Abstract
The analysis of the cerebrospinal fluid (CSF) proteome in recent years has resulted in a valuable repository of data for targeting and diagnosing a variety of diseases, such as Parkinson’s disease, Alzheimer’s disease, traumatic brain injury, and amyotrophic lateral sclerosis. Human ventricular CSF contains numerous proteins that are unique to CSF due in part to the interaction of the biofluid with the brain. This allows researchers to obtain information from a region that would otherwise be inaccessible except through invasive surgery or during autopsy. Characterization of the CSF proteome requires that strict care be taken so that sample integrity and fidelity are maintained to ensure data reproducibility. Standardized methods in sample collection, storage, preparation, analysis, and data mining must be used for meaningful information to be obtained. The following method describes a simple and robust approach for preparing CSF samples for analysis via reversed-phase liquid chromatography (RPLC) and mass spectrometry (MS).
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References
Mischak H, Allmaier G, Apweiler R et al (2010) Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med 2:46ps42
Goonetilleke UR, Scarborough M, Ward SA et al (2010) Proteomic analysis of cerebrospinal fluid in pneumococcal meningitis reveals potential biomarkers associated with survival. J Infect Dis 202:542–550
Gini B, Lovato L, Cianti R et al (2008) Novel autoantigens recognized by CSF IgG from Hashimoto’s encephalitis revealed by a proteomic approach. J Neuroimmunol 196:153–158
Tian XJ, Li JY, Huang Y et al (2009) Preliminary analysis of cerebrospinal fluid proteome in patients with neurocysticercosis. Chin Med J (Engl) 122:1003–1008
Bai S, Liu S, Guo X et al (2009) Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients. Mol Vis 15:1638–1648
Hwang HJ, Quinn T, Zhang J (2009) Identification of glycoproteins in human cerebrospinal fluid. Methods Mol Biol 566:263–276
Mouton-Barbosa E, Roux-Dalvai F, Bouyssie D et al (2010) In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol Cell Proteomics 9:1006–1021
Waybright T, Avellino AM, Ellenbogen RG et al (2010) Characterization of the human ventricular cerebrospinal fluid proteome obtained from hydrocephalic patients. J Proteomics 73:1156–1162
Hu WT, Chen-Plotkin A, Arnold SE et al (2010) Novel CSF biomarkers for Alzheimer’s disease and mild cognitive impairment. Acta Neuropathol 119:669–678
Maarouf CL, Andacht TM, Kokjohn TA et al (2009) Proteomic analysis of Alzheimer’s disease cerebrospinal fluid from neuropathologically diagnosed subjects. Curr Alzheimer Res 6:399–406
Harris VK, Diamanduros A, Good P et al (2010) Bri2-23 is a potential cerebrospinal fluid biomarker in multiple sclerosis. Neurobiol Dis 40:331–339
Liu S, Bai S, Qin Z et al (2009) Quantitative proteomic analysis of the cerebrospinal fluid of patients with multiple sclerosis. J Cell Mol Med 13:1586–1603
Sinha A, Srivastava N, Singh S et al (2009) Identification of differentially displayed proteins in cerebrospinal fluid of Parkinson’s disease patients: a proteomic approach. Clin Chim Acta 400:14–20
Cadosch D, Thyer M, Gautschi OP et al (2010) Functional and proteomic analysis of serum and cerebrospinal fluid derived from patients with traumatic brain injury: a pilot study. ANZ J Surg 80:542–547
Xiao F, Chen D, Lu Y et al (2009) Proteomic analysis of cerebrospinal fluid from patients with idiopathic temporal lobe epilepsy. Brain Res 1255:180–189
Barnea E, Sorkin R, Ziv T et al (2005) Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins. Proteomics 5:3367–3375
Barnidge DR, Tschumper RC, Jelinek DF et al (2005) Protein expression profiling of CLL B cells using replicate off-line strong cation exchange chromatography and LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 819:33–39
Blonder J, Chan KC, Issaq HJ et al (2006) Identification of membrane proteins from mammalian cell/tissue using methanol-facilitated solubilization and tryptic digestion coupled with 2D-LC-MS/MS. Nat Protoc 1:2784–2790
Conrads KA, Yu LR, Lucas DA et al (2004) Quantitative proteomic analysis of inorganic phosphate-induced murine MC3T3-E1 osteoblast cells. Electrophoresis 25:1342–1352
Cutillas PR, Norden AG, Cramer R et al (2003) Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond) 104:483–490
Dai J, Wang J, Zhang Y et al (2005) Enrichment and identification of cysteine-containing peptides from tryptic digests of performic oxidized proteins by strong cation exchange LC and MALDI-TOF/TOF MS. Anal Chem 77:7594–7604
Das S, Bosley AD, Ye X et al (2010) Comparison of strong cation exchange and SDS-PAGE fractionation for analysis of multiprotein complexes. J Proteome Res 9:6696–6704
Gao M, Deng C, Yu W et al (2008) Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography. Proteomics 8:939–947
Le Bihan T, Goh T, Stewart II et al (2006) Differential analysis of membrane proteins in mouse fore- and hindbrain using a label-free approach. J Proteome Res 5:2701–2710
Liu X, Valentine SJ, Plasencia MD et al (2007) Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom 18:1249–1264
Zhang C, Liu P, Wang N et al (2007) Comparison of two tandem mass spectrometry-based methods for analyzing the proteome of healthy human lens fibers. Mol Vis 13:1873–1877
Manley GT, Diaz-Arrastia R, Brophy M et al (2010) Common data elements for traumatic brain injury: recommendations from the biospecimens and biomarkers working group. Arch Phys Med Rehabil 91:1667–1672
Acknowledgments
This project has been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the United States Government.
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Waybright, T.J. (2013). Preparation of Human Cerebrospinal Fluid for Proteomics Biomarker Analysis. In: Zhou, M., Veenstra, T. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1002. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-360-2_5
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DOI: https://doi.org/10.1007/978-1-62703-360-2_5
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