Identification of the peptides was performed in the nanoAcquity UPLCXevo QTof MS system (Waters, Manchester, UK), as previously described [18 (link)]. Differences in protein expression between the groups were obtained by the t test, embedded in the Protein Lynx Global Service (PLGS) software version 3.03, (Monte Carlo algorithm) and expressed as p < 0.05 for down-regulated proteins and 1 − p > 0.95 for upregulated proteins. Comparisons were made between the strains, for each treatment (SI vs. RI, SII vs. RII and SIII vs. RIII).
To understand the biological significance of the quantitative results of the proteomic analysis, the differentially altered proteins in each comparison were analyzed using bioinformatics tools, as previously reported [18 (link),50 (link),51 (link),52 (link)]. The software CYTOSCAPE® 3.0.4 (Java®) was used to build networks of molecular interaction between the identified proteins, with the aid of ClueGo and ClusterMark applications [53 (link)].
To understand the biological significance of the quantitative results of the proteomic analysis, the differentially altered proteins in each comparison were analyzed using bioinformatics tools, as previously reported [18 (link),50 (link),51 (link),52 (link)]. The software CYTOSCAPE® 3.0.4 (Java®) was used to build networks of molecular interaction between the identified proteins, with the aid of ClueGo and ClusterMark applications [53 (link)].
Free full text: Click here
