Established procedures allow the exploratory analysis of the protein content of cells and organisms and their temporal qualitative and quantitative changes that accompany development, reaction to environmental impacts and pathophysiological processes. Targeted proteomics strategies of high accuracy and sensitivity, such as multiple reaction monitoring (MRM), have been set up for quantitative analysis of known protein networks. Furthermore, the conformation of proteins can be analyzed using amide hydrogen exchange (HDX) mass spectrometry, which allows the analysis of protein mechanics, protein-protein interaction interfaces and ligand-induced allosteric conformational changes.