Mass spectrometry has evolved into a powerful tool to study thousands of proteins in an unbiased and systematic manner in a single experiment. The current improvements in identification accuracy, sample throughput and data analysis allows us to answer biological questions at unprecedented speeds and with increased comprehensiveness. We apply these techniques in a variety of biological research areas and several model organisms to answer questions of fundamental importance in transcriptional and translational gene regulation, epigenomics, genome stability and evolution. We recently developed phylointeractomics as a new experimental approach for evolutionary research and apply it to study changes in telomere binding protein across the vertebrate lineage. Additionally, we generated a large scale developmental proteome of Drosophila melanogaster to complement previous transcriptomics studies. During the talk, a selection of application of quantitative proteomics and interactomics will be presented.