Proteomics analysis of Echinococcus granulosus protoscolex stage

•We standardized the two-dimensional electrophoresis technique, achieving reproducibility of our results.•Peptide Mass Fingerprint of the data acquired using MASCOT software allowed us to identify 61 unique proteins, 28 of which are described in the protoscolex stage for the first time.•Of these 28 new proteins, eleven are not described in parasites of any kind. We propose Prostaglandin-H2 D-isomerase, Endophillin B1, Protein DJ 1 and Nuclear DBF2-related kinase as novel protein candidates involved in cyst fertility molecular mechanisms.