We then investigated how IsoDec performs in the context of a proteomics database search. We found that each tool produced a similar number of proteoform-spectrum matches (PrSMs; Figure ). A PrSM refers to a match of the combination of an experimental precursor mass and fragmentation spectrum to their synthetic or catalogued counterparts from a database or spectral library. The number of unambiguous PrSMs was statistically similar between tools, but FLD and TopFD produced higher numbers of ambiguous PrSMs.