Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry

Abstract

Cerebrospinal fluid (CSF) is a biofluid in direct contact with the brain and as such constitutes a sample of choice in neurological disorder research, including neurodegenerative diseases such as Alzheimer or Parkinson. Human CSF has still been less studied using proteomic technologies compared to other biological fluids such as blood plasma or serum. In this work, a pool of "normal" human CSF samples was analysed using a shotgun proteomic workflow that combined removal of highly abundant proteins by immunoaffinity depletion and isoelectric focussing fractionation of tryptic peptides to alleviate the complexity of the biofluid. The resulting 24 fractions were analysed using liquid chromatography coupled to a high-resolution and high-accuracy timsTOF Pro mass spectrometer. This state-of-the-art mass spectrometry-based proteomic workflow allowed the identification of 3'174 proteins in CSF. The dataset reported herein completes the pool of the most comprehensive human CSF proteomes obtained so far. An overview of the identified proteins is provided based on gene ontology annotation. Mass and tandem mass spectra are made available as a possible starting point for further studies exploring the human CSF proteome.

Keywords: Cerebrospinal fluid; LC-MS/MS; Large-scale proteome; Mass spectrometry; Proteomics.

Fig. 1

GO terms of the genes representative of the 3’174 proteins identified in the CSF dataset. The Panther software was used for the GO annotation on the three ontologies, (a) molecular function (b) biological process and (c) cellular component.

Fig. 2

Comparison of protein and peptide identifications in CSF between our previously published dataset obtained with an Orbitrap Fusion Lumos instrument , and the current dataset obtained with a timsTOF Pro mass spectrometer.