CSF proteome is the real time protein content that may reveal useful biomarkers for diagnosis and therapeutic decision-making. But the low protein concentration in CSF and the low volumes typically obtained after lumbar puncture precludes the conventional use of proteomic analysis. We miniaturized the method to be compatible with low-volume samples by combination of nanoLC-MS/MS analysis and combinatorial peptide ligand library technology to reduce the dynamic range of protein concentration in CSF and unmask previously undetected proteins. We demonstrated that this deep proteomic analysis allows profiling the CSF proteome with a reasonable depth, in short analytical times and good accuracy. We settled a clinically-compatible proteomics strategy targeting the deep CSF proteome discovery.