Fig. 1. Overview of proteomics approaches in Tritryps. The proteome of each life cycle stage of a protozoan parasite of interest (Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei) undergoes characteristic modulations as the parasite responds to a perturbation trigger. The perturbation trigger can either be a natural factor that regulates the development of the parasite (such as changes in pH or temperature, variations in availability of nutrients, and other environmental changes during its transition to a different host species) or a therapeutic intervention such as an inhibitor/growth modulator treatment or a chemical probe treatment. The proteins extracted from a specific life cycle stage of the protozoan parasite of interest following the perturbation window are typically digested to peptides using a protease such as trypsin. The proteomic samples often require additional treatments such as reduction of disulphide bonds, alkylation of free thiols and extensive clean-up or desalting procedures. The relative expression changes in several hundreds to thousands of proteins across different conditions are then measured with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique following a suitable quantitative proteomics approach such as label-free quantification or one of the different types of label-based quantification methods. Processing, analyses and visualisation of the large proteomics data sets are carried out using dedicated software programmes.