The knowledge of three dimensional structures of molecules helps to better understand their biological functionality. Conventional methods for determination of proteins structure based on crystallization suffer by many limitations. The drawback of these methods is mainly in non-reflectiveness of physiological conditions. So called MS3D approach, which includes hydrogen-deuterium exchange (H/D exchange), chemical cross-linking, limited proteolysis and ion mobility, enables to fulfill the task of monitoring the proteins three dimensional structures under different native conditions.
We have developed an easy and straight forward workflow for elucidation of changes in proteins structure under different conditions by using functionalized MALDI targets. The presented technology enables to modify the MALDI targets with different proteases such as pepsin, nepenthesin or others to optimally digest the protein for H/D exchange experiment and limited proteolysis.