RIME-MASCOT Based Proteomic Analysis

The MS/MS data obtained by RIME was processed using DataAnalysis version 5.2 (Bruker Daltoniks), and proteins were identified using MASCOT version 2.7.0 (Matrix Science, London, UK) against the Uniprot_Plasmodium_berghei_ANKA_strain database (4,948 sequences; 3,412,795 residues). Protease specificity was set for trypsin (C-term, KR; Restrict, P; Independent, no; Semispecific, no; two missed and/or nonspecific cleavages permitted). Variable modifications considered were N-terminal Gln to pyro-Glu, and oxidation of methionine. The mass tolerance for precursor ions was ±15 ppm. The mass tolerance for fragment ions was ±0.05 Da. The threshold score/expectation value for accepting individual spectra was p < 0.05. Quantitative value and fold enrichment were calculated by Scaffold5 version5.1.2 (Proteome Software, Portland, OR, USA) [70 (link)] and Microsoft Excel, respectively, for MS/MS-based proteomic studies. Proteins that were unique or more than fivefold enriched with p-value < 0.05 by two-tailed Student’s t-test in PbAP2-FG2 compared to WT were identified as a possible interaction partner of PbAP2-FG2.