Fig. 1: Characteristics of the study participants.

The flowchart outlines the longitudinal sampling and proteomic workflow employed in the study. Fifty-four individuals from two distinct geographical regions provided three matched samples each. Plasma samples were prepared both with and without depletion of the top 14 most abundant proteins. These samples were then analyzed using Data-Independent Acquisition (DIA)/SWATH LC-MS/MS. Arrows indicate the flow of samples through each stage of processing, including plasma preparation, mass spectrometry analysis, and subsequent computational analyses, which were used to explore protein dynamics over time. Abbreviations: V0 visit 0 (collected before estimated date of infection), V1 visit 1 (collected 10–14 days post estimated date of infection), V2 visit 2 (collected 15–42 days before estimated date of infection), IAVI International AIDS Vaccine Initiative, SA South Africa, KE Kenya, DIA data-independent acquisition, SWATH sequential window acquisition of all theoretical mass spectra, MS mass spectrometry.