1. A computer controlled method comprising: accessing dissociation spectrum data comprising a plurality of spectral peaks representing a plurality of fragments of a parent ion, said parent ion comprising a plurality of molecular subunits and a plurality of cleavage sites, each of said plurality of cleavage sites connecting a first one of said plurality of molecular subunits and a second one of said plurality of molecular subunits; determining a reference mass of one of said plurality of fragments from said dissociation spectrum data, wherein at least one of said plurality of molecular subunits in said one of said plurality of fragments is unknown; selecting a candidate parent ion description from a database of molecule descriptions where a computed ion mass of said candidate parent ion description matches said reference mass; and scoring said candidate parent ion description.