AbstractPurposeThis pilot study aimed to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus‐associated periprosthetic joint infection (PJI) and non‐infected arthroplasty failure (NIAF) and identify potential novel biomarkers differentiating the two.Experimental designIn this pilot study, eight sonicate fluid samples (four from NIAF and four from S. aureus PJI) were studied. Samples were reduced, alkylated, and trypsinized overnight, followed by analysis using liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) on a high‐resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label‐free quantitation.ResultsPrincipal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were identified based on their detection in at least three out of four samples from each group; 35 statistically significant differentially abundant proteins (DAPs) were found (two‐sample t‐test p‐values ≤0.05 and log₂fold‐change values ≥2 or ≤−2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, to be increased in S. aureus PJI compared to NIAF samples.Conclusion and clinical relevanceProteomic profiling of sonicate fluid using LC‐MS/MS differentiated S. aureus PJI and NIAF in this pilot study. Further work is needed using a larger sample size and including non‐S. aureus PJI and a diversty of NIAF‐types.