The research area Proteomics focuses on the analysis of proteins and peptides in biological data sets. Proteins are essential building blocks for every living organism and over the last years, mass spectrometry has become the method of choice for the analysis of those. To understand and investigate cell processes or gain new insights in illnesses triggered by certain proteins or the absence or oversupply of those, the identification and quantification of proteins in the tissue is of primary importance. Since 2011 and in close collaboration with the Mechtler group at the IMP, Vienna, our research group has focused on the area of computational proteomics and therein on the development of algorithms to identify proteins and peptides in biological samples. This has led to the emergence of the MS Amanda algorithm, a database search engine especially designed for high resolution data sets and perfectly capable of identifying chimeric spectra. In addition, we are currently working on a library search engine, MS Ana, that is able to identify peptides based on a previously created library of mass spectra with known peptide identifications. To complement that, also a search engine for the identification of peptides connected with a cleavable cross-linker, called MS Annika, is in progress.