https://doi.org/10.5061/dryad.3r2280gnx

Description

Summary

Trypanosoma cruzi is a protozoan parasite that causes Chagas disease. Globally 6 to 7 million people are infected by this parasite of which 20-30% will progress to develop Chronic Chagasic Cardiomyopathy (CCC). Despite its high disease burden, no clinically approved vaccine exists for the prevention or treatment of CCC. Developing vaccines that can stimulate T. cruzi–specific CD8+ cytotoxic T cells and eliminate infected cells requires targeting parasitic antigens presented on major histocompatibility complex class I (MHC-I) molecules. We utilized mass spectrometry-based immunopeptidomics to investigate which parasitic peptides are displayed on MHC-I of T. cruzi–infected cells. More than a dozen T. cruzi peptides were identified.

Experimental procedures

Murine MC57G fibroblasts were infected with T. cruzi trypomastigotes strain Tulahuen. After 48 hours, extracellular parasites were washed away and T. cruzi – infected fibroblasts were harvested. Peptides presented on Major Histocompatibility Complex I (MHC-I) were isolated and analyzed by mass spectrometry using an ThermoScientific Orbitrap Eclipse instrument. Proteomes databases *T. cruzi *strain CL Brener (https://www.uniprot.org/proteomes/UP000002296) and C57BL/6 mus musculus (https://www.uniprot.org/proteomes/UP000000589) were used for peptide identification.

Data files

In this dataset, we submitted the raw data files obtained from sample analysis using a ThermoScientific Orbitrap Eclipse mass spectrometer instrument. Experiment #1 (file Mass_spec_run_experiment__1.raw), #2a (file Mass_spec_run_experiment__2a.raw) and #2b (file Mass_spec_run_experiment__2b.raw) represents raw data files from mass spec runs on peptides from T. cruzi – infected MC57G fibroblasts. The file called “Run control experiment” (file Mass_spec_run_control_experiment.raw) contains raw data from uninfected MC57G cells.

Sharing/Access information

Data can be downloaded here https://doi.org/10.5061/dryad.3r2280gnx

Publication can be found here: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012764 

Code/software:

Raw data files can be imported to PRISM X software or similar mass spectrometry data analysis software. We used the proteomes databases T. cruzi strain CL Brener (https://www.uniprot.org/proteomes/UP000002296) and C57BL/6 mus musculus (https://www.uniprot.org/proteomes/UP000000589) for peptide identification. Additionally, the following data analysis parameters were used to obtain our results: enzyme set to none, digest mode set to unspecific, up to three variable modifications including oxidation of methionine as well as deamidation of asparagine and glutamine, parent mass error tolerance of 15 ppm, fragment mass error tolerance of 0.02 Da, charge states between 1 and 7 were accepted, the peptide -10LgP score was left at the default 15 and the protein -10LgP score was left at the default 20 corresponding to protein false discovery rates of 1.6% and 2.5%. Peptide sequence lengths between 8 and 15 amino acids were selected for further analysis.