Proposal for a standard representation of two‐dimensional gel electrophoresis data

Abstract

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.

PEDRo: A database for storing, searching and disseminating experimental proteomics data

“…Thus, for example, there is no detailed description of the image analysis software used, the descriptions of individual spots are fairly minimal, and no details are captured on spot excision. An earlier critique of the PEDRo model for gels, and some possible extensions, is provided by [21]. It seems that, in order to provide insights for the developers of gel-based experiments, it would be appropriate for the model to be revised to provide additional details on gels.…”

An object model and database for functional genomics

“…The model also stores experimental protocols, raw data and data analysis and is known as Functional Genomics Experiment Object Model (FGE-OM). FGE-OM was developed from three main sources: the MAGE model for microarrays (Spellman et al, 2002), the PEDRo model developed at the University of Manchester (Taylor et al, 2003), and a model developed at the University of Glasgow, referred to as Gla-PSI (Jones et al, 2003). PEDRo is a proposal for a standard format for proteomics, covering 2-DE and MS, with limited support for describing the origin of a biological sample.…”