In-depth Exploration of Cerebrospinal Fluid by Combining Peptide Ligand Library Treatment and Label-free Protein Quantification

Abstract

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 of method thus to with low volume We the is with this and the dynamic range of protein concentration is with of to an of of the of proteins in one a analytical we the method is and for of of in 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 of method thus to with low volume We the is with this and the dynamic range of protein concentration is with of to an of of the of proteins in one a analytical we the method is and for of of in of biological a a in clinical this are a particularly is with in the the of a fluid in to a the of a from a fluid used abundance and and used abundance and and is in closest contact with the a of biomarkers for neurological diseases. of CSF lumbar is an is and a brain fluid fluid protein abundance and and proteins fluid fluid protein abundance and and proteins CSF of the brain of biological for of the and of and analysis in current and of fluid challenges in and the of the the large the the and CSF is in the a in the of a of a of and on the the the of from the cell into the CSF and is as the CSF a on of a in the CSF and thus a for the brain of concentration of CSF by the protein content of the CSF in the from proteins, the by a on analysis in current and of fluid to and to in neurological of the of this the protein concentration in CSF is in CSF proteins, on the other are to and by the of the as of the for and protein in a of the CSF is by the from the fluid the of the This is with the the as CSF into the and the of the the in in into the by the cell brain and proteins from the brain to of the CSF protein content of proteins in is a of from to and CSF is a biochemical window into the brain and an of neurological analysis in CSF the to to a clinical a protein and on to protein as of a analysis in current and a of the proteins in CSF and the dynamic range of protein of the protein of CSF protein and the detected proteins in in the This very large dynamic range as for other fluids, a analytical and largely studies CSF proteomic first 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