Mass spectrometry based proteomics is a critical technology in life science research. The tremendous increase in instrument capacity resulting in large data file production and the development of several new data acquisition workflows puts increasing demands on the bioinformatics solutions to perform data analysis and data integration. In this proposal we aim at establishing high-end bioinformatics solutions for rapid and accurate data analysis in Sweden. These bioinformatics solutions referred to as openBIS, iportal and the trans-proteomics pipeline were developed by scientists in Switzerland and in the USA, are fully operational outside Sweden and can facilitate the analysis of several types of mass spectrometry proteomics based experiments. A successful project will have far reaching consequences for performing data analysis within proteomics for researchers at the medical faculty at Lund University and can potentially also impact proteomics researchers at a national level.