Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs

Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite.  In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30% more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3) The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids.