Proteome of peripheral mononuclear cells (PBMCs) from asymptomatic malaria and uninfected individuals and the ensuing malaria episodes

Cumulative malaria parasite exposure in endemic regions often results in the acquisition of partial immunity and asymptomatic infections. There is limited information on how host-parasite interactions mediate maintenance of chronic symptomless infections that sustain malaria transmission. Here, we have determined the gene expression profiles of the parasite population and the corresponding host peripheral blood mononuclear cells (PBMCs) from 21 children (<15 years). We compared children who were defined as uninfected, asymptomatic and those with febrile malaria. Children with asymptomatic infections had a parasite transcriptional profile characterized by a bias toward trophozoite stage (~12 hours-post invasion) parasites and low parasite levels, while earlier ring stage parasites were characteristic of febrile malaria. The host response of asymptomatic children was characterized by downregulated transcription of genes associated with inflammatory responses, compared to children with ..., Proteins were extracted from PBMCs by resuspending the pellet with 5µl of 6M UREA (Thermo scientific). The protein samples were then adjusted with 50mM Triethylamonium bicarbonate (TEAB, Sigma-Aldrich) to 100µl and the protein concentration determined using the Bicinchoninic acid (BCA) protein assay (Thermo scientific). The protein samples were then reduced with 40mM dithiothretol, alkylated with 80mM iodoacetamide in the dark, and quenched with 80mM iodoacetamide at room temperature, followed by digestion with1µg/µl of trypsin (57). Nine pools, each containing 9 samples and 1 control for batch correction, were prepared by combining 1µl aliquots from each sample. The samples were pooled using a custom randomization R script. The pooled samples were then individually labelled using the Tandem Mass Tag (TMT) 10-plex kit (Thermo Scientific) according to the manufacturer’s instructions. One isobaric tag was used solely for the pooled samples and combined with peptides samples labelled with ..., The files can be opened using MaxQuant software, specifically version 2.0.3.0 was used for analysis.
Differential protein abundance analysis of MaxQuant output was done using PERSEUS version 2.05.0 software.
Protein-protein interaction and Gene ontology analyses was perforened using STRING database version 11.5 (https://string-db.org/)., # Proteome of peripheral mononuclear cells (PBMCs) from asymptomatic malaria and uninfected individuals and the ensuing febrile malaria episodes

Proteins were extracted from peripheral mononuclear cells (PBMCs), pooled using Tandem Mass Tags (TMT) (10-plex) and injected into the LC-MS/MS for proteomics analysis. The output raw files were loaded into MaxQuant software v2.0.3.0 for protein quantification. The output from MaxQuant was then read using PERSEUS software v2.05.0 and differential protein abundance analysis performed.
The Proteomics_metadata file contains the metadata that links each sample to the raw data files and the treatment group (condition).

## Description of the data and file structure

The RAW data files provided contains the output data from the LC-MS/MS per each pool. The pools serve as the input data for MaxQuant software.

The Proteomics_metadata contains the metadata information that links each sample to the condition/treatment group (i.e. asymptomatic, uninfecte...