Study of proteome maps using partial ordering

This paper describes numerical characterization of proteome maps based on partial ordering of protein spots with respect to the mass and the charge. The partial ordering diagram is embedded directly over the 2D map and the corresponding adjacency matrix is constructed. The adjacency matrix is augmented by including the information on the abundance of proteins in a gel as suitably scaled diagonal entries of the matrix. The approach is illustrated on proteome maps of Anderson et al. (1996) based on experimental results from liver cells of rats exposed to four peroxisome proliferators. We used the leading eigenvectors of the adjacency matrices as maps descriptors in order to determine the degree of similarity between proteome maps.