In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification.
Cerebrospinal fluid (CSF) is the biological fluid in closest contact with the brain and thus contains proteins of neural cell origin. Hence, CSF is a biochemical window into the brain and is particularly attractive for the search for biomarkers of neurological diseases. However, as in the case of other biological fluids, one of the main analytical challenges in proteomic characterization of the CSF is the very wide concentration range of proteins, largely exceeding the dynamic range of current analytical approaches. Here, we used the combinatorial peptide ligand library technology (ProteoMiner) to reduce the dynamic range of protein concentration in CSF and unmask previously undetected proteins by nano-LC-MS/MS analysis on an LTQ-Orbitrap mass spectrometer. This method was first applied on a large pool of CSF from different sources with the aim to better characterize the protein content of this fluid, especially for the low abundance components. We were able to identify 1212 proteins in CSF, and among these, 745 were only detected after peptide library treatment. However, additional difficulties for clinical studies of CSF are the low protein concentration of this fluid and the low volumes typically obtained after lumbar puncture, precluding the conventional use of ProteoMiner with large volume columns for treatment of patient samples. The method has thus been optimized to be compatible with low volume samples. We could show that the treatment is still efficient with this miniaturized protocol and that the dynamic range of protein concentration is actually reduced even with small amounts of beads, leading to an increase of more than 100% of the number of identified proteins in one LC-MS/MS run. Moreover, using a dedicated bioinformatics analytical work flow, we found that the method is reproducible and applicable for label-free quantification of series of samples processed in parallel.
Mouton-Barbosa
Emmanuelle
E
Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, 31077 Toulouse, France.
Roux-Dalvai
Florence
F
Bouyssié
David
D
Berger
François
F
Schmidt
Eric
E
Righetti
Pier Giorgio
PG
Guerrier
Luc
L
Boschetti
Egisto
E
Burlet-Schiltz
Odile
O
Monsarrat
Bernard
B
Gonzalez de Peredo
Anne
A
D002556:Cerebrospinal Fluid Proteins / Q000032:analysis*; D002853:Chromatography, Liquid; D006801:Humans; D008024:Ligands; D013058:Mass Spectrometry; D008863:Microspheres; D055495:Neurogenesis; D019151:Peptide Library; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D013194:Staining and Labeling
D002556:Cerebrospinal Fluid Proteins; D008024:Ligands; D019151:Peptide Library