Quantitative Proteomic Analysis of Paracoccidioides brasiliensis

Data processing were performed as previously described (Lima Pde et al. 2015 (link)). In brief, for proteomic analyzes of the data obtained from the LC-MS^E, the ProteinLynx Global Server version 3.0.2 (Waters, Manchester, UK) was employed. The processed spectra were searched against P. brasiliensis (Pb18) protein sequences (https://www.uniprot.org/proteomes/). The protein identification criteria also included the detection of at least 2 fragment ions per peptide, 5 fragments per protein and the determination of at least 1 peptide per protein. A protein that showed a variance coefficient of 0.057 and that was detected in all replicates was used to normalize the protein expression levels in the samples (PADG_04570). Expression^E informatics v.3.0.2 was used for quantitative comparisons. The mathematical model used to calculate the ratios was part of the Expression^E algorithm inside the PLGS software from the Waters Corporation (Geromanos et al. 2009 (link)). The minimum repeat rate for each protein in all replicates was 2. Protein tables generated by ProteinLynx Global Server were merged, and the dynamic range of the experiment was calculated using the software program MassPivot v1.0.1. The data obtained by NanoUPLC-MS^E were subjected to in silico analysis to identify functional classification. For this analysis, it was used FungiDBdatabase (https://fungidb.org/fungidb/).