Fig. 8

Generating the fragmentation graph. a DEREPLICATOR[32] generates the theoretical spectrum of a PNP by first constructing a peptide graph, where each node is an amino acid and each edge is a peptide bond. Afterwards, it considers various fragmentations of the peptide graph by removing each possible bridge and 2-cut (each such removal breaks the peptide graph into two connected components). DEREPLICATOR generates the theoretical spectrum of a peptide as the set of masses of all resulting connected components, where the mass of a component is defined as the total mass of its constituent amino acids. b DEREPLICATOR+ sequentially breaks the metabolite graph at multiple bridges and 2-cuts, and models a theoretical spectrum of a metabolite as a fragmentation graph. Only a small subgraph of the fragmentation graph is shown