In-depth Characterization of the Cerebrospinal Fluid (CSF) Proteome Displayed Through the CSF Proteome Resource (CSF-PR)

Overview

Journal Mol Cell Proteomics

Specialties Biochemistry
Cell Biology
Molecular Biology

Date 2014 Jul 20

PMID 25038066

Citations 51

Authors

Astrid Guldbrandsen

Heidrun Vethe

Yehia Farag

Eystein Oveland

Hilde Garberg

Magnus Berle

Kjell-Morten Myhr

Jill A Opsahl

Harald Barsnes

Frode S Berven

Affiliations

Soon will be listed here.

Abstract

In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.

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References

Berven F, Ahmad R, Clauser K, Carr S . Optimizing performance of glycopeptide capture for plasma proteomics. J Proteome Res. 2010; 9(4):1706-15. PMC: 2855884. DOI: 10.1021/pr900845m. View

Teunissen C, Petzold A, Bennett J, Berven F, Brundin L, Comabella M . A consensus protocol for the standardization of cerebrospinal fluid collection and biobanking. Neurology. 2009; 73(22):1914-22. PMC: 2839806. DOI: 10.1212/WNL.0b013e3181c47cc2. View

Maccarrone G, Milfay D, Birg I, Rosenhagen M, Holsboer F, Grimm R . Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry. Electrophoresis. 2004; 25(14):2402-12. DOI: 10.1002/elps.200305909. View

Kroksveen A, Aasebo E, Vethe H, van Pesch V, Franciotta D, Teunissen C . Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. J Proteomics. 2012; 78:312-25. DOI: 10.1016/j.jprot.2012.09.037. View

Berger M, Locher G, Saurer S, Gullick W, Waterfield M, Groner B . Correlation of c-erbB-2 gene amplification and protein expression in human breast carcinoma with nodal status and nuclear grading. Cancer Res. 1988; 48(5):1238-43. View

Yuan X, Desiderio D . Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics. 2005; 5(2):541-50. DOI: 10.1002/pmic.200400934. View

McComb J . Recent research into the nature of cerebrospinal fluid formation and absorption. J Neurosurg. 1983; 59(3):369-83. DOI: 10.3171/jns.1983.59.3.0369. View

Hudziak R, Schlessinger J, Ullrich A . Increased expression of the putative growth factor receptor p185HER2 causes transformation and tumorigenesis of NIH 3T3 cells. Proc Natl Acad Sci U S A. 1987; 84(20):7159-63. PMC: 299249. DOI: 10.1073/pnas.84.20.7159. View

Helle K . Chromogranins A and B and secretogranin II as prohormones for regulatory peptides from the diffuse neuroendocrine system. Results Probl Cell Differ. 2010; 50:21-44. DOI: 10.1007/400_2009_26. View

10.

Benjannet S, Leduc R, Adrouche N, Falgueyret J, Marcinkiewicz M, Seidah N . Chromogranin B (secretogranin I), a putative precursor of two novel pituitary peptides through processing at paired basic residues. FEBS Lett. 1987; 224(1):142-8. DOI: 10.1016/0014-5793(87)80438-6. View

11.

Simonsen A, McGuire J, Hansson O, Zetterberg H, Podust V, Davies H . Novel panel of cerebrospinal fluid biomarkers for the prediction of progression to Alzheimer dementia in patients with mild cognitive impairment. Arch Neurol. 2007; 64(3):366-70. DOI: 10.1001/archneur.64.3.366. View

12.

Constantinescu R, Andreasson U, Li S, Podust V, Mattsson N, Anckarsater R . Proteomic profiling of cerebrospinal fluid in parkinsonian disorders. Parkinsonism Relat Disord. 2010; 16(8):545-9. DOI: 10.1016/j.parkreldis.2010.06.011. View

13.

Fenyo D, Beavis R . A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem. 2003; 75(4):768-74. DOI: 10.1021/ac0258709. View

14.

Zougman A, Pilch B, Podtelejnikov A, Kiehntopf M, Schnabel C, Kumar C . Integrated analysis of the cerebrospinal fluid peptidome and proteome. J Proteome Res. 2007; 7(1):386-99. DOI: 10.1021/pr070501k. View

15.

Kroksveen A, Opsahl J, Aye T, Ulvik R, Berven F . Proteomics of human cerebrospinal fluid: discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J Proteomics. 2010; 74(4):371-88. DOI: 10.1016/j.jprot.2010.11.010. View

16.

Chambers M, MacLean B, Burke R, Amodei D, Ruderman D, Neumann S . A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012; 30(10):918-20. PMC: 3471674. DOI: 10.1038/nbt.2377. View

17.

Vizcaino J, Cote R, Csordas A, Dianes J, Fabregat A, Foster J . The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2012; 41(Database issue):D1063-9. PMC: 3531176. DOI: 10.1093/nar/gks1262. View

18.

Thompson D, Haddow J . Serial monitoring of serum alpha-fetoprotein and chorionic gonadotropin in males with germ cell tumors. Cancer. 1979; 43(5):1820-9. DOI: 10.1002/1097-0142(197905)43:5<1820::aid-cncr2820430535>3.0.co;2-g. View

19.

Tian Y, Zhou Y, Elliott S, Aebersold R, Zhang H . Solid-phase extraction of N-linked glycopeptides. Nat Protoc. 2007; 2(2):334-9. PMC: 2971528. DOI: 10.1038/nprot.2007.42. View

20.

Regeniter A, Kuhle J, Mehling M, Moller H, Wurster U, Freidank H . A modern approach to CSF analysis: pathophysiology, clinical application, proof of concept and laboratory reporting. Clin Neurol Neurosurg. 2009; 111(4):313-8. DOI: 10.1016/j.clineuro.2008.12.004. View