Mass spectrometry based proteomics is widely used to study cellular processes in model organisms. However, it has not much been applied in environmental research because it was thought that free proteins would not be sufficiently stable in the environments. Based on recent observations that protein can readily be detected as a component of dissolve organic carbon, this article gives an overview about the possible use of proteomic methods in ecology and environmental sciences. At this stage, there are two areas of interest: (1) the identification of phylogenetic groups contributing to the DOC pool, and (2) identification of the origin of specific enzymes that are important for ecosystem processes. In this paper methods of mass spectrometry based proteomics were applied to identify proteins from DOC and water samples from different environments. It is demonstrated, that environmental proteomics is capable to distinguish the active set of organisms of different horizons of soils, and from various sources of surface water. Currently the limitation is given by the present knowledge of the genome of soil organisms. In addition, environmental proteomics allows to relate protein presence to biogeochemical processes, and to identify the source organisms for specific enzymes. Taking laccases as an example, it is shown that this enzyme is excreted into soils by a whole range of organisms from different phylogenetic groups. Further applications, such as in pollution reseach are conceivable. In summary, environmental proteomcis opens a new area of research between the fields of microbiology and biogeochemistry.