Global Protein Interaction Network for <i>Trypanosoma cruzi</i>

<i>Trypanosoma cruzi</i>, the causative agent of Chagas disease, poses a significant health challenge due to limited therapeutic options and an incomplete understanding of its biology. Approximately half of the genome encodes hypothetical proteins with unknown functions, underscoring the need for systematic functional annotation. Protein-protein interactions (PPIs) underpin essential cellular processes, yet no large-scale PPI map has been developed for <i>T. cruzi</i> ─a critical gap that impedes both functional annotation of its proteome and drug discovery. This study presents the first comprehensive PPI network for <i>T. cruzi</i>, constructed using quantitative mass spectrometry-based cofractionation data. The network includes 1319 proteins and more than 16,000 predicted interactions, with 47% of the proteins classified as hypothetical, consistent with the 49% hypothetical annotation rate in the proteome. Their placement within functionally enriched network modules provides unprecedented insights into their potential biological roles. Network analysis revealed densely interconnected cores enriched with essential cellular functions. This PPI network exhibits small-world properties, with conserved proteins showing higher connectivity, reinforcing their central roles in the parasite's biology. This resource, publicly available at https://2025.trypsnetdb.org/, offers a powerful platform for exploring <i>T. cruzi</i> biology and prioritizing novel therapeutic targets, revealing central hubs of protein organization, resolving ribosomal and proteasomal complexes, and enabling functional predictions for numerous hypothetical proteins through integrative structural modeling.