Large-scale proteomic tree. This is a simplified version of Additional file 1, a large-scale proteomic tree of 843 microbes. Only major phyla and classes are shown here. Most species are clustered in accordance with their taxonomic classifications. The red sectors highlighted the species situated differently from their taxonomic positions. Epsilon proteobacteria and Delta proteobacteria are mainly chemosynthesis organisms. Although they belong to the Proteobacteria phylum, they are clustered with Cyabobacteria, Aquificae and Chlorobi, which are species with unique ways of energy production. The other Proteobacteria species are mainly parasitic organisms; they are clustered with Chlamydiae and Spirochaete, which are parasitic species as well. The clustering results of these species demonstrate that the probe-set method tends to cluster organisms according to their metabolic or phenotypic similarities, especially at lower taxonomic levels.