The methodology of neuroproteomics

Methods in Molecular Biology

Volumn 566, Issue , 2009, Pages 1-21

  Ottens, Andrew K ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Brain; Chromatography; Disease; Injury; Mass spectrometry; Neurodegenerative; Neuroproteomics; Proteomics

Indexed keywords

ANIMALIA;

NERVE PROTEIN;

ANIMAL; ARTICLE; AUDIOVISUAL EQUIPMENT; BIOLOGY; CHEMISTRY; DEGENERATIVE DISEASE; HUMAN; MEDLINE; METHODOLOGY; NERVOUS SYSTEM; NEUROLOGIC DISEASE; NEUROSCIENCE; PATHOPHYSIOLOGY; PROTEIN PROCESSING; PROTEOMICS; SYNAPSE VESICLE; TRANSLATIONAL RESEARCH; ULTRASTRUCTURE;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, ANATOMIC; NERVE TISSUE PROTEINS; NERVOUS SYSTEM; NERVOUS SYSTEM DISEASES; NEURODEGENERATIVE DISEASES; NEUROSCIENCES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; PUBMED; SYNAPTIC VESICLES; TRANSLATIONAL RESEARCH;

EID: 77449106117     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-562-6_1     Document Type: Article

References (133)

1. Kim, S. I., Voshol, H., van Oostrum, J., Hastings, T. G., Cascio, M., and Glucksman, M. J. (2004) Neuroproteomics: Expression profiling of the brain's proteomes in health and disease. Neurochem. Res. 29, 1317-1331.
2. Butcher, J. (2007) Neuroproteomics comes of age. Lancet Neurol. 6, 850-851.
3. Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., Duncan, M. W., Harris, R., Williams, K. L., and Humphery-Smith, I. (1995) Progress with gene-product mapping of the mollicutes: Mycoplasma genitalium. Electrophoresis 16, 1090-1094.
4. Pocklington, A. J., Armstrong, J. D., and Grant, S. G. (2006) Organization of brain complexity -synapse proteome form and function. Brief Funct. Genomic Proteomic. 5, 66-73.
5. Temburni, M. K., and Jacob, M. H. (2001) New functions for glia in the brain. Proc. Natl Acad. Sci. USA 98, 3631-3632.
6. Masland, R. H. (2004) Neuronal cell types. Curr. Biol. 14, R497-R500.
7. Becker, M., Schindler, J., and Nothwang, H. G. (2006) Neuroproteomics -the tasks lying ahead. Electrophoresis 27, 2819-2829.
8. Ekegren, T., Hanrieder, J., and Bergquist, J. (2008) Clinical perspectives of high-resolution mass spectrometry-based proteomics in neuroscience: Exemplified in amyotrophic lateral sclerosis biomarker discovery research. J. Mass Spectrom. 43, 559-571.
9. Gustincich, S., Sandelin, A., Plessy, C., Katayama, S., Simone, R., Lazarevic, D., Hayashizaki, Y., and Carninci, P. (2006) The complexity of the mammalian transcriptome. J. Physiol. 575, 321-332.
10. Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., and Burge, C. B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476.
11. Jensen, O. N. (2006) Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol. 7, 391-403.
12. Kalume, D. E., Molina, H., and Pandey, A. (2003) Tackling the phosphoproteome: Tools and strategies. Curr. Opin. Chem. Biol. 7, 64-69.
13. Paradela, A., and Albar, J. P. (2008) Advances in the analysis of protein phosphorylation. J. Proteome Res. 7, 1809-1818.
14. Yang, X. J. (2005) Multisite Protein Modification and Intramolecular Signaling. Oncogene 24, 1653-1662.
15. Dube, D. H., and Bertozzi, C. R. (2005) Glycans in cancer and inflammation -potential for therapeutics and diagnostics. Nat. Rev. Drug Discov. 4, 477-488.
16. Carpentier, S. C., Panis, B., Swennen, R., and Lammertyn, J. (2008) Finding the significant markers: Statistical analysis of proteomic data. Methods Mol. Biol. 428, 327-347.
17. Isserlin, R., and Emili, A. (2008) Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery. Curr. Opin. Mol. Ther. 10, 231-242.
18. Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. A., Julian, R. K. Jr., Jones, A. R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T. A., Patterson, S. D., Ping, P., Seymour, S. L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T. M., Whitelegge, J. P., Wilkins, M. R., Xenarios, I., Yates, J. R. 3rd, and Hermjakob, H. (2007) The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25, 887-893.
19. Eisenacher, M., Hardt, T., Martens, L., Hakkinen, J., Apweiler, R., Hamacher, M., Meyer, H. E., and Stephan, C. (2008) Proteomics data collection -3rd ProDaC Workshop April 22nd 2008, Toledo, Spain. Proteomics 8, 4163-4167.
20. Lu, Q., Murugesan, N., Macdonald, J. A., Wu, S. L., Pachter, J. S., and Hancock, W. S. (2008) Analysis of mouse brain microvascular endothelium using immuno-laser capture microdissection coupled to a hybrid linear ion trap with fourier transform-mass spectrometry proteomics platform. Electrophoresis 29, 2689-2695.
21. Mustafa, D., Kros, J. M., and Luider, T. (2008) Combining laser capture microdissection and proteomics techniques. Methods Mol. Biol. 428, 159-178.
22. Ferrer, I., Santpere, G., Arzberger, T., Bell, J., Blanco, R., Boluda, S., Budka, H., Carmona, M., Giaccone, G., Krebs, B., Limido, L., Parchi, P., Puig, B., Strammiello, R., Strobel, T., and Kretzschmar, H. (2007) Brain protein preservation largely depends on the postmortem storage temperature: Implications for study of proteins in human neurologic diseases and management of brain banks: A brainnet europe study. J. Neuropathol. Exp. Neurol. 66, 35-46.
23. Van Elzen, R., Moens, L., and Dewilde, S. (2008) Expression profiling of the cerebral ischemic and hypoxic response. Expert Rev. Proteomics 5, 263-282.
24. Lipton, P. (1999) Ischemic cell death in brain neurons. Physiol. Rev. 79, 1431-1568.
25. Stanimirovic, D., and Satoh, K. (2000) Inflammatory mediators of cerebral endothelium: A role in ischemic brain inflammation. Brain Pathol. 10, 113-126.
26. Won, S. J., Kim, D. Y., and Gwag, B. J. (2002) Cellular and molecular pathways of ischemic neuronal death. J. Biochem. Mol. Biol. 35, 67-86.
27. Danton, G. H., and Dietrich, W. D. (2003) Inflammatory mechanisms after ischemia and stroke. J. Neuropathol. Exp. Neurol. 62, 127-136.
28. Aurell, A., Rosengren, L. E., Karlsson, B., Olsson, J. E., Zbornikova, V., and Haglid, K. G. (1991) Determination of S-100 and glial fibrillary acidic protein concentrations in cerebrospinal fluid after brain infarction. Stroke 22, 1254-1258.
29. Sotgiu, S., Zanda, B., Marchetti, B., Fois, M. L., Arru, G., Pes, G. M., Salaris, F. S., Arru, A., Pirisi, A., and Rosati, G. (2006) Inflammatory biomarkers in blood of patients with acute brain ischemia. Eur. J. Neurol. 13, 505-513.
30. Longa, E. Z., Weinstein, P. R., Carlson, S., and Cummins, R. (1989) Reversible middle cerebral artery occlusion without craniectomy in rats. Stroke 20, 84-91.
31. Bao, W. L., Williams, A. J., Faden, A. I., and Tortella, F. C. (2001) Selective mGluR5 receptor antagonist or agonist provides neuroprotection in a rat model of focal cerebral ischemia. Brain Res. 922, 173-179.
32. Berti, R., Williams, A. J., Velarde, L. C., Moffett, J. R., Elliott, P. J., Adams, J., Yao, C., Dave, J. R., and Tortella, F. C. (2003) Effect of the proteasome inhibitor MLN519 on the expression of inflammatory molecules following middle cerebral artery occlusion and reperfusion in the rat. Neurotox. Res. 5, 505-514.
33. Phillips, J. B., Williams, A. J., Adams, J., Elliott, P. J., and Tortella, F. C. (2000) Proteasome inhibitor PS519 reduces infarction and attenuates leukocyte infiltration in a rat model of focal cerebral ischemia. Stroke 31, 1686-1693.
34. Williams, A. J., Dave, J. R., Phillips, J. B., Lin, Y., McCabe, R. T., and Tortella, F. C. (2000) Neuroprotective efficacy and therapeutic window of the high-affinity N-methyl-d-aspartate antagonist conantokin-G: In vitro (primary cerebellar neurons) and in vivo (rat model of transient focal brain ischemia) studies. J. Pharmacol. Exp. Ther. 294, 378-386.
35. Williams, A. J., Hale, S. L., Moffett, J. R., Dave, J. R., Elliott, P. J., Adams, J., and Tortella, F. C. (2003) Delayed treatment with MLN519 reduces infarction and associated neurologic deficit caused by focal ischemic brain injury in rats via antiinflammatory mechanisms involving nuclear factor-kappaB activation, gliosis, and leukocyte infiltration. J. Cereb. Blood Flow Metab. 23, 75-87.
36. Williams, A. J., Ling, G., Berti, R., Moffett, J. R., Yao, C., Lu, X. M., Dave, J. R., and Tortella, F. C. (2003) Treatment with the snail peptide CGX-1007 reduces DNA damage and alters gene expression of c-Fos and Bcl-2 following focal ischemic brain injury in rats. Exp. Brain Res. 153, 16-26.
37. Williams, A. J., Ling, G., McCabe, R. T., and Tortella, F. C. (2002) Intrathecal CGX-1007 is neuroprotective in a rat model of focal cerebral ischemia. Neuroreport 13, 821-824.
38. Williams, A. J., and Tortella, F. C. (2002) Neuroprotective effects of the sodium channel blocker RS100642 and attenuation of ischemia-induced brain seizures in the rat. Brain Res. 932, 45-55.
39. Yao, C., Williams, A. J., Lu, X. C., Price, R. A., Cunningham, B. S., Berti, R., Tortella, F. C., and Dave, J. R. (2003) The sodium channel blocker RS100642 reverses downregulation of the sodium channel alpha-subunit Na(v) 1.1 expression caused by transient ischemic brain injury in rats. Neurotox. Res. 5, 245-253.
40. Cernak, I. (2005) Animal models of head trauma. NeuroRx 2, 410-422.
41. Onifer, S. M., Rabchevsky, A. G., and Scheff, S. W. (2007) Rat models of traumatic spinal cord injury to assess motor recovery. ILAR J. 48, 385-395.
42. Pearse, D. D., and Bunge, M. B. (2006) Designing cell-and gene-based regeneration strategies to repair the injured spinal cord. J. Neurotrauma 23, 438-452.
43. Ravikumar, R., McEwen, M. L., and Springer, J. E. (2007) Post-treatment with the cyclosporin derivative, NIM811, reduced indices of cell death and increased the volume of spared tissue in the acute period following spinal cord contusion. J. Neurotrauma 24, 1618-1630.
44. Reilly, P. L. (2001) Brain injury: The pathophysiology of the first hours. 'Talk and Die revisited'. J. Clin. Neurosci. 8, 398-403.
45. Stiefel, M. F., Tomita, Y., and Marmarou, A. (2005) Secondary ischemia impairing the restoration of ion homeostasis following traumatic brain injury. J. Neurosurg. 103, 707-714.
46. Prieto, D. A., Ye, X., and Veenstra, T. D. (2008) Proteomic analysis of traumatic brain injury: The search for biomarkers. Expert Rev. Proteomics 5, 283-291.
47. Ottens, A. K., Kobeissy, F. H., Fuller, B. F., Liu, M. C., Oli, M. W., Hayes, R. L., and Wang, K. K. (2007) Novel neuroproteomic approaches to studying traumatic brain injury. Prog. Brain Res. 161, 401-418.
48. Ottens, A. K., Kobeissy, F. H., Golden, E. C., Zhang, Z., Haskins, W. E., Chen, S. S., Hayes, R. L., Wang, K. K., and Denslow, N. D. (2006) Neuroproteomics in neurotrauma. Mass Spectrom. Rev. 25, 380-408.
49. Matsumoto, I., Alexander-Kaufman, K., Iwazaki, T., Kashem, M. A., and Matsuda-Matsumoto, H. (2007) CNS proteomes in alcohol and drug abuse and dependence. Expert Rev. Proteomics 4, 539-552.
50. Kobeissy, F. H., Sadasivan, S., Liu, J., Gold, M. S., and Wang, K. K. (2008) Psychiatric research: Psychoproteomics, degradomics and systems biology. Expert Rev. Proteomics 5, 293-314.
51. Matsumoto, H., and Matsumoto, I. (2008) Alcoholism: Protein expression profiles in a human hippocampal model. Expert Rev. Proteomics 5, 321-331.
52. Hemby, S. E. (2006) Assessment of genome and proteome profiles in cocaine abuse. Prog. Brain Res. 158, 173-195.
53. Bodzon-Kulakowska, A., Bierczynska-Krzysik, A., Drabik, A., Noga, M., Kraj, A., Suder, P., and Silberring, J. (2005) Morphinome-Proteome of the Nervous System After Morphine Treatment. Amino Acids 28, 13-19.
54. Iwazaki, T., McGregor, I. S., and Matsumoto, I. (2008) Protein expression profile in the amygdala of rats with methamphetamineinduced behavioral sensitization. Neurosci. Lett. 435, 113-119.
55. Iwazaki, T., McGregor, I. S., and Matsumoto, I. (2007) Protein expression profile in the striatum of rats with methamphetamineinduced behavioral sensitization. Proteomics 7, 1131-1139.
56. Kobeissy, F. H., Warren, M. W., Ottens, A. K., Sadasivan, S., Zhang, Z., Gold, M. S., and Wang, K. K. (2008) Psychoproteomic analysis of rat cortex following acute methamphetamine exposure. J. Proteome Res. 7, 1971-1983.
57. Freeman, W. M., Brebner, K., Amara, S. G., Reed, M. S., Pohl, J., and Phillips, A. G. (2005) Distinct proteomic profiles of amphetamine self-administration transitional states. Pharmacogenomics J. 5, 203-214.
58. Hwang, Y. Y., and Li, M. D. (2006) Proteins differentially expressed in response to nicotine in five rat brain regions: Identification using a 2-DE/MS-based proteomics approach. Proteomics 6, 3138-3153.
59. Yeom, M., Shim, I., Lee, H. J., and Hahm, D. H. (2005) Proteomic analysis of nicotineassociated protein expression in the striatum of repeated nicotine-treated rats. Biochem. Biophys. Res. Commun. 326, 321-328.
60. Thompson, P. M., Hayashi, K. M., Simon, S. L., Geaga, J. A., Hong, M. S., Sui, Y., Lee, J. Y., Toga, A. W., Ling, W., and London, E. D. (2004) Structural abnormalities in the brains of human subjects who use methamphetamine. J. Neurosci. 24, 6028-6036.
61. Pierce, R. C., and Kumaresan, V. (2006) The mesolimbic dopamine system: The final common pathway for the reinforcing effect of drugs of abuse? Neurosci. Biobehav. Rev. 30, 215-238.
62. Gotz, J., Deters, N., Doldissen, A., Bokhari, L., Ke, Y., Wiesner, A., Schonrock, N., and Ittner, L. M. (2007) A decade of tau transgenic animal models and beyond. Brain Pathol. 17, 91-103.
63. Games, D., Adams, D., Alessandrini, R., Barbour, R., Berthelette, P., Blackwell, C., Carr, T., Clemens, J., Donaldson, T., and Gillespie, F. (1995) Alzheimer-type neuropathology in transgenic mice overexpressing V717F beta-amyloid precursor protein. Nature 373, 523-527.
64. Hsiao, K., Chapman, P., Nilsen, S., Eckman, C., Harigaya, Y., Younkin, S., Yang, F., and Cole, G. (1996) Correlative memory deficits, abeta elevation, and amyloid plaques in transgenic mice. Science 274, 99-102.
65. Sturchler-Pierrat, C., Abramowski, D., Duke, M., Wiederhold, K. H., Mistl, C., Rothacher, S., Ledermann, B., Burki, K., Frey, P., Paganetti, P. A., Waridel, C., Calhoun, M. E., Jucker, M., Probst, A., Staufenbiel, M., and Sommer, B. (1997) Two amyloid precursor protein transgenic mouse models with alzheimer diseaselike pathology. Proc. Natl Acad. Sci. USA 94, 13287-13292.
66. Stalder, M., Phinney, A., Probst, A., Sommer, B., Staufenbiel, M., and Jucker, M. (1999) Association of microglia with amyloid plaques in brains of APP23 transgenic mice. Am. J. Pathol. 154, 1673-1684.
67. Lewis, J., McGowan, E., Rockwood, J., Melrose, H., Nacharaju, P., Van Slegtenhorst, M., Gwinn-Hardy, K., Paul Murphy, M., Baker, M., Yu, X., Duff, K., Hardy, J., Corral, A., Lin, W. L., Yen, S. H., Dickson, D. W., Davies, P., and Hutton, M. (2000) Neurofibrillary tangles, amyotrophy and progressive motor disturbance in mice expressing mutant (P301L) tau protein. Nat. Genet. 25, 402-405.
68. Lewis, J., Dickson, D. W., Lin, W. L., Chisholm, L., Corral, A., Jones, G., Yen, S. H., Sahara, N., Skipper, L., Yager, D., Eckman, C., Hardy, J., Hutton, M., and McGowan, E. (2001) Enhanced neurofibrillary degeneration in transgenic mice expressing mutant tau and APP. Science 293, 1487-1491.
69. Gotz, J., Chen, F., van Dorpe, J., and Nitsch, R. M. (2001) Formation of neurofibrillary tangles in P301l tau transgenic mice induced by abeta 42 fibrils. Science 293, 1491-1495.
70. Gotz, J., Streffer, J. R., David, D., Schild, A., Hoerndli, F., Pennanen, L., Kurosinski, P., and Chen, F. (2004) Transgenic animal models of Alzheimer's disease and related disorders: Histopathology, behavior and therapy. Mol. Psychiatry 9, 664-683.
71. Abdul, H. M., Sultana, R., St. Clair, D. K., Markesbery, W. R., and Butterfield, D. A. (2008) Oxidative damage in brain from human mutant APP/PS-1 double knock-in mice as a function of age. Free Radic. Biol. Med. 45, 1420-1425.
72. Owen, J. B., Opii, W. O., Ramassamy, C., Pierce, W. M., and Butterfield, D. A. (2008) Proteomic analysis of brain protein expression levels in NF-Kappabeta p50 (-/-) homozygous knockout mice. Brain Res. 1240, 22-30.
73. Hartl, D., Rohe, M., Mao, L., Staufenbiel, M., Zabel, C., and Klose, J. (2008) Impairment of adolescent hippocampal plasticity in a mouse model for Alzheimer's disease precedes disease phenotype. PLoS ONE 3, e2759.
74. Martin, B., Brenneman, R., Becker, K. G., Gucek, M., Cole, R. N., and Maudsley, S. (2008) ITRAQ analysis of complex proteome alterations in 3xTgAD Alzheimer's mice: Understanding the interface between physiology and disease. PLoS ONE 3, e2750.
75. Vonsattel, J. P. (2008) Huntington disease models and human neuropathology: Similarities and differences. Acta Neuropathol. 115, 55-69.
76. Perluigi, M., Poon, H. F., Maragos, W., Pierce, W. M., Klein, J. B., Calabrese, V., Cini, C., De Marco, C., and Butterfield, D. A. (2005) Proteomic analysis of protein expression and oxidative modification in r6/2 transgenic mice: A model of Huntington disease. Mol. Cell. Proteomics 4, 1849-1861.
77. Chiang, M. C., Juo, C. G., Chang, H. H., Chen, H. M., Yi, E. C., and Chern, Y. (2007) Systematic uncovering of multiple pathways underlying the pathology of Huntington disease by an acid-cleavable isotope-coded affinity tag approach. Mol. Cell. Proteomics 6, 781-797.
78. Fasano, M., and Lopiano, L. (2008) Alphasynuclein and Parkinson's disease: A proteomic view. Expert Rev. Proteomics 5, 239-248.
79. Betarbet, R., Canet-Aviles, R. M., Sherer, T. B., Mastroberardino, P. G., McLendon, C., Kim, J. H., Lund, S., Na, H. M., Taylor, G., Bence, N. F., Kopito, R., Seo, B. B., Yagi, T., Yagi, A., Klinefelter, G., Cookson, M. R., and Greenamyre, J. T. (2006) Intersecting pathways to neurodegeneration in Parkinson's disease: Effects of the pesticide rotenone on DJ-1, alpha-synuclein, and the ubiquitin-proteasome system. Neurobiol. Dis. 22, 404-420.
80. Betarbet, R., Sherer, T. B., and Greenamyre, J. T. (2005) Ubiquitin-proteasome system and Parkinson's diseases. Exp. Neurol. 191, S17-S27.
81. Ichibangase, T., Saimaru, H., Takamura, N., Kuwahara, T., Koyama, A., Iwatsubo, T., and Imai, K. (2008) Proteomics of caenorhabditis elegans over-expressing human alpha-synuclein analyzed by fluorogenic derivatization-liquid chromatography/tandem mass spectrometry: Identification of actin and several ribosomal proteins as negative markers at early Parkinson's disease stages. Biomed. Chromatogr. 22, 232-234.
82. Zabel, C., Andreew, A., Mao, L., and Hartl, D. (2008) Protein expression overlap: More important than which proteins change in expression? Expert Rev. Proteomics 5, 187-205.
83. Tribl, F., Meyer, H. E., and Marcus, K. (2008) Analysis of organelles within the nervous system: Impact on brain and organelle functions. Expert Rev. Proteomics 5, 333-351.
84. Fasano, M., Giraudo, S., Coha, S., Bergamasco, B., and Lopiano, L. (2003) Residual substantia nigra neuromelanin in Parkinson's disease is cross-linked to alpha-synuclein. Neurochem. Int. 42, 603-606.
85. Halliday, G. M., Ophof, A., Broe, M., Jensen, P. H., Kettle, E., Fedorow, H., Cartwright, M. I., Griffiths, F. M., Shepherd, C. E., and Double, K. L. (2005) Alpha-synuclein redistributes to neuromelanin lipid in the substantia nigra early in Parkinson's disease. Brain 128, 2654-2664.
86. Stevens, S. M. Jr., Duncan, R. S., Koulen, P., and Prokai, L. (2008) Proteomic analysis of mouse brain microsomes: Identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system. J. Proteome Res. 7, 1046-1054.
87. Grant, K. J., and Wu, C. C. (2007) Advances in neuromembrane proteomics: Efforts towards a comprehensive analysis of membrane proteins in the brain. Brief Funct. Genomic Proteomic. 6, 59-69.
88. Macher, B. A., and Yen, T. Y. (2007) Proteins at membrane surfaces -a review of approaches. Mol. Biosyst. 3, 705-713.
89. Emes, R. D., Pocklington, A. J., Anderson, C. N., Bayes, A., Collins, M. O., Vickers, C. A., Croning, M. D., Malik, B. R., Choudhary, J. S., Armstrong, J. D., and Grant, S. G. (2008) Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nat. Neurosci. 11, 799-806.
90. Li, K. W., and Jimenez, C. R. (2008) Synapse proteomics: Current status and quantitative applications. Expert Rev. Proteomics 5, 353-360.
91. Bai, F., and Witzmann, F. A. (2007) Synaptosome proteomics. Subcell. Biochem. 43, 77-98.
92. Cheng, D., Hoogenraad, C. C., Rush, J., Ramm, E., Schlager, M. A., Duong, D. M., Xu, P., Wijayawardana, S. R., Hanfelt, J., Nakagawa, T., Sheng, M., and Peng, J. (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol. Cell. Proteomics 5, 1158-1170.
93. Liu, S. H., Cheng, H. H., Huang, S. Y., Yiu, P. C., and Chang, Y. C. (2006) Studying the protein organization of the postsynaptic density by a novel solid phase-and chemical cross-linking-based technology. Mol. Cell. Proteomics 5, 1019-1032.
94. Burre, J., Beckhaus, T., Schagger, H., Corvey, C., Hofmann, S., Karas, M., Zimmermann, H., and Volknandt, W. (2006) Analysis of the synaptic vesicle proteome using three gel-based protein separation techniques. Proteomics 6, 6250-6262.
95. Burre, J., Zimmermann, H., and Volknandt, W. (2007) Immunoisolation and subfractionation of synaptic vesicle proteins. Anal. Biochem. 362, 172-181.
96. Morciano, M., Burre, J., Corvey, C., Karas, M., Zimmermann, H., and Volknandt, W. (2005) Immunoisolation of two synaptic vesicle pools from synaptosomes: A proteomics analysis. J. Neurochem. 95, 1732-1745.
97. Dosemeci, A., Tao-Cheng, J. H., Vinade, L., and Jaffe, H. (2006) Preparation of postsynaptic density fraction from hippocampal slices and proteomic analysis. Biochem. Biophys. Res. Commun. 339, 687-694.
98. Trinidad, J. C., Specht, C. G., Thalhammer, A., Schoepfer, R., and Burlingame, A. L. (2006) Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol. Cell. Proteomics 5, 914-922.
99. Trinidad, J. C., Thalhammer, A., Specht, C. G., Lynn, A. J., Baker, P. R., Schoepfer, R., and Burlingame, A. L. (2008) Quantitative analysis of synaptic phosphorylation and protein expression. Mol. Cell. Proteomics 7, 684-696.
100. Vosseller, K., Trinidad, J. C., Chalkley, R. J., Specht, C. G., Thalhammer, A., Lynn, A. J., Snedecor, J. O., Guan, S., Medzihradszky, K. F., Maltby, D. A., Schoepfer, R., and Burlingame, A. L. (2006) O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol. Cell. Proteomics 5, 923-934.
101. Augustinack, J. C., Schneider, A., Mandelkow, E. M., and Hyman, B. T. (2002) Specific tau phosphorylation sites correlate with severity of neuronal cytopathology in Alzheimer's disease. Acta Neuropathol. 103, 26-35.
102. Hampel, H., Burger, K., Pruessner, J. C., Zinkowski, R., DeBernardis, J., Kerkman, D., Leinsinger, G., Evans, A. C., Davies, P., Moller, H. J., and Teipel, S. J. (2005) Correlation of cerebrospinal fluid levels of tau protein phosphorylated at threonine 231 with rates of hippocampal atrophy in Alzheimer disease. Arch. Neurol. 62, 770-773.
103. Cripps, D., Thomas, S. N., Jeng, Y., Yang, F., Davies, P., and Yang, A. J. (2006) Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation. J. Biol. Chem. 281, 10825-10838.
104. Butterfield, D. A., Reed, T., Newman, S. F., and Sultana, R. (2007) Roles of amyloid beta-peptide-associated oxidative stress and brain protein modifications in the pathogenesis of Alzheimer's disease and mild cognitive impairment. Free Radic. Biol. Med. 43, 658-677.
105. Zhan, X., and Desiderio, D. M. (2004) The human pituitary nitroproteome: Detection of nitrotyrosyl-proteins with two-dimensional western blotting, and amino acid sequence determination with mass spectrometry. Biochem. Biophys. Res. Commun. 325, 1180-1186.
106. Zhan, X., and Desiderio, D. M. (2006) Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry. Anal. Biochem. 354, 279-289.
107. Azarkan, M., Huet, J., Baeyens-Volant, D., Looze, Y., and Vandenbussche, G. (2007) Affinity chromatography: A useful tool in proteomics studies. J. Chromatogr. B. Analyt Technol. Biomed. Life. Sci. 849, 81-90.
108. Karlsson, K., Cairns, N., Lubec, G., and Fountoulakis, M. (1999) Enrichment of human brain proteins by heparin chromatography. Electrophoresis 20, 2970-2976.
109. Xiong, S., Zhang, L., and He, Q. Y. (2008) Fractionation of proteins by heparin chromatography. Methods Mol. Biol. 424, 213-221.
110. Abu-Farha, M., Elisma, F., and Figeys, D. (2008) Identification of protein-protein interactions by mass spectrometry coupled techniques. Adv. Biochem. Eng. Biotechnol. 110, 67-80.
111. Berggard, T., Linse, S., and James, P. (2007) Methods for the detection and analysis of protein-protein interactions. Proteomics 7, 2833-2842.
112. Zhang, Z., Ottens, A. K., Golden, E. C., Hayes, R. L., and Wang, K. K. (2006) Using calmodulin-affinity capture to study the rat brain calmodulin binding proteome and its vulnerability to calpain and caspase proteolysis. Calcium Binding Proteins 1, 125-134.
113. Klose, J. (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231-243.
114. O'Farrell, P. H. (1975) High resolution twodimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021.
115. Alban, A., David, S. O., Bjorkesten, L., Andersson, C., Sloge, E., Lewis, S., and Currie, I. (2003) A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 36-44.
116. Tannu, N. S., and Hemby, S. E. (2006) Methods for proteomics in neuroscience. Prog. Brain Res. 158, 41-82.
117. Shin, J. H., Krapfenbauer, K., and Lubec, G. (2006) Large-scale identification of cytosolic mouse brain proteins by chromatographic prefractionation. Electrophoresis 27, 2799-2813.
118. McDonald, W. H., and Yates, J. R. 3rd. (2002) Shotgun proteomics and biomarker discovery. Dis. Markers 18, 99-105.
119. Wolters, D. A., Washburn, M. P., and Yates, J. R. 3rd. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690.
120. Nakamura, T., Kuromitsu, J., and Oda, Y. (2008) Evaluation of comprehensive multidimensional separations using reversed-phase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics. J. Proteome Res. 7, 1007-1011.
121. Gilar, M., Olivova, P., Daly, A. E., and Gebler, J. C. (2005) Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J. Sep. Sci. 28, 1694-1703.
122. Righetti, P. G., Boschetti, E., Lomas, L., and Citterio, A. (2006) Protein equalizer technology: The quest for a "democratic proteome". Proteomics 6, 3980-3992.
123. Panchaud, A., Affolter, M., Moreillon, P., and Kussmann, M. (2008) Experimental and computational approaches to quantitative proteomics: Status quo and outlook. J. Proteomics 71, 19-33.
124. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999.
125. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951.
126. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386.
127. Yao, X., Freas, A., Ramirez, J., Demirev, P. A., and Fenselau, C. (2001) Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus. Anal. Chem. 73, 2836-2842.
128. Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K., and Hamon, C. (2003) Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904.
129. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169.
130. Zetterberg, H., Ruetschi, U., Portelius, E., Brinkmalm, G., Andreasson, U., Blennow, K., and Brinkmalm, A. (2008) Clinical proteomics in neurodegenerative disorders. Acta Neurol. Scand. 118, 1-11.
131. Hsich, G., Kenney, K., Gibbs, C. J., Lee, K. H., and Harrington, M. G. (1996) The 14-3-3 brain protein in cerebrospinal fluid as a marker for transmissible spongiform encephalopathies. N. Engl. J. Med. 335, 924-930.
132. Veenstra, T. D., and Marcus, K. (2008) Multidimensional advancement of neuroproteomics. Expert Rev. Proteomics 5, 149-151.
133. Takamori, S., Holt, M., Stenius, K., Lemke, E. A., Gronborg, M., Riedel, D., Urlaub, H., Schenck, S., Brugger, B., Ringler, P., Muller, S. A., Rammner, B., Grater, F., Hub, J. S., De Groot, B. L., Mieskes, G., Moriyama, Y., Klingauf, J., Grubmuller, H., Heuser, J., Wieland, F., and Jahn, R. (2006) Molecular anatomy of a trafficking organelle. Cell 127, 831-846.