Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification

J Proteome Res. 2018 Dec 7;17(12):4113-4126. doi: 10.1021/acs.jproteome.8b00300. Epub 2018 Aug 31.


Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared with other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of donors. After immunoaffinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20 689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained data set constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes whose transcripts are highly expressed in brain according to the Human Protein Atlas. The principal Alzheimer's disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E, and neurogranin) were detected. Importantly, our data set significantly contributes to the Chromosome-centric Human Proteome Project (C-HPP), and 12 proteins considered as missing are proposed for validation in accordance with the HPP guidelines. Of these 12 proteins, 8 proteins are based on 2 to 6 uniquely mapping peptides from this CSF analysis, and 4 match a new peptide with a "stranded" single peptide in PeptideAtlas from previous CSF studies. The MS proteomic data are available to the ProteomeXchange Consortium ( ) with the data set identifier PXD009646.

Keywords: Human Proteome Project; augurin; brain; cerebrospinal fluid; mass spectrometry; missing proteins; proteomics; tandem mass tag.

MeSH terms

  • Biomarkers / cerebrospinal fluid
  • Brain Chemistry / genetics
  • Cerebrospinal Fluid / chemistry*
  • Cerebrospinal Fluid Proteins / analysis*
  • Humans
  • Proteome / analysis*
  • Proteomics / methods
  • Tandem Mass Spectrometry


  • Biomarkers
  • Cerebrospinal Fluid Proteins
  • Proteome