The operation of waste water treatment plants (WWTP) was discovered decades ago by Srinath et al. (1959), and is now a well characterized, and established method in civil engineering. However, the biological processes in wastewater treatment is not fully understood, and increased knowledge is required to further develop new, and existing WWTP’s. Improved control of the WWTP’s can be established by learning more about the community ecology of the different WWTP’s, which is the main goal for the EcoDesign project. In recent years, the application of genomics, transcriptomics, and proteomics have undergone continuing development, and the fields are maturing to encompass more complex systems, among others WWTP’s. Since proteins expression is a direct reflection of microbial activity, they have a major importance in the function and stability of WWTP’s. In this research, the application of protein extraction is investigated, and proteins associated with the biofilm formation is sought to be identified. These protein exists in the biofilm matrix, which consists of extracellular polymeric substances (EPS), in which proteins are included. Crude extracts were run on sodium dodecyl sulfate polyacrylamide (SDS-PAGE) gels, and analyzed by tandem mass spectrometry (LC-MS/MS). It was found that the extraction methods did not seem to be sufficient, which resulted in only few identified proteins. However, human Elastase-3A where identified in all applied extraction methods providing more evidence of the existence of this resistant protein inWWTP’s. This report provides the current knowledge, and results obtained in this exciting field of study, and has already motivated further investigations.