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Proteomic Studies on the Development of the Central Nervous System and Beyond

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Abstract

Neuroproteomics has become a ‘symbol’ or even a ‘sign’ for neuroscientists in the post-genomic era. During the last several decades, a number of proteomic approaches have been used widely to decipher the complexity of the brain, including the study of embryonic stages of human or non-human animal brain development. The use of proteomic techniques has allowed for great scientific advancements, including the quantitative analysis of proteomic data using 2D-DIGE, ICAT and iTRAQ. In addition, proteomic studies of the brain have expanded into fields such as subproteomics, synaptoproteomics, neural plasma membrane proteomics and even mitochondrial proteomics. The rapid progress that has been made in this field will not only increase the knowledge based on the neuroproteomics of the developing brain but also help to increase the understanding of human neurological diseases. This paper will focus on proteomic studies in the central nervous system and especially those conducted on the development of the brain in order to summarize the advances in this rapidly developing field.

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References

  1. Choudhary J, Grant SG (2004) Proteomics in postgenomic neuroscience: the end of the beginning. Nat Neurosci 7(5):440–445

    Article  CAS  PubMed  Google Scholar 

  2. Becker M, Schindler J, Nothwang HG (2006) Neuroproteomics—the tasks lying ahead. Electrophoresis 27(13):2819–2829

    Article  CAS  PubMed  Google Scholar 

  3. Bayes A, Grant SG (2009) Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat Rev Neurosci 10(9):635–646

    Article  CAS  PubMed  Google Scholar 

  4. Svensson M, Skold K, Nilsson A, Falth M, Nydahl K, Svenningsson P, Andren PE (2007) Neuropeptidomics: MS applied to the discovery of novel peptides from the brain. Anal Chem 79(1):15–16–18–21

    Article  PubMed  Google Scholar 

  5. Andrade EC, Krueger DD, Nairn AC (2007) Recent advances in neuroproteomics. Curr Opin Mol Ther 9(3):270–281

    CAS  PubMed  Google Scholar 

  6. Shin JH, Krapfenbauer K, Lubec G (2005) Column chromatographic prefractionation leads to the detection of 543 different gene products in human fetal brain. Electrophoresis 26(14):2759–2778

    Article  CAS  PubMed  Google Scholar 

  7. Fountoulakis M, Juranville JF, Dierssen M, Lubec G (2002) Proteomic analysis of the fetal brain. Proteomics 2(11):1547–1576

    Article  CAS  PubMed  Google Scholar 

  8. Carrette O, Burkhard PR, Hochstrasser DF, Sanchez JC (2006) Age-related proteome analysis of the mouse brain: a 2-DE study. Proteomics 6(18):4940–4949

    Article  CAS  PubMed  Google Scholar 

  9. Chen W, Ji J, Xu X, He S, Ru B (2003) Proteomic comparison between human young and old brains by two-dimensional gel electrophoresis and identification of proteins. Int J Dev Neurosci 21(4):209–216

    CAS  PubMed  Google Scholar 

  10. Wang J, Gu Y, Wang L, Hang X, Gao Y, Wang H, Zhang C (2007) HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages. Proteomics 7(21):4008–4015

    Article  CAS  PubMed  Google Scholar 

  11. Seefeldt I, Nebrich G, Romer I, Mao L, Klose J (2006) Evaluation of 2-DE protein patterns from pre- and postnatal stages of the mouse brain. Proteomics 6(18):4932–4939

    Article  CAS  PubMed  Google Scholar 

  12. Yang S, Liu T, Li S, Zhang X, Ding Q, Que H, Yan X, Wei K, Liu S (2008) Comparative proteomic analysis of brains of naturally aging mice. Neuroscience 154(3):1107–1120

    Article  CAS  PubMed  Google Scholar 

  13. Hartl D, Irmler M, Romer I, Mader MT, Mao L, Zabel C, de Angelis MH, Beckers J, Klose J (2008) Transcriptome and proteome analysis of early embryonic mouse brain development. Proteomics 8(6):1257–1265

    Article  CAS  PubMed  Google Scholar 

  14. Tribl F, Marcus K, Bringmann G, Meyer HE, Gerlach M, Riederer P (2006) Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity. J Neural Transm 113(8):1041–1054

    Article  CAS  PubMed  Google Scholar 

  15. Van den Bergh G, Clerens S, Firestein BL, Burnat K, Arckens L (2006) Development and plasticity-related changes in protein expression patterns in cat visual cortex: a fluorescent two-dimensional difference gel electrophoresis approach. Proteomics 6(13):3821–3832

    Article  PubMed  CAS  Google Scholar 

  16. Baudet ML, Hassanali Z, Sawicki G, List EO, Kopchick JJ, Harvey S (2008) Growth hormone action in the developing neural retina: a proteomic analysis. Proteomics 8(2):389–401

    Article  CAS  PubMed  Google Scholar 

  17. Beranova-Giorgianni S, Pabst MJ, Russell TM, Giorgianni F, Goldowitz D, Desiderio DM (2002) Preliminary analysis of the mouse cerebellum proteome. Brain Res Mol Brain Res 98(1–2):135–140

    Article  CAS  PubMed  Google Scholar 

  18. Weitzdorfer R, Hoger H, Shim KS, Cekici L, Pollak A, Lubec G (2008) Changes of hippocampal signaling protein levels during postnatal brain development in the rat. Hippocampus 18(8):807–813

    Article  PubMed  Google Scholar 

  19. Chen P, Li X, Sun Y, Liu Z, Cao R, He Q, Wang M, Xiong J, Xie J, Wang X et al (2006) Proteomic analysis of rat hippocampal plasma membrane: characterization of potential neuronal-specific plasma membrane proteins. J Neurochem 98(4):1126–1140

    Article  CAS  PubMed  Google Scholar 

  20. McNair K, Davies CH, Cobb SR (2006) Plasticity-related regulation of the hippocampal proteome. Eur J Neurosci 23(2):575–580

    Article  PubMed  Google Scholar 

  21. Cobb SR, Pitt A (2008) Proteomics in the study of hippocampal plasticity. Expert Rev Proteomics 5(3):393–404

    Article  CAS  PubMed  Google Scholar 

  22. Romeo MJ, Espina V, Lowenthal M, Espina BH, Petricoin EF 3rd, Liotta LA (2005) CSF proteome: a protein repository for potential biomarker identification. Expert Rev Proteomics 2(1):57–70

    Article  CAS  PubMed  Google Scholar 

  23. Hale JE, Gelfanova V, You JS, Knierman MD, Dean RA (2008) Proteomics of cerebrospinal fluid: methods for sample processing. Methods Mol Biol 425:53–66

    Article  CAS  PubMed  Google Scholar 

  24. Zappaterra MD, Lisgo SN, Lindsay S, Gygi SP, Walsh CA, Ballif BA (2007) A comparative proteomic analysis of human and rat embryonic cerebrospinal fluid. J Proteome Res 6(9):3537–3548

    Article  CAS  PubMed  Google Scholar 

  25. Parada C, Gato A, Aparicio M, Bueno D (2006) Proteome analysis of chick embryonic cerebrospinal fluid. Proteomics 6(1):312–320

    Article  CAS  PubMed  Google Scholar 

  26. Parada C, Gato A, Bueno D (2005) Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. J Proteome Res 4(6):2420–2428

    Article  CAS  PubMed  Google Scholar 

  27. Blennow K, Hampel H, Weiner M, Zetterberg H (2010) Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat Rev Neurol 6(3):131–144

    Article  CAS  PubMed  Google Scholar 

  28. Raedler TJ, Wiedemann K (2006) CSF-studies in neuropsychiatric disorders. Neuro Endocrinol Lett 27(3):297–305

    CAS  PubMed  Google Scholar 

  29. Zhang J, Montine TJ (2007) Proteomic discovery of CSF biomarkers for Alzheimer’s disease. Ann Neurol 61(5):497 author reply 497–498

    Article  PubMed  Google Scholar 

  30. Guo J, Sun Z, Xiao S, Liu D, Jin G, Wang E, Zhou J (2009) Proteomic analysis of the cerebrospinal fluid of Parkinson’s disease patients. Cell Res 19(12):1401–1403

    Article  CAS  PubMed  Google Scholar 

  31. Thambisetty M, Lovestone S (2010) Blood-based biomarkers of Alzheimer’s disease: challenging but feasible. Biomark Med 4(1):65–79

    Article  CAS  PubMed  Google Scholar 

  32. Blakeley P, Siepen JA, Lawless C, Hubbard SJ (2010) Investigating protein isoforms via proteomics: a feasibility study. Proteomics 10(6):1127–1140

    Article  CAS  PubMed  Google Scholar 

  33. Stoop MP, Lamers RJ, Burgers PC, Sillevis Smitt PA, Hintzen RQ, Luider TM (2008) The rate of false positive sequence matches of peptides profiled by MALDI MS and identified by MS/MS. J Proteome Res 7(11):4841–4847

    Article  CAS  PubMed  Google Scholar 

  34. Portelius E, Dean RA, Gustavsson MK, Andreasson U, Zetterberg H, Siemers E, Blennow K (2010) A novel Abeta isoform pattern in CSF reflects gamma-secretase inhibition in Alzheimer disease. Alzheimers Res Ther 2(2):7

    Article  PubMed  CAS  Google Scholar 

  35. Westman-Brinkmalm A, Ruetschi U, Portelius E, Andreasson U, Brinkmalm G, Karlsson G, Hansson S, Zetterberg H, Blennow K (2009) Proteomics/peptidomics tools to find CSF biomarkers for neurodegenerative diseases. Front Biosci 14:1793–1806

    Article  CAS  PubMed  Google Scholar 

  36. D’Aguanno S, Del Boccio P, Bernardini S, Ballone E, Di Ilio C, Federici G, Urbani A (2007) Electrophoretic separations of cerebrospinal fluid proteins in clinical investigations. Clin Chem Lab Med 45(4):437–449

    Article  PubMed  CAS  Google Scholar 

  37. Verhoeven NM, Guerand WS, Struys EA, Bouman AA, van der Knaap MS, Jakobs C (2000) Plasma creatinine assessment in creatine deficiency: A diagnostic pitfall. J Inherit Metab Dis 23(8):835–840

    Article  CAS  PubMed  Google Scholar 

  38. Skalnikova H, Vodicka P, Gadher SJ, Kovarova H (2008) Proteomics of neural stem cells. Expert Rev Proteomics 5(2):175–186

    Article  CAS  PubMed  Google Scholar 

  39. Chae JI, Kim J, Woo SM, Han HW, Cho YK, Oh KB, Nam KH, Kang YK (2009) Cytoskeleton-associated proteins are enriched in human embryonic-stem cell-derived neuroectodermal spheres. Proteomics 9(5):1128–1141

    Article  CAS  PubMed  Google Scholar 

  40. Akama K, Tatsuno R, Otsu M, Horikoshi T, Nakayama T, Nakamura M, Toda T, Inoue N (2008) Proteomic identification of differentially expressed genes in mouse neural stem cells and neurons differentiated from embryonic stem cells in vitro. Biochim Biophys Acta 1784(5):773–782

    CAS  PubMed  Google Scholar 

  41. Li KW, Jimenez CR (2008) Synapse proteomics: current status and quantitative applications. Expert Rev Proteomics 5(2):353–360

    Article  CAS  PubMed  Google Scholar 

  42. Grant SG (2006) The synapse proteome and phosphoproteome: a new paradigm for synapse biology. Biochem Soc Trans 34(Pt 1):59–63

    CAS  PubMed  Google Scholar 

  43. McClatchy DB, Liao L, Park SK, Venable JD, Yates JR (2007) Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res 17(9):1378–1388

    Article  CAS  PubMed  Google Scholar 

  44. Bai F, Witzmann FA (2007) Synaptosome proteomics. Subcell Biochem 43:77–98

    Article  PubMed  Google Scholar 

  45. Dencher NA, Goto S, Reifschneider NH, Sugawa M, Krause F (2006) Unraveling age-dependent variation of the mitochondrial proteome. Ann N Y Acad Sci 1067:116–119

    Article  CAS  PubMed  Google Scholar 

  46. Nielsen PA, Olsen JV, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR (2005) Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 4(4):402–408

    Article  CAS  PubMed  Google Scholar 

  47. Lu A, Wisniewski JR, Mann M (2009) Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve. J Proteome Res 8(5):2418–2425

    Article  CAS  PubMed  Google Scholar 

  48. Pottiez G, Flahaut C, Cecchelli R, Karamanos Y (2009) Understanding the blood-brain barrier using gene and protein expression profiling technologies. Brain Res Rev 62(1):83–98

    Article  CAS  PubMed  Google Scholar 

  49. Pardridge WM (2003) Molecular biology of the blood-brain barrier. Methods Mol Med 89:385–399

    CAS  PubMed  Google Scholar 

  50. Pardridge WM (2005) Molecular biology of the blood-brain barrier. Mol Biotechnol 30(1):57–70

    Article  CAS  PubMed  Google Scholar 

  51. Calabria AR, Shusta EV (2006) Blood-brain barrier genomics and proteomics: elucidating phenotype, identifying disease targets and enabling brain drug delivery. Drug Discov Today 11(17–18):792–799

    Article  CAS  PubMed  Google Scholar 

  52. Shin JH, Krapfenbauer K, Lubec G (2006) Mass-spectrometrical analysis of proteins encoded on chromosome 21 in human fetal brain. Amino Acids 31(4):435–447

    Article  CAS  PubMed  Google Scholar 

  53. Pollak DD, John J, Hoeger H, Lubec G (2006) An integrated map of the murine hippocampal proteome based upon five mouse strains. Electrophoresis 27(13):2787–2798

    Article  CAS  PubMed  Google Scholar 

  54. Saiga T, Fukuda T, Matsumoto M, Tada H, Okano HJ, Okano H, Nakayama KI (2009) Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development. Mol Cell Biol 29(13):3529–3543

    Article  CAS  PubMed  Google Scholar 

  55. Jin K, Mao XO, Cottrell B, Schilling B, Xie L, Row RH, Sun Y, Peel A, Childs J, Gendeh G et al (2004) Proteomic and immunochemical characterization of a role for stathmin in adult neurogenesis. FASEB J 18(2):287–299

    Article  CAS  PubMed  Google Scholar 

  56. Svensson M, Skold K, Nilsson A, Falth M, Svenningsson P, Andren PE (2007) Neuropeptidomics: expanding proteomics downwards. Biochem Soc Trans 35(Pt 3):588–593

    CAS  PubMed  Google Scholar 

  57. Kim SI, Voshol H, van Oostrum J, Hastings TG, Cascio M, Glucksman MJ (2004) Neuroproteomics: expression profiling of the brain’s proteomes in health and disease. Neurochem Res 29(6):1317–1331

    Article  CAS  PubMed  Google Scholar 

  58. Fountoulakis M, Kossida S (2006) Proteomics-driven progress in neurodegeneration research. Electrophoresis 27(8):1556–1573

    Article  CAS  PubMed  Google Scholar 

  59. Kolla V, Jeno P, Moes S, Tercanli S, Lapaire O, Choolani M, Hahn S (2010) Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ). J Biomed Biotechnol 952047

  60. Muntane G, Dalfo E, Martinez A, Rey MJ, Avila J, Perez M, Portero M, Pamplona R, Ayala V, Ferrer I (2006) Glial fibrillary acidic protein is a major target of glycoxidative and lipoxidative damage in Pick’s disease. J Neurochem 99(1):177–185

    Article  CAS  PubMed  Google Scholar 

  61. Srivastava G, Singh K, Tiwari MN, Singh MP (2010) Proteomics in Parkinson’s disease: current trends, translational snags and future possibilities. Expert Rev Proteomics 7(1):127–139

    Article  CAS  PubMed  Google Scholar 

  62. van Dijk KD, Teunissen CE, Drukarch B, Jimenez CR, Groenewegen HJ, Berendse HW, van de Berg WD (2010) Diagnostic cerebrospinal fluid biomarkers for Parkinson’s disease: a pathogenetically based approach. Neurobiol Dis

  63. Baloyianni N, Tsangaris GT (2009) The audacity of proteomics: a chance to overcome current challenges in schizophrenia research. Expert Rev Proteomics 6(6):661–674

    Article  PubMed  Google Scholar 

  64. Jiang L, Lindpaintner K, Li HF, Gu NF, Langen H, He L, Fountoulakis M (2003) Proteomic analysis of the cerebrospinal fluid of patients with schizophrenia. Amino Acids 25(1):49–57

    CAS  PubMed  Google Scholar 

  65. Lakhan SE (2006) Schizophrenia proteomics: biomarkers on the path to laboratory medicine? Diagn Pathol 1:11

    Article  PubMed  CAS  Google Scholar 

  66. Thaker GK, Carpenter WT Jr (2001) Advances in schizophrenia. Nat Med 7(6):667–671

    Article  CAS  PubMed  Google Scholar 

  67. Hye A, Lynham S, Thambisetty M, Causevic M, Campbell J, Byers HL, Hooper C, Rijsdijk F, Tabrizi SJ, Banner S et al (2006) Proteome-based plasma biomarkers for Alzheimer’s disease. Brain 129(Pt 11):3042–3050

    Article  CAS  PubMed  Google Scholar 

  68. Blennow K (2005) CSF biomarkers for Alzheimer’s disease: use in early diagnosis and evaluation of drug treatment. Expert Rev Mol Diagn 5(5):661–672

    Article  CAS  PubMed  Google Scholar 

  69. German DC, Gurnani P, Nandi A, Garner HR, Fisher W, Diaz-Arrastia R, O’Suilleabhain P, Rosenblatt KP (2007) Serum biomarkers for Alzheimer’s disease: proteomic discovery. Biomed Pharmacother 61(7):383–389

    Article  CAS  PubMed  Google Scholar 

  70. Kovacech B, Zilka N, Novak M (2009) New age of neuroproteomics in Alzheimer’s disease research. Cell Mol Neurobiol 29(6–7):799–805

    Article  CAS  PubMed  Google Scholar 

  71. Butterfield DA, Boyd-Kimball D, Castegna A (2003) Proteomics in Alzheimer’s disease: insights into potential mechanisms of neurodegeneration. J Neurochem 86(6):1313–1327

    Article  CAS  PubMed  Google Scholar 

  72. Lovestone S, Guntert A, Hye A, Lynham S, Thambisetty M, Ward M (2007) Proteomics of Alzheimer’s disease: understanding mechanisms and seeking biomarkers. Expert Rev Proteomics 4(2):227–238

    Article  CAS  PubMed  Google Scholar 

  73. Korolainen MA, Nyman TA, Aittokallio T, Pirttila T (2010) An update on clinical proteomics in Alzheimer’s research. J Neurochem 112(6):1386–1414

    Article  CAS  PubMed  Google Scholar 

  74. Holsboer F (2008) How can we realize the promise of personalized antidepressant medicines? Nat Rev Neurosci 9(8):638–646

    Article  CAS  PubMed  Google Scholar 

  75. Ottervald J, Franzen B, Nilsson K, Andersson LI, Khademi M, Eriksson B, Kjellstrom S, Marko-Varga G, Vegvari A, Harris RA et al. (2010) Multiple sclerosis: Identification and clinical evaluation of novel CSF biomarkers. J Proteomics 73(6):1117–1132

    Article  CAS  PubMed  Google Scholar 

  76. Stoop MP, Dekker LJ, Titulaer MK, Burgers PC, Sillevis Smitt PA, Luider TM, Hintzen RQ (2008) Multiple sclerosis-related proteins identified in cerebrospinal fluid by advanced mass spectrometry. Proteomics 8(8):1576–1585

    Article  CAS  PubMed  Google Scholar 

  77. Sultana R, Poon HF, Cai J, Pierce WM, Merchant M, Klein JB, Markesbery WR, Butterfield DA (2006) Identification of nitrated proteins in Alzheimer’s disease brain using a redox proteomics approach. Neurobiol Dis 22(1):76–87

    Article  CAS  PubMed  Google Scholar 

  78. Butterfield DA, Perluigi M, Sultana R (2006) Oxidative stress in Alzheimer’s disease brain: new insights from redox proteomics. Eur J Pharmacol 545(1):39–50

    Article  CAS  PubMed  Google Scholar 

  79. Sultana R, Boyd-Kimball D, Poon HF, Cai J, Pierce WM, Klein JB, Merchant M, Markesbery WR, Butterfield DA (2006) Redox proteomics identification of oxidized proteins in Alzheimer’s disease hippocampus and cerebellum: an approach to understand pathological and biochemical alterations in AD. Neurobiol Aging 27(11):1564–1576

    Article  CAS  PubMed  Google Scholar 

  80. Butterfield DA, Gnjec A, Poon HF, Castegna A, Pierce WM, Klein JB, Martins RN (2006) Redox proteomics identification of oxidatively modified brain proteins in inherited Alzheimer’s disease: an initial assessment. J Alzheimers Dis 10(4):391–397

    CAS  PubMed  Google Scholar 

  81. Sultana R, Perluigi M, Butterfield DA (2006) Redox proteomics identification of oxidatively modified proteins in Alzheimer’s disease brain and in vivo and in vitro models of AD centered around Abeta (1–42). J Chromatogr B Analyt Technol Biomed Life Sci 833(1):3–11

    Article  CAS  PubMed  Google Scholar 

  82. Martins-de-Souza D, Harris LW, Guest PC, Turck CW, Bahn S (2009) The role of proteomics in depression research. Eur Arch Psychiatry Clin Neurosci, 2009 Dec 9 [Epub ahead of print]

  83. Taurines R, Dudley E, Grassl J, Warnke A, Gerlach M, Coogan AN, Thome J (2010) Proteomic research in psychiatry. J Psychopharmacol, 2010 Feb 16 [Epub ahead of print]

  84. Portelius E, Zetterberg H, Gobom J, Andreasson U, Blennow K (2008) Targeted proteomics in Alzheimer’s disease: focus on amyloid-beta. Expert Rev Proteomics 5(2):225–237

    Article  CAS  PubMed  Google Scholar 

  85. Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q et al (2005) Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J Alzheimers Dis 7(2):125–133 discussion 173–180

    CAS  PubMed  Google Scholar 

  86. Lakhan SE, Kramer A (2009) Schizophrenia genomics and proteomics: are we any closer to biomarker discovery? Behav Brain Funct 5:2

    Article  PubMed  CAS  Google Scholar 

  87. Stevens SM Jr, Zharikova AD, Prokai L (2003) Proteomic analysis of the synaptic plasma membrane fraction isolated from rat forebrain. Brain Res Mol Brain Res 117(2):116–128

    Article  CAS  PubMed  Google Scholar 

  88. Li KW, Smit AB (2008) Subcellular proteomics in neuroscience. Front Biosci 13:4416–4425

    Article  CAS  PubMed  Google Scholar 

  89. Tannu NS, Hemby SE (2006) Methods for proteomics in neuroscience. Prog Brain Res 158:41–82

    Article  CAS  PubMed  Google Scholar 

  90. Garbis S, Lubec G, Fountoulakis M (2005) Limitations of current proteomics technologies. J Chromatogr A 1077(1):1–18

    Article  CAS  PubMed  Google Scholar 

  91. Olsen JV, Nielsen PA, Andersen JR, Mann M, Wisniewski JR (2007) Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels. Brain Res 1134(1):95–106

    Article  CAS  PubMed  Google Scholar 

  92. Lemaire R, Stauber J, Wisztorski M, Van Camp C, Desmons A, Deschamps M, Proess G, Rudlof I, Woods AS, Day R et al (2007) Tag-mass: specific molecular imaging of transcriptome and proteome by mass spectrometry based on photocleavable tag. J Proteome Res 6(6):2057–2067

    Article  CAS  PubMed  Google Scholar 

  93. Yang ZJ, Appleby VJ, Coyle B, Chan WI, Tahmaseb M, Wigmore PM, Scotting PJ (2004) Novel strategy to study gene expression and function in developing cerebellar granule cells. J Neurosci Methods 132(2):149–160

    Article  CAS  PubMed  Google Scholar 

  94. Ericsson C, Peredo I, Nister M (2007) Optimized protein extraction from cryopreserved brain tissue samples. Acta Oncol 46(1):10–20

    Article  CAS  PubMed  Google Scholar 

  95. Irmler M, Hartl D, Schmidt T, Schuchhardt J, Lach C, Meyer HE, Hrabe de Angelis M, Klose J, Beckers J (2008) An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons. Proteomics 8(6):1165–1169

    Article  CAS  PubMed  Google Scholar 

  96. Deighton RF, Short DM, McGregor RJ, Gow AJ, Whittle IR, McCulloch J (2009) The utility of functional interaction and cluster analysis in CNS proteomics. J Neurosci Methods 180(2):321–329

    Article  CAS  PubMed  Google Scholar 

  97. Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H (2008) PRIDE: new developments and new datasets. Nucleic Acids Res 36(Database issue):D878–883

    Google Scholar 

  98. Schuchhardt J, Glintschert A, Hartl D, Irmler M, Beckers J, Stephan C, Marcus K, Klose J, Meyer HE, Malik A (2008) BrainProfileDB - a platform for integration of functional genomics data. Proteomics 8(6):1162–1164

    Article  CAS  PubMed  Google Scholar 

  99. Hamacher M, Stephan C, Eisenacher M, Hardt T, Marcus K, Meyer HE (2008) Maintaining standardization: an update of the HUPO Brain Proteome Project. Expert Rev Proteomics 5(2):165–173

    Article  PubMed  Google Scholar 

  100. Reidegeld KA, Muller M, Stephan C, Bluggel M, Hamacher M, Martens L, Korting G, Chamrad DC, Parkinson D, Apweiler R et al (2006) The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics 6(18):4997–5014

    Article  CAS  PubMed  Google Scholar 

  101. Bluggel M, Bailey S, Korting G, Stephan C, Reidegeld KA, Thiele H, Apweiler R, Hamacher M, Meyer HE (2004) Towards data management of the HUPO Human Brain Proteome Project pilot phase. Proteomics 4(8):2361–2362

    Article  PubMed  CAS  Google Scholar 

  102. Hamacher M, Apweiler R, Arnold G, Becker A, Bluggel M, Carrette O, Colvis C, Dunn MJ, Frohlich T, Fountoulakis M et al (2006) HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics 6(18):4890–4898

    Article  CAS  PubMed  Google Scholar 

  103. Hamacher M, Marcus K, van Hall A, Meyer HE, Stephan C (2006) The HUPO Brain Proteome Project–no need to hurry? J Neural Transm 113(8):963–971

    Article  CAS  PubMed  Google Scholar 

  104. Hamacher M, Meyer HE (2005) HUPO Brain Proteome Project: aims and needs in proteomics. Expert Rev Proteomics 2(1):1–3

    Article  PubMed  Google Scholar 

  105. Hamacher M, Marcus K, Stephan C, Klose J, Park YM, Meyer HE (2008) HUPO Brain Proteome Project: toward a code of conduct. Mol Cell Proteomics 7(2):457

    CAS  PubMed  Google Scholar 

  106. Stuhler K, Pfeiffer K, Joppich C, Stephan C, Jung K, Muller M, Schmidt O, van Hall A, Hamacher M, Urfer W et al (2006) Pilot study of the Human Proteome Organisation Brain Proteome Project: applying different 2-DE techniques to monitor proteomic changes during murine brain development. Proteomics 6(18):4899–4913

    Article  PubMed  CAS  Google Scholar 

  107. Focking M, Boersema PJ, O’Donoghue N, Lubec G, Pennington SR, Cotter DR, Dunn MJ (2006) 2-D DIGE as a quantitative tool for investigating the HUPO Brain Proteome Project mouse series. Proteomics 6(18):4914–4931

    Article  CAS  PubMed  Google Scholar 

  108. Mueller M, Martens L, Reidegeld KA, Hamacher M, Stephan C, Bluggel M, Korting G, Chamrad D, Scheer C, Marcus K et al (2006) Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. Proteomics 6(18):5059–5075

    Article  CAS  PubMed  Google Scholar 

  109. Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Muller M, Apweiler R, Martens L et al (2006) Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics 6(18):5015–5029

    Article  CAS  PubMed  Google Scholar 

  110. Dowsey AW, English J, Pennington K, Cotter D, Stuehler K, Marcus K, Meyer HE, Dunn MJ, Yang GZ (2006) Examination of 2-DE in the Human Proteome Organisation Brain Proteome Project pilot studies with the new RAIN gel matching technique. Proteomics 6(18):5030–5047

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We wish to thank the anonymous reviewers for their valuable suggestions for this manuscript. This work is supported by the National Basic Research Project (973 program) (2006CB504100), The National Key Technologies R&D Program for New Drugs (2009ZX09103-616, 2009ZX09503-002, 2009ZX09301-002), General Program (30900830, 30973107, 30800196, 30772293) of General Program of National Natural Science Foundation of China, Major Program for Science and Technology Research of Beijing Municipal Bureau (7061004).

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Correspondence to Chenggang Zhang.

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Zhang, C. Proteomic Studies on the Development of the Central Nervous System and Beyond. Neurochem Res 35, 1487–1500 (2010). https://doi.org/10.1007/s11064-010-0218-z

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