We have developed a software to investigate the fragmentation dynamics of a protein exposed to an ionizing laser pulse. Proteins are ionized(charged) and what follows is a coloumbic explosion. By studying the dynamics of the fragmentation we can learn more about the fundamental interaction between photons and matter. The obtained data also can be used to classify and separate protein from each other. Long term we want to build a database containing data from many proteins which we can use to draw more general conclusion and hopefully can aid in protein structure determination.