Comparing fragmentation spectra from two parasitic worm species to discover unique peptides

Mass spectrometry (MS) is a technique used in proteomics to identify proteins. Fragmentation spectra (MS2) are commonly assigned to peptides by database searches to identify proteins. Assignment of identified peptides to a genome can be achieved by the field of proteogenomics. Complete genomes, and therefore derived proteome databases, are available for some well-studied species but not for all other species. Taenia solium and Taenia hydatigena are two closely related tapeworm species with limited and almost complete lack of sequenced genome. The larval stages of both these parasites can infect pigs, while humans can only be infected by T. solium. When investigating the prevalence of T. solium in pigs, one needs a diagnostic test that is able to distinguish between the two Taenia species. Current tests, however, cannot make any distinctions. A possible solution would be identifying species-specific proteins for a possible diagnostic test despite limitations at genome-level. To achieve this, we compare spectra between datasets from each species to determine unique spectra. Full proteogenomics searches are then used as a follow-up for interesting leads.