*2.8. Data Analysis*

The mass spectra were searched against a database containing *L. braziliensis* sequences available at UniProtKB/Swiss-Prot, using the Andromeda search engine included in the MaxQuant Software (Ver. 1.2.6.20). Reversed proteins were used as decoys. The option "matching between runs" was used for searching, and parameters such as fragment ion mass tolerance of 0.5 Da and parent ion tolerance of 20 ppm were included. Cysteine carbamidomethylation was set as fixed modification, methionine oxidation as variable modification, and up to two missed cleavages were allowed. The maximum false peptide and protein discovery rate was set as 1%. Protein absolute abundances were calculated based on the spectral protein intensity (raw intensities) using the 'Total Protein Approach' (TPA), and absolute protein copy numbers per cell were estimated using the 'Proteomic Ruler' approach [29]. Calculations of total protein, protein concentration, and copy number were performed in Microsoft Excel. Perseus software (Ver. 1.6.5.0) [30] was used for statistical analysis. Minimal number of valid values was set to 4 per protein in at least one group, and missing values were imputed from a normal distribution. Significances were calculated using the t test for pairwise comparisons, with a threshold of false discovery rate (FDR) of 3%. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE [31] partner repository with the dataset identifier PXD029462.
