The project for which I wrote my dissertation in the fourth year of my degree in Computer Science at the University of Glasgow. This project 'Pep2Path v2' was an implementation of several algorithms bundled together, including some mass spectrometry dereplication, and the Pep2Path algorithm presented by Medema et al used to identify the chemical composition of RiPPs and NRPs, two classes of biological compound. This algorithm (and a couple of other simple scoring functions) matches gene data from an organism's genome to chemical data from mass spectrometry and scores this match. Details can be found in the dissertation, where the algorithms and various properties of scoring functions are explored. The version which was submitted for assessment can be found frozen in the Submission branch. Otherwise, this is a work in progress.