Pathways enriched in PD-specific proteins were predominantly linked to the ‘ER-Phagosome pathway’ (endoplasmic reticulum–phagosome; P = 2.9 × 10−3) and ‘ECM proteoglycans’ (P = 0.04), involving HLA proteins (HLA-C and HLA-E) and proteasomes (PSME1, PSMD5, PSMB10 and PSMD11). Here, HLA-E is linked to Parkinson disease.