<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>The global analysis of proteins is now feasible due to improvements in techniques such as two-dimensional gel electrophoresis (2-DE), mass spectrometry, yeast two-hybrid
systems and the development of bioinformatics applications. The experiments form
the basis of proteomics, and present significant challenges in data analysis, storage and
querying. We argue that a standard format for proteome data is required to enable
the storage, exchange and subsequent re-analysis of large datasets. We describe the
criteria that must be met for the development of a standard for proteomics. We have
developed a model to represent data from 2-DE experiments, including difference
gel electrophoresis along with image analysis and statistical analysis across multiple
gels. This part of proteomics analysis is not represented in current proposals for
proteomics standards. We are working with the Proteomics Standards Initiative to
develop a model encompassing biological sample origin, experimental protocols, a
number of separation techniques and mass spectrometry. The standard format will
facilitate the development of central repositories of data, enabling results to be verified
or re-analysed, and the correlation of results produced by different research groups
using a variety of laboratory techniques.</p>
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Comp Funct Genomics. 2003 Oct; 4(5):492-501