In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)

Molecular and Cellular Proteomics

Volumn 13, Issue 11, 2014, Pages 3152-3163

  Guldbrandsen, Astrid ^a   Vethe, Heidrun ^a   Farag, Yehia ^a   Oveland, Eystein ^a   Garberg, Hilde ^a   Berle, Magnus ^a,b   Myhr, Kjell Morten ^a,b   Opsahl, Jill A ^a   Barsnes, Harald ^a   Berven, Frode S ^a,b  

^a UNIVERSITY OF BERGEN   (Norway)

^b HAUKELAND UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 1 ANTICHYMOTRYPSIN; ASPARAGINE; CHROMOGRANIN B; CONTACTIN 1; GLYCOPEPTIDE; GLYCOPROTEIN; VITAMIN D BINDING PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ANTIBODY AFFINITY; ARTICLE; CEREBROSPINAL FLUID; CEREBROSPINAL FLUID PROTEOME RESOURCE; CONTROLLED STUDY; HUMAN; LUMBAR PUNCTURE; MASS SPECTROMETRY; NORMAL HUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN CEREBROSPINAL FLUID LEVEL; PROTEIN DEPLETION; PROTEIN FUNCTION; PROTEIN GLYCOSYLATION; PROTEIN STRUCTURE; PROTEOMICS; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; CHEMISTRY; GENE EXPRESSION PROFILING; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; METABOLISM; PROCEDURES; TANDEM MASS SPECTROMETRY;

CEREBROSPINAL FLUID; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENE EXPRESSION PROFILING; GLYCOPEPTIDES; GLYCOPROTEINS; HEALTHY VOLUNTEERS; HUMANS; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84910044581     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.038554     Document Type: Article

References (63)

1. Segal, M. B. (1993) Extracellular and cerebrospinal fluids. J. Inherit. Metab. Dis. 16, 617-638
2. Kroksveen, A. C., Opsahl, J. A., Aye, T. T., Ulvik, R. J., and Berven, F. S. (2011) Proteomics of human cerebrospinal fluid: discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J. Proteomics 74, 371-388
3. McComb, J. G. (1983) Recent research into the nature of cerebrospinal fluid formation and absorption. J. Neurosurg. 59, 369-383
4. Regeniter, A., Kuhle, J., Mehling, M., Moller, H., Wurster, U., Freidank, H., and Siede, W. H. (2009) A modern approach to CSF analysis: pathophysiology, clinical application, proof of concept, and laboratory reporting. Clin. Neurol. Neurosurg. 111, 313-318
5. Schutzer, S. E., Liu, T., Natelson, B. H., Angel, T. E., Schepmoes, A. A., Purvine, S. O., Hixson, K. K., Lipton, M. S., Camp, D. G., Coyle, P. K., Smith, R. D., and Bergquist, J. (2010) Establishing the proteome of normal human cerebrospinal fluid. PLoS One 5, e10980
6. Zougman, A., Pilch, B., Podtelejnikov, A., Kiehntopf, M., Schnabel, C., Kumar, C., and Mann, M. (2008) Integrated analysis of the cerebrospinal fluid peptidome and proteome. J. Proteome Res. 7, 386-399
7. Yuan, X., and Desiderio, D. M. (2005) Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics 5, 541-550
8. Pan, S., Wang, Y., Quinn, J. F., Peskind, E. R., Waichunas, D., Wimberger, J. T., Jin, J., Li, J. G., Zhu, D., Pan, C., and Zhang, J. (2006) Identification of glycoproteins in human cerebrospinal fluid with a complementary proteomic approach. J. Proteome Res. 5, 2769-2779
9. Noben, J. P., Dumont, D., Kwasnikowska, N., Verhaert, P., Somers, V., Hupperts, R., Stinissen, P., and Robben, J. (2006) Lumbar cerebrospinal fluid proteome in multiple sclerosis: characterization by ultrafiltration, liquid chromatography, and mass spectrometry. J. Proteome Res. 5, 1647-1657
10. Sickmann, A., Dormeyer, W., Wortelkamp, S., Woitalla, D., Kuhn, W., and Meyer, H. E. (2000) Identification of proteins from human cerebrospinal fluid, separated by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 21, 2721-2728
11. Maccarrone, G., Milfay, D., Birg, I., Rosenhagen, M., Holsboer, F., Grimm, R., Bailey, J., Zolotarjova, N., and Turck, C. W. (2004) Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry. Electrophoresis 25, 2402-2412
12. Davidsson, P., Folkesson, S., Christiansson, M., Lindbjer, M., Dellheden, B., Blennow, K., and Westman-Brinkmalm, A. (2002) Identification of proteins in human cerebrospinal fluid using liquid-phase isoelectric focusing as a prefractionation step followed by two-dimensional gel electrophoresis and matrix-Assisted laser desorption/ionisation mass spectrometry. Rapid Commun. Mass Spectrom. 16, 2083-2088
13. Ogata, Y., Charlesworth, M. C., and Muddiman, D. C. (2005) Evaluation of protein depletion methods for the analysis of total-, phospho-And glycoproteins in lumbar cerebrospinal fluid. J. Proteome Res. 4, 837-845
14. Wenner, B. R., Lovell, M. A., and Lynn, B. C. (2004) Proteomic analysis of human ventricular cerebrospinal fluid from neurologically normal, elderly subjects using two-dimensional LC-MS/MS. J. Proteome Res. 3, 97-103
15. Xu, J., Chen, J., Peskind, E. R., Jin, J., Eng, J., Pan, C., Montine, T. J., Goodlett, D. R., and Zhang, J. (2006) Characterization of proteome of human cerebrospinal fluid. Int. Rev. Neurobiol. 73, 29-98
16. Pan, S., Zhu, D., Quinn, J. F., Peskind, E. R., Montine, T. J., Lin, B., Goodlett, D. R., Taylor, G., Eng, J., and Zhang, J. (2007) A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics 7, 469-473
17. Li, S. J., Peng, M., Li, H., Liu, B. S., Wang, C., Wu, J. R., Li, Y. X., and Zeng, R. (2009) Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res. 37, D907-912
18. Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545
19. Berger, M. S., Locher, G. W., Saurer, S., Gullick, W. J., Waterfield, M. D., Groner, B., and Hynes, N. E. (1988) Correlation of c-erbB-2 gene amplification and protein expression in human breast carcinoma with nodal status and nuclear grading. Cancer Res. 48, 1238-1243
20. Hudziak, R. M., Schlessinger, J., and Ullrich, A. (1987) Increased expression of the putative growth factor receptor p185HER2 causes transformation and tumorigenesis of NIH 3T3 cells. Proc. Natl. Acad. Sci. U. S. A. 84, 7159-7163
21. Vogelzang, N. J., Lange, P. H., Goldman, A., Vessela, R. H., Fraley, E. E., and Kennedy, B. J. (1982) Acute changes of alpha-fetoprotein and human chorionic gonadotropin during induction chemotherapy of germ cell tumors. Cancer Res. 42, 4855-4861
22. Bosl, G. J., Lange, P. H., Fraley, E. E., Goldman, A., Nochomovitz, L. E., Rosai, J., Waldmann, T. A., Johnson, K., and Kennedy, B. J. (1981) Human chorionic gonadotropin and alphafetoprotein in the staging of nonseminomatous testicular cancer. Cancer 47, 328-332
23. Thompson, D. K., and Haddow, J. E. (1979) Serial monitoring of serum alpha-fetoprotein and chorionic gonadotropin in males with germ cell tumors. Cancer 43, 1820-1829
24. Catalona, W. J., Richie, J. P., Ahmann, F. R., Hudson, M. A., Scardino, P. T., Flanigan, R. C., Dekernion, J. B., Ratliff, T. L., Kavoussi, L. R., Dalkin, B. L., Waters, W.B., MacFarlane, M. T., and Southwick, P. C. (1994) Comparison of digital rectal examination and serum prostate specific antigen in the early detection of prostate cancer: results of a multicenter clinical trial of 6630 men. J. Urol. 151, 1283-1290
25. Canney, P. A., Moore, M., Wilkinson, P. M., and James, R. D. (1984) Ovarian cancer antigen CA125: a prospective clinical assessment of its role as a tumour marker. Br. J. Cancer 50, 765-769
26. Roth, J. (2002) Protein N-glycosylation along the secretory pathway: relationship to organelle topography and function, protein quality control, and cell interactions. Chem. Rev. 102, 285-303
27. Sato, Y., and Endo, T. (2010) Alteration of brain glycoproteins during aging. Geriatr. Gerontol. Int. 1, S32-40
28. Nilsson, J., Ruetschi, U., Halim, A., Hesse, C., Carlsohn, E., Brinkmalm, G., and Larson, G. (2009) Enrichment of glycopeptides for glycan structure and attachment site identification. Nat. Methods 6, 809-811
29. Teunissen, C., Menge, T., Altintas, A., Alvarez-Cermeno, J. C., Bertolotto, A., Berven, F. S., Brundin, L., Comabella, M., Degn, M., Deisenhammer, F., Fazekas, F., Franciotta, D., Frederiksen, J. L., Galimberti, D., Gnanapavan, S., Hegen, H., Hemmer, B., Hintzen, R., Hughes, S., Iacobaeus, E., Kroksveen, A. C., Kuhle, J., Richert, J., Tumani, H., Villar, L. M., Drulovic, J., Dujmovic, I., Khalil, M., and Bartos, A. (2013) Consensus definitions and application guidelines for control groups in cerebrospinal fluid biomarker studies in multiple sclerosis. Mult. Scler.
30. Teunissen, C. E., Petzold, A., Bennett, J. L., Berven, F. S., Brundin, L., Comabella, M., Franciotta, D., Frederiksen, J. L., Fleming, J. O., Furlan, R., Hintzen, R. Q., Hughes, S. G., Johnson, M. H., Krasulova, E., Kuhle, J., Magnone, M. C., Rajda, C., Rejdak, K., Schmidt, H. K., van Pesch, V., Waubant, E., Wolf, C., Giovannoni, G., Hemmer, B., Tumani, H., and Deisenhammer, F. (2009) A consensus protocol for the standardization of cerebrospinal fluid collection and biobanking. Neurology 73, 1914-1922
31. Kroksveen, A. C., Aasebo, E., Vethe, H., Van Pesch, V., Franciotta, D., Teunissen, C. E., Ulvik, R. J., Vedeler, C., Myhr, K. M., Barsnes, H., and Berven, F. S. (2012) Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. J. Proteomics 78, 312-325
32. Phillips, H. L., Williamson, J. C., van Elburg, K. A., Snijders, A. P., Wright, P. C., and Dickman, M. J. (2010) Shotgun proteome analysis utilizing mixed mode (reversed phase-Anion exchange chromatography) in conjunction with reversed phase liquid chromatography mass spectrometry analysis. Proteomics 10, 2950-2960
33. Tian, Y., Zhou, Y., Elliott, S., Aebersold, R., and Zhang, H. (2007) Solidphase extraction of N-linked glycopeptides. Nat. Protoc. 2, 334-339
34. Berven, F. S., Ahmad, R., Clauser, K. R., and Carr, S. A. (2010) Optimizing performance of glycopeptide capture for plasma proteomics. J. Proteome Res. 9, 1706-1715
35. Vaudel, M., Barsnes, H., Berven, F. S., Sickmann, A., and Martens, L. (2011) SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 11, 996-999
36. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
37. Fenyo, D., and Beavis, R. C. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768-774
38. Barsnes, H., Vaudel, M., Colaert, N., Helsens, K., Sickmann, A., Berven, F. S., and Martens, L. (2011) Compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics 12, 70
39. Nesvizhskii, A. I. (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 73, 2092-2123
40. Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M. Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S. L., Nuwaysir, L. M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E. W., Moritz, R. L., Katz, J. E., Agus, D. B., MacCoss, M., Tabb, D. L., and Mallick, P. (2012) A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918-920
41. Mi, H., Muruganujan, A., and Thomas, P. D. (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41, D377-386
42. Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1292
43. Vaudel, M., Breiter, D., Beck, F., Rahnenfuhrer, J., Martens, L., and Zahedi, R. P. (2013) D-score: a search engine independent MD-score. Proteomics 13, 1036-1041
44. Frank, M., and Kemler, R. (2002) Protocadherins. Curr. Opin. Cell Biol. 14, 557-562
45. Kroksveen, A. C., Guldbrandsen, A., Vedeler, C., Myhr, K. M., Opsahl, J. A., and Berven, F. S. (2012) Cerebrospinal fluid proteome comparison between multiple sclerosis patients and controls. Acta Neurol. Scand. 126, Supplement s195, 90-96
46. Ottervald, J., Franzén, B., Nilsson, K., Andersson, L., Khademi, M., Eriksson, B., Kjellström, S., Marko-Varga, G., Végvári, A., Harris, R., Laurell, T., Miliotis, T., Matusevicius, D., Salter, H., Ferm, M., and Olsson, T. (2010) Multiple sclerosis: identification and clinical evaluation of novel CSF biomarkers. J. Proteomics 73, 1117-1132
47. Abdi, F., Quinn, J. F., Jankovic, J., McIntosh, M., Leverenz, J. B., Peskind, E., Nixon, R., Nutt, J., Chung, K., Zabetian, C., Samii, A., Lin, M., Hattan, S., Pan, C., Wang, Y., Jin, J., Zhu, D., Li, G. J., Liu, Y., Waichunas, D., Montine, T. J., and Zhang, J. (2006) Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders. J. Alzheimer's Dis. 9, 293-348
48. Simonsen, A. H., McGuire, J., Podust, V. N., Davies, H., Minthon, L., Skoog, I., Andreasen, N., Wallin, A., Waldemar, G., and Blennow, K. (2008) Identification of a novel panel of cerebrospinal fluid biomarkers for Alzheimer's disease. Neurobiol. Aging 29, 961-968
49. Davidsson, P., Westman-Brinkmalm, A., Nilsson, C. L., Lindbjer, M., Paulson, L., Andreasen, N., Sjogren, M., and Blennow, K. (2002) Proteome analysis of cerebrospinal fluid proteins in Alzheimer patients. Neuroreport 13, 611-615
50. Simonsen, A. H., McGuire, J., Hansson, O., Zetterberg, H., Podust, V. N., Davies, H. A., Waldemar, G., Minthon, L., and Blennow, K. (2007) Novel panel of cerebrospinal fluid biomarkers for the prediction of progression to Alzheimer dementia in patients with mild cognitive impairment. Arch. Neurol. 64, 366-370
51. Kroksveen, A. C., Opsahl, J. A., Aye, T. T., Ulvik, R. J., and Berven, F. S. (2011) Proteomics of human cerebrospinal fluid: discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J. Proteomics 74, 371-388
52. Kroksveen, A. C., Aasebo, E., Vethe, H., Van Pesch, V., Franciotta, D., Teunissen, C. E., Ulvik, R. J., Vedeler, C., Myhr, K. M., Barsnes, H., and Berven, F. S. (2013) Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. J. Proteomics 78, 312-325
53. Benjannet, S., Leduc, R., Adrouche, N., Falgueyret, J. P., Marcinkiewicz, M., Seidah, N. G., Mbikay, M., Lazure, C., and Chretien, M. (1987) Chromogranin B (secretogranin I), a putative precursor of two novel pituitary peptides through processing at paired basic residues. FEBS Lett. 224, 142-148
54. Helle, K. (2010) Chromogranins A and B and secretogranin II as prohormones for regulatory peptides from the diffuse neuroendocrine system. Results Probl. Cell Differ. 50, 21-44
55. Haddad, J. G. (1995) Plasma vitamin D-binding protein (Gc-globulin): multiple tasks. J. Steroid Biochem. Mol. Biol. 53, 579-582
56. Kim, J. S., Monroe, M. E., Camp, D. G., 2nd, Smith, R. D., and Qian, W. J. (2013) In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. J. Proteome Res. 12, 910-916
57. Wein, S. P., Cote, R. G., Dumousseau, M., Reisinger, F., Hermjakob, H., and Vizcaino, J. A. (2012) Improvements in the Protein Identifier Cross-Reference service. Nucleic Acids Res. 40, W276-280
58. Martins-de-Souza, D., Maccarrone, G., Wobrock, T., Zerr, I., Gormanns, P., Reckow, S., Falkai, P., Schmitt, A., and Turck, C. W. (2010) Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia. J. Psychiatr. Res. 44, 1176-1189
59. Constantinescu, R., Andreasson, U., Li, S., Podust, V. N., Mattsson, N., Anckarsater, R., Anckarsater, H., Rosengren, L., Holmberg, B., Blennow, K., Wikkelso, C., Ruetschi, U., and Zetterberg, H. (2010) Proteomic profiling of cerebrospinal fluid in parkinsonian disorders. Parkinsonism Relat. Disord. 16, 545-549
60. Wright, B. L., Lai, J. T., and Sinclair, A. J. (2012) Cerebrospinal fluid and lumbar puncture: a practical review. J. Neurol. 259, 1530-1545
61. Aasebo, E., Opsahl, J. A., Bjorlykke, Y., Myhr, K. M., Kroksveen, A. C., and Berven, F. S. (2014) Effects of blood contamination and the rostro-caudal gradient on the human cerebrospinal fluid proteome. PLoS One 9, e90429
62. Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440
63. Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Rios, D., Wang, R., and Hermjakob, H. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-1069