In line with the results of the combined MRM cohort, the independent analysis of these two cohorts revealed four proteins (CNTNAP4, SERPINI1, NRXN3, and GRIA4) that were significantly downregulated in the CSF of MDD patients in both cohorts (iTRAQ-MDD vs iTRAQ-Con, p < 0.05 and new-MDD vs new-Con, p < 0.05). The gene discussed is CNTNAP4; the disease is major depressive disorder.