Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research

PLoS One. 2018 Nov 29;13(11):e0206478. doi: 10.1371/journal.pone.0206478. eCollection 2018.


Cerebrospinal fluid is investigated in biomarker studies for various neurological disorders of the central nervous system due to its proximity to the brain. Currently, only a limited number of biomarkers have been validated in independent studies. The high variability in the protein composition and protein abundance of cerebrospinal fluid between as well as within individuals might be an important reason for this phenomenon. To evaluate this possibility, we investigated the inter- and intraindividual variability in the cerebrospinal fluid proteome globally, with a specific focus on disease biomarkers described in the literature. Cerebrospinal fluid from a longitudinal study group including 12 healthy control subjects was analyzed by label-free quantification (LFQ) via LC-MS/MS. Data were quantified via MaxQuant. Then, the intra- and interindividual variability and the reference change value were calculated for every protein. We identified and quantified 791 proteins, and 216 of these proteins were abundant in all samples and were selected for further analysis. For these proteins, we found an interindividual coefficient of variation of up to 101.5% and an intraindividual coefficient of variation of up to 29.3%. Remarkably, these values were comparably high for both proteins that were published as disease biomarkers and other proteins. Our results support the hypothesis that natural variability greatly impacts cerebrospinal fluid protein biomarkers because high variability can lead to unreliable results. Thus, we suggest controlling the variability of each protein to distinguish between good and bad biomarker candidates, e.g., by utilizing reference change values to improve the process of evaluating potential biomarkers in future studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers / cerebrospinal fluid
  • Cerebrospinal Fluid Proteins / metabolism*
  • Female
  • Healthy Volunteers
  • Humans
  • Longitudinal Studies
  • Male
  • Middle Aged
  • Nervous System Diseases / cerebrospinal fluid*
  • Proteomics


  • Biomarkers
  • Cerebrospinal Fluid Proteins

Grant support

This work was supported by the Deutsche Parkinson Gesellschaft, Medical Faculty at RUB (FoRUM), the European Union (NISCI, GA no. 681094), the German Federal Ministry of Ecucation and Research (WTZ with Brasil, FKZ 01DN14023), the HUPO Brain Proteome Project (HBPP), PURE, a project of Northrhine Westfalia, a federal German state and by de.NBI, a project of the German Federal Ministry of Ecucation and Research [FKZ 031 A 534A]. No funding bodies had any role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.