughput technology. While researchers and practitioners are generally aware of some of the information quality issues associated with public proteomics data, there are few accepted criteria and guidelines for dealing with them. In this article, we highlight factors that impact on the quality of experimental data and review current approaches to information quality management in proteomics. Data quality issues are considered throughout the lifecycle of a proteomics experiment, from experiment design and technique selection, through data analysis, to archiving and sharing.

Keywords: information quality, proteomics, standards, quality assessment, information management

Submitted: July 12, 2007. Received (in revised form): January 11, 2008.


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