Proposal for a Standard Representation of Two-Dimensional Gel Electrophoresis Data
2003
Jones, Andrew(Department of Computing Science, University of Glasgow) | Wastling, Jonathan(Institute of Biomedical and Life Sciences, University of Glasgow) | Hunt, Ela(Department of Computing Science, University of Glasgow)
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-hybridsystems and the development of bioinformatics applications. The experiments formthe basis of proteomics, and present significant challenges in data analysis, storage andquerying. We argue that a standard format for proteome data is required to enablethe storage, exchange and subsequent re-analysis of large datasets. We describe thecriteria that must be met for the development of a standard for proteomics. We havedeveloped a model to represent data from 2-DE experiments, including differencegel electrophoresis along with image analysis and statistical analysis across multiplegels. This part of proteomics analysis is not represented in current proposals forproteomics standards. We are working with the Proteomics Standards Initiative todevelop a model encompassing biological sample origin, experimental protocols, anumber of separation techniques and mass spectrometry. The standard format willfacilitate the development of central repositories of data, enabling results to be verifiedor re-analysed, and the correlation of results produced by different research groupsusing a variety of laboratory techniques.
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