Functional Annotation of 2D Protein Maps: The GelMap Portal

Abstract

In classical proteome analyses, final experimental data are (a) images of 2D protein separations obtained by gel electrophoresis and (b) corresponding lists of proteins which were identified by mass spectrometry (MS). For data annotation, software tools were developed which allow the linking of protein identity data directly to 2D gels ("clickable gels"). GelMap is a new online software tool to annotate 2D protein maps. It allows (i) functional annotation of all identified proteins according to biological categories defined by the user, e.g., subcellular localization, metabolic pathway, or assignment to a protein complex and (ii) annotation of several proteins per analyzed protein "spot" according to MS primary data. Options to differentially display proteins of functional categories offer new opportunities for data evaluation. For instance, if used for the annotation of 2D Blue native/SDS gels, GelMap allows the identification of protein complexes of low abundance. A web portal has been established for presentation and evaluation of protein identity data related to 2D gels and is freely accessible at http://www.gelmap.de/.

Keywords: data annotation; data visualization; mass spectrometry; proteomics; software; two-dimensional gel electrophoresis; web portal.

Figure 1

Reference map of the mitochondrial proteome of Arabidopsis thaliana (Klodmann et al., ; http://www.gelmap.de/47). Proteins were separated by 2D Blue native/SDS PAGE. The two icons given in the header allow access to the “protein spreadsheet” and the “peptide spreadsheet.”

Figure 2

Integration of the mitochondrial reference maps at GelMap into MASCP Gator (http://gator.masc-proteomics.org/). Upon submission of a protein accession (here: At2g47260), matching peptides from GelMap are graphically displayed at the Gator site. Direct access to GelMap is provided by links in the left side menu of the Gator.