A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome

Ghizal Siddiqui; Amanda De Paoli; Christopher A MacRaild; Anna E Sexton; Coralie Boulet; Anup D Shah; Mitchell B Batty; Ralf B Schittenhelm; Teresa G Carvalho; Darren J Creek

doi:10.1093/gigascience/giac008

A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome

Gigascience. 2022 Mar 7:11:giac008. doi: 10.1093/gigascience/giac008.

Affiliations

¹ Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
² Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.
³ Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
⁴ Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.

Abstract

Background: Plasmodium falciparum 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 has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility.

Results: Here, we present a comprehensive P. falciparum-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites.

Conclusion: A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria.

Keywords: LC-MS/MS; Plasmodium falciparum; data-dependent acquisition; data-independent acquisition; malaria; proteomics; red blood cells.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Erythrocytes / metabolism
Erythrocytes / parasitology
Humans
Malaria, Falciparum* / metabolism
Malaria, Falciparum* / parasitology
Plasmodium falciparum* / metabolism
Proteome / metabolism
Reproducibility of Results

Substances

Proteome