Modified Enrichment Method for Identification of Human Cerebrospinal Fluid Proteins by Mass Spectrometry

Current methods used for the proteomic analysis of human cerebrospinal fluid (CSF) focus on depleting highly abundant proteins, to facilitate the detection of less abundant proteins. However most such methods are time-consuming and not highly effective. In the present study, we tested a newly developed hollow-fiber-membrane-based (HFM) protein separation device as a tool in preparing CSF samples for 2-D-LC-MS/MS proteomic analysis. Within 1 h, the HFM pretreatment device efficiently depleted a CSF sample for highly abundant high molecular weight proteins, thus enriching the sample for less abundant, low molecular weight proteins and peptides. Six CSF samples of three different volumes (1 mL, 2 mL and 10 mL) from three healthy subjects were pretreated with this device, and subsequent 2-D-LC-MS/MS analysis yielded 82,731 MS/MS spectra with statistically positive hits for 160 proteins. Thirty-four of these proteins, including 4 brain-specific proteins, were found in CSF for the first time. This pretreatment method may assist with the identification of new biomarkers for the diagnosis and treatment of CNS diseases.