An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

Abstract

Background: Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data.

Results: In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here.

Conclusion: The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.

Figure 1

Unified Modeling Language (UML) representation of AGML data model. The dashed line separates the spot-specific from the gel-specific data described in the text as distinct AGML sections. The separation reflects an analytical distinction between the electrophoretic component from the image analysis and mass spectrometry. However, the integration in the common AGML document is seamless. It is represented here for explanatory purposes only. The UML diagram represented was generated using FUJABA .

Figure 2

A Sample screenshot of the AGML Visualizer in action. AGML Visualizer software is capable of reading AGML documents and display a visual representation of virtual and real gels described in the AGML document instance. In this representative figure, the real gel is shown as the small figure atop the virtual gel. Left side of the gel depicts all the pertinent information regarding the gel (gel information as described in methods). The right side of the gel displays the information on a particular spot (spot information as described in methods). The AGML Visualizer is based on the AGML schema proposed in this paper.