This project identifies and quantitates Hydroxyapatite binding proteins (HAP) in plasma genotyped for complement factor H (CFH) polymorphism in late stage age-related macular degeneration (AMD) patients by sequential window acquisition of all theoretical mass spectra (SWATH). This study provides insights into factors contributing to the formation of sub-retinal pigment epithelial (RPE) deposits and explores the effect of AMD-associated CFH polymorphism on deposit composition.