We have analysed the protein composition of wild-type, a T7Cas9 strain used generate CRISPR/Cas9 deletion of VPS23 gene in Trypanosoma cruzi. The main objective was to compare the quantitative changes observed in a clone that only one copy of the gene was replaced with the parental parasite line used to make the deletion. The obtained clone presented several phenotypes both related to cell infection in vitro and animal progression of the disease.