Molecular phenotype in primary angiitis of the CNS (PACNS) CSF is informed by proteomic comparison of CSF between PACNS and noninflammatory control (NIC) cohorts. Molecular data are overlaid onto the complement cascade pathway (adapted from KEGG, hsa04610). Fold change in protein abundance between PACNS and NIC was evaluated for all proteins annotated in the pathway. Proteins are reported as elevated (red, >1.5 fold significant increase in PACNS), unchanged (pink, not significantly changed in PACNS), decreased (blue, >1.5 fold significant reduction in PACNS), or not observed (white, no abundance in NIC or PACNS). The prediction for C3 and C5 convertase activity (activated, yellow; inhibited, gray) is informed specifically by molecular changes observed in the complement regulatory proteins CFP, complement C4 binding protein (C4BP), CD59, and CD55. The proposed model predicts a shift toward activation of the alternative pathway (CFP, CD55), active inhibition of classical pathway (C4BPA and C4BPB), and elevated signaling from the terminal cascade (CD59).