Although management of risk factors, including hyperglycemia, hyperlipidemia, and hypertension, have been shown to ameliorate diabetes-induced vision loss, effective noninvasive medical therapies for the prevention of PDR remain an unmet clinical need. We intended to find differentially expressed proteins that play crucial roles in proliferative diabetic retinopathy. We provide a novel strategy for biomarker screening, combining recent MS techniques with public database analysis, and identified plasma FCGR3A, DPEP2 and ADGRF5 as potential biomarkers for patients with PDR. Identifying the key molecules of the disease is essential for the development of new therapeutic molecules and new uses of existing drugs.