Supporting data for "A new mass spectral library for high-coverage and reproducible analysis of the <i>Plasmodium falciparum</i>-infected red blood cell proteome."

<i>Plasmodium falciparum</i> causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry-based proteomics using Data Dependent Acquisition (DDA) has been extensively used to understand the biochemical processes within the parasite. However, DDA is problematic for the detection of low abundance proteins, proteome coverage, and has poor run-to-run reproducibility. <br>Here, we present a comprehensive <i>P. falciparum</i>-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 <i>P. falciparum</i> and 1,617 RBC proteins using a Data Independent Acquisition (DIA) mass spectrometric approach. The spectral library includes proteins expressed in the three morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs (uRBC). This spectral library contains 87% of all <i>P. falciparum</i> proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The <i>P. falciparum</i> spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterise the three distinct asexual parasite stages in RBCs, and compared artemisinin resistant (Cam3.IIR539T) and sensitive (Cam3.IIrev) parasites. <br>A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of <i>P. falciparum</i> malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms and vaccine candidate discovery for malaria. Data are available via ProteomeXchange with identifier PXD027241 and PXD027301