Intact Protein Analysis by LC-MS for Characterizing Biomarkers in Cerebrospinal Fluid

Methods Mol Biol. 2019:1959:163-172. doi: 10.1007/978-1-4939-9164-8_11.


In the field of proteomics, the emerging "top-down" MS-based proteomics approach can be used to obtain a bird's eye view of all intact proteoforms present in a sample. This alternative to the "bottom-up" approach based on tryptic protein digestion processes has some unique advantages for assessing PTMs and sequence variations. However, it requires some dedicated tools for sample preparation and LC-MS analysis, which makes it more complex to handle than the bottom-up approach. In this study, a simple methodology is presented for characterizing intact proteins in biological fluid. This method yields quantitative information using an MS1 profiling approach and makes it possible to identify the proteins regulated under various clinical conditions.

Keywords: Biomarker; Cerebrospinal fluid; LC-MS; Protein precipitation; SPE; Top-down.

MeSH terms

  • Biomarkers*
  • Cerebrospinal Fluid Proteins* / isolation & purification
  • Cerebrospinal Fluid Proteins* / metabolism
  • Chromatography, Liquid*
  • Data Interpretation, Statistical
  • Humans
  • Mass Spectrometry*
  • Proteome*
  • Proteomics* / methods
  • Solid Phase Extraction


  • Biomarkers
  • Cerebrospinal Fluid Proteins
  • Proteome