%0 Journal Article %T In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. %+ Institut de pharmacologie et de biologie structurale (IPBS) %+ Grenoble Institut des Neurosciences (GIN) %+ Service Neurochirurgie [CHU Toulouse] %+ Politecnico di Milano [Milan] (POLIMI) %+ Bio-Rad %A Mouton-Barbosa, Emmanuelle %A Roux-Dalvai, Florence %A Bouyssié, David %A Berger, François, R. %A Schmidt, Eric %A Righetti, Pier Giorgio %A Guerrier, Luc %A Boschetti, Egisto %A Burlet-Schiltz, Odile %A Monsarrat, Bernard %A de Peredo, Anne Gonzalez %Z This work was supported by grants from the Institut National du Cancer (INCa), Agence Nationale de la Recherche (ANR/INCa Programme Plates-formes technologiques du vivant), Fondation pour la Recherche Médicale (Programme Grands Equipements), Cancéropole Grand Sud-Ouest, Génopole, and Région Midi-Pyrénées. %< avec comité de lecture %@ 1535-9476 %J Molecular and Cellular Proteomics %I American Society for Biochemistry and Molecular Biology %V 9 %N 5 %P 1006-21 %8 2010-05 %D 2010 %R 10.1074/mcp.M900513-MCP200 %M 20093276 %Z Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]Journal articles %X 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. %G English %2 https://inserm.hal.science/inserm-00498129/document %2 https://inserm.hal.science/inserm-00498129/file/Mouton-Barbosa-2010-In_depth_exploration.pdf %L inserm-00498129 %U https://inserm.hal.science/inserm-00498129 %~ INSERM %~ UNIV-TLSE3 %~ UGA %~ CNRS %~ UNIV-GRENOBLE1 %~ U836 %~ IPBS %~ UNIV-UT3 %~ UT3-INP %~ UT3-TOULOUSEINP %~ FRM