Sepsis is a frequent complication among newborns and accounts for >400,000 deaths globally. Infection-related inflammation contributes to long-term adverse neurodevelopmental outcomes in infants that survive sepsis. Preterm infants, particularly those born <28 weeks gestational age, are at the highest risk, affecting up to 50%, for developing late-onset sepsis (LOS; >72 hours of age). A rapid and accurate diagnosis of LOS is critical to minimise inflammation and antibiotic therapy, but early diagnosis is complicated by slow (up to 36 hours) and inaccurate diagnostic tests. Consequently, 2/3 of infants receive unnecessary antibiotic therapy, which is associated with adverse outcomes, including mortality, and contributes to antibiotic resistant organisms in the community. Innate immune development and response to infection are critical for fighting pathogens, yet are incompletely characterised in preterm infants. It is unclear if immune defence pathways differ between infants with and without sepsis and if differences are related to changes in the proteome. Proteome differences can be used to identify biomarkers that can improve the current diagnostic approach and potentially identify novel immune modulators for the prevention and treatment of LOS. We’re using targeted and untargeted approaches to explore and quantify the plasma proteome of preterm infants with and without LOS. To date, our targeted immunoassay approach has revealed a number of cytokines are elevated and favour a regulatory response in infants with LOS. We have begun our untargeted quantification of the proteome using label-free data-independent acquisition mass spectrometry-based proteomics, and data analysis is in progress.