Quantitative Neuroproteomics: Classical and Novel Tools for Studying Neural Differentiation and Function

详细信息    查看全文

• 作者：Luca Colucci-D’Amato (1) (2)
  Annarita Farina (3)
  Johannes P. C. Vissers (4)
  Angela Chambery (1)
  
• 关键词：Neuroproteomics ; Neural differentiation ; Mass spectrometry ; 2DE (2D ; PAGE) ; MALDI ; TOF ; LC ; MS ; Label ; free ; Isotopic labeling ; Proteomic profiling ; Neurodegeneration
• 刊名：Stem Cell Reviews and Reports
• 出版年：2011
• 出版时间：March 2011
• 年：2011
• 卷：7
• 期：1
• 页码：77-93
• 全文大小：641KB
• 参考文献：1. Schurov, I. L., Handford, E. J., Brandon, N. J., & Whiting, P. J. (2004). Expression of disrupted in schizophrenia 1 (DISC1) protein in the adult and developing mouse brain indicates its role in neurodevelopment. / Molecular Psychiatry, 9, 1100-110.
  2. Dranovsky, A., & Hen, R. (2007). DISC1 puts the brakes on neurogenesis. / Cell, 130, 981-83.
  3. Mackie, S., Millar, J. K., & Porteous, D. J. (2007). Role of DISC1 in neural development and schizophrenia. / Current Opinion in Neurobiology, 17, 95-02.
  4. Leo, D., Sorrentino, E., Volpicelli, F., et al. (2003). Altered midbrain dopaminergic neurotransmission during development in an animal model of ADHD. / Neuroscience and Biobehavioral Reviews, 27, 661-69.
  5. Pouget, P., Wattiez, N., Rivaud-Pechoux, S., & Gaymard, B. (2009). A fragile balance: Perturbation of GABA mediated circuit in prefrontal cortex generates high intraindividual performance variability. / PLoS ONE, 4, e5208.
  6. Calegari, F., & Huttner, W. B. (2003). An inhibition of cyclin-dependent kinases that lengthens, but does not arrest, neuroepithelial cell cycle induces premature neurogenesis. / Journal of Cell Science, 116, 4947-955.
  7. Wang, W., Bu, B., Xie, M., Zhang, M., Yu, Z., & Tao, D. (2009). Neural cell cycle dysregulation and central nervous system diseases. / Progress in Neurobiology, 89, 1-7.
  8. Greene, L. A., & Tischler, A. S. (1976). Establishment of a noradrenergic clonal line of rat adrenal pheochromocytoma cells which respond to nerve growth factor. / Proceedings of the National Academy of Sciences of the United States of America, 73, 2424-428.
  9. Huang, E. J., & Reichardt, L. F. (2001). Neurotrophins: Roles in neuronal development and function. / Annual Review of Neuroscience, 24, 677-36.
  10. Aebersold, R., Rist, B., & Gygi, S. P. (2000). Quantitative proteome analysis: Methods and applications. / Annals of the New York Academy of Sciences, 919, 33-7.
  11. Gygi, S. P., & Aebersold, R. (2000). Mass spectrometry and proteomics. / Current Opinion in Chemical Biology, 4, 489-94.
  12. Hoffrogge, R., Beyer, S., Volker, U., Uhrmacher, A. M., & Rolfs, A. (2006). 2-DE proteomic profiling of neuronal stem cells. / Neuro-degenerative Diseases, 3, 112-21.
  13. Bottcher, T., Mix, E., Koczan, D., et al. (2003). Gene expression profiling of ciliary neurotrophic factor-overexpressing rat striatal progenitor cells (ST14A) indicates improved stress response during the early stage of differentiation. / Journal of Neuroscience Research, 73, 42-3.
  14. Kwak, D. H., Yu, K., Kim, S. M., et al. (2006). Dynamic changes of gangliosides expression during the differentiation of embryonic and mesenchymal stem cells into neural cells. / Experimental and Molecular Medicine, 38, 668-76.
  15. Gygi, S. P., Rochon, Y., Franza, B. R., & Aebersold, R. (1999). Correlation between protein and mRNA abundance in yeast. / Molecular and Cellular Biology, 19, 1720-730.
  16. Becker, M., Schindler, J., & Nothwang, H. G. (2006). Neuroproteomics-- the tasks lying ahead. / Electrophoresis, 27, 2819-829.
  17. Andrade, E. C., Krueger, D. D., & Nairn, A. C. (2007). Recent advances in neuroproteomics. / Current Opinion in Molecular Therapeutics, 9, 270-81.
  18. Beyer, S., Mix, E., Hoffrogge, R., Lünser, K., V?lker, U., & Rolfs, A. (2007). Neuroproteomics in stem cell differentiation. / Proteomics Clinical Applications, 1, 1513-523.
  19. Butcher, J. (2007). Neuroproteomics comes of age. / Lancet Neurology, 6, 850-51.
  20. Maurer, M. H., Feldmann, R. E., Jr., Futterer, C. D., & Kuschinsky, W. (2003). The proteome of neural stem cells from adult rat hippocampus. / Proteome Science, 1, 4.
  21. Maurer, M. H., Feldmann, R. E., Jr., Futterer, C. D., Butlin, J., & Kuschinsky, W. (2004). Comprehensive proteome expression profiling of undifferentiated versus differentiated neural stem cells from adult rat hippocampus. / Neurochemical Research, 29, 1129-144.
  22. Dahl, A., Eriksson, P. S., Persson, A. I., et al. (2003). Proteome analysis of conditioned medium from cultured adult hippocampal progenitors. / Rapid Communications in Mass Spectrometry, 17, 2195-202.
  23. Ianora, A., Miralto, A., Poulet, S. A., et al. (2004). Aldehyde suppression of copepod recruitment in blooms of a ubiquitous planktonic diatom. / Nature, 429, 403-07.
  24. Di Lieto, A., Leo, D., Volpicelli, F., di Porzio, U., & Colucci-D’Amato, L. (2007). FLUOXETINE modifies the expression of serotonergic markers in a differentiation-dependent fashion in the mesencephalic neural cell line A1 mes c-myc. / Brain Research, 1143, 1-0.
  25. Baharvand, H., Hajheidari, M., Ashtiani, S. K., & Salekdeh, G. H. (2006). Proteomic signature of human embryonic stem cells. / Proteomics, 6, 3544-549.
  26. Baharvand, H., Hajheidari, M., Zonouzi, R., Ashtiani, S. K., Hosseinkhani, S., & Salekdeh, G. H. (2006). Comparative proteomic analysis of mouse embryonic stem cells and neonatal-derived cardiomyocytes. / Biochemical and Biophysical Research Communications, 349, 1041-049.
  27. Hoffrogge, R., Mikkat, S., Scharf, C., et al. (2006). 2-DE proteome analysis of a proliferating and differentiating human neuronal stem cell line (ReNcell VM). / Proteomics, 6, 1833-847.
  28. Hoffrogge, R., Beyer, S., Hubner, R., et al. (2007). 2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells. / Proteomics, 7, 33-6.
  29. An, J., Yuan, Q., Wang, C., et al. (2005). Differential display of proteins involved in the neural differentiation of mouse embryonic carcinoma P19 cells by comparative proteomic analysis. / Proteomics, 5, 1656-668.
  30. Inberg, A., Bogoch, Y., Bledi, Y., & Linial, M. (2007). Cellular processes underlying maturation of P19 neurons: Changes in protein folding regimen and cytoskeleton organization. / Proteomics, 7, 910-20.
  31. Chambery, A., Colucci-D’Amato, L., Vissers, J. P., Scarpella, S., Langridge, J. I., & Parente, A. (2009). Proteomic profiling of proliferating and differentiated neural mes-c-myc A1 cell line from mouse embryonic mesencephalon by LC-MS. / Journal of Proteome Research, 8, 227-38.
  32. Colucci-D’Amato, G. L., Tino, A., Pernas-Alonso, R., ffrench-Mullen, J. M., & di Porzio, U. (1999). Neuronal and glial properties coexist in a novel mouse CNS immortalized cell line. / Experimental Cell Research, 252, 383-91.
  33. Watkins, J., Basu, S., & Bogenhagen, D. F. (2008). A quantitative proteomic analysis of mitochondrial participation in p19 cell neuronal differentiation. / Journal of Proteome Research, 7, 328-38.
  34. Au, C. E., Bell, A. W., Gilchrist, A., Hiding, J., Nilsson, T., & Bergeron, J. J. (2007). Organellar proteomics to create the cell map. / Current Opinion in Cell Biology, 19, 376-85.
  35. Li, K. W., & Smit, A. B. (2008). Subcellular proteomics in neuroscience. / Frontiers in Bioscience, 13, 4416-425.
  36. Blondeau, F., Ritter, B., Allaire, P. D., et al. (2004). Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. / Proceedings of the National Academy of Sciences of the United States of America, 101, 3833-838.
  37. Coughenour, H. D., Spaulding, R. S., & Thompson, C. M. (2004). The synaptic vesicle proteome: A comparative study in membrane protein identification. / Proteomics, 4, 3141-155.
  38. Li, K. W. (2007). Proteomics of synapse. / Analytical and Bioanalytical Chemistry, 387, 25-8.
  39. Huttner, W. B., Schiebler, W., Greengard, P., & De Camilli, P. (1983). Synapsin I (protein I), a nerve terminal-specific phosphoprotein. III. Its association with synaptic vesicles studied in a highly purified synaptic vesicle preparation. / Journal of Cell Biology, 96, 1374-388.
  40. Hartinger, J., Stenius, K., Hogemann, D., & Jahn, R. (1996). 16-BAC/SDS-PAGE: A two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. / Analytical Biochemistry, 240, 126-33.
  41. Burre, J., Zimmermann, H., & Volknandt, W. (2007). Immunoisolation and subfractionation of synaptic vesicle proteins. / Analytical Biochemistry, 362, 172-81.
  42. Witzmann, F. A., Arnold, R. J., Bai, F., et al. (2005). A proteomic survey of rat cerebral cortical synaptosomes. / Proteomics, 5, 2177-201.
  43. Schrimpf, S. P., Meskenaite, V., Brunner, E., et al. (2005). Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. / Proteomics, 5, 2531-541.
  44. Godovac-Zimmermann, J., & Brown, L. R. (2001). Perspectives for mass spectrometry and functional proteomics. / Mass Spectrometry Reviews, 20, 1-7.
  45. Kriegsheim, A., Preisinger, C., & Kolch, W. (2008). Mapping of signaling pathways by functional interaction proteomics. / Methods in Molecular Biology, 484, 177-92.
  46. Colucci-D’Amato, L., Perrone-Capano, C., & di Porzio, U. (2003). Chronic activation of ERK and neurodegenerative diseases. / Bioessays, 25, 1085-095.
  47. Dowell, J. A., Johnson, J. A., & Li, L. (2009). Identification of astrocyte secreted proteins with a combination of shotgun proteomics and bioinformatics. / Journal of Proteome Research, 8, 4135-143.
  48. Schubert, D., Herrera, F., Cumming, R., et al. (2009). Neural cells secrete a unique repertoire of proteins. / Journal of Neurochemistry, 109, 427-35.
  49. Mor-Vaknin, N., Punturieri, A., Sitwala, K., & Markovitz, D. M. (2003). Vimentin is secreted by activated macrophages. / Nature Cell Biology, 5, 59-3.
  50. Tytell, M. (2005). Release of heat shock proteins (Hsps) and the effects of extracellular Hsps on neural cells and tissues. / International Journal of Hyperthermia, 21, 445-55.
  51. Johnson, M. D., Yu, L. R., Conrads, T. P., et al. (2005). The proteomics of neurodegeneration. / American Journal of Pharmacogenomics, 5, 259-70.
  52. Sun, F., & Cavalli, V. (2009). Neuroproteomics: Towards understanding neuronal regeneration and degeneration. / Molecular & Cellular Proteomics.
  53. Perrin, R. J., Fagan, A. M., & Holtzman, D. M. (2009). Multimodal techniques for diagnosis and prognosis of Alzheimer’s disease. / Nature, 461, 916-22.
  54. Zetterberg, H., Ruetschi, U., Portelius, E., et al. (2008). Clinical proteomics in neurodegenerative disorders. / Acta Neurologica Scandinavica, 118, 1-1.
  55. Han, M. H., Hwang, S. I., Roy, D. B., et al. (2008). Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. / Nature, 451, 1076-081.
  56. Noorbakhsh, F., Overall, C. M., & Power, C. (2009). Deciphering complex mechanisms in neurodegenerative diseases: The advent of systems biology. / Trends in Neurosciences, 32, 88-00.
  57. Wilkins, M. R., Pasquali, C., Appel, R. D., et al. (1996). From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. / Biotechnology (N Y), 14, 61-5.
  58. Gorg, A., Boguth, G., Obermaier, C., Posch, A., & Weiss, W. (1995). Two-dimensional polyacrylamide gel electrophoresis with immobilized pH gradients in the first dimension (IPG-Dalt): The state of the art and the controversy of vertical versus horizontal systems. / Electrophoresis, 16, 1079-086.
  59. Gorg, A., Drews, O., Luck, C., Weiland, F., & Weiss, W. (2009). 2-DE with IPGs. / Electrophoresis, 30(Suppl 1), S122–S132.
  60. Altland, K., Becher, P., Rossmann, U., & Bjellqvist, B. (1988). Isoelectric focusing of basic proteins: The problem of oxidation of cysteines. / Electrophoresis, 9, 474-85.
  61. Smejkal, G. B. (2006). The promise of gel-based proteomics. / Expert Opinion on Drug Discovery, 1, 7-0.
  62. Vercauteren, F. G., Arckens, L., & Quirion, R. (2007). Applications and current challenges of proteomic approaches, focusing on two-dimensional electrophoresis. / Amino Acids, 33, 405-14.
  63. Pearce, A., & Svendsen, C. N. (1999). Characterisation of stem cell expression using two-dimensional electrophoresis. / Electrophoresis, 20, 969-70.
  64. Romeo, M. J., Espina, V., Lowenthal, M., Espina, B. H., Petricoin, E. F., 3rd, & Liotta, L. A. (2005). CSF proteome: A protein repository for potential biomarker identification. / Expert Review of Proteomics, 2, 57-0.
  65. Unlu, M., Morgan, M. E., & Minden, J. S. (1997). Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. / Electrophoresis, 18, 2071-077.
  66. Barthéléry, M., Jaishankar, A., Salli, U., Freeman, W. M., & Vrana, K. E. (2009). 2-D DIGE identification of differentially expressed heterogeneous nuclear ribonucleoproteins and transcription factors during neural differentiation of human embryonic stem cells. / Proteomics Clinical Applications, 3, 505-14.
  67. Schirle, M., Heurtier, M. A., & Kuster, B. (2003). Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry. / Molecular & Cellular Proteomics, 2, 1297-305.
  68. Burre, J., Beckhaus, T., Schagger, H., et al. (2006). Analysis of the synaptic vesicle proteome using three gel-based protein separation techniques. / Proteomics, 6, 6250-262.
  69. Takamori, S., Holt, M., Stenius, K., et al. (2006). Molecular anatomy of a trafficking organelle. / Cell, 127, 831-46.
  70. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., & Watanabe, C. (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. / Proceedings of the National Academy of Sciences of the United States of America, 90, 5011-015.
  71. Ishii, D., Hibi, K., Asai, K., Nagaya, M., Mochizuki, K., & Mochida, Y. (1978). Studies of microhigh-performance liquid chromatography. IV. Application of the micro pre-column method to the analysis of corticosteroids in serum. / Journal of Chromatography, 156, 173-80.
  72. Tsuda, T., & Novotny, M. V. (1978). Packed microcapillary columns in high performance liquid chromatography. / Analytical Chemistry, 50, 271-75.
  73. Scott, R. P., & Kucera, P. (1979). Use of microbore columns for the separation of substances of biological origin. / Journal of Chromatography, 185, 27-1.
  74. Tomer, K. B., Moseley, M. A., Deterding, L. J., & Parker, C. E. (1994). Capillary liquid chromatography/mass spectrometry. / Mass Spectrometry Reviews, 13, 431-57.
  75. Vissers, J. P. (1999). Recent developments in microcolumn liquid chromatography. / Journal of Chromatography A, 856, 117-43.
  76. Shen, Y., Zhao, R., Berger, S. J., Anderson, G. A., Rodriguez, N., & Smith, R. D. (2002). High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. / Analytical Chemistry, 74, 4235-249.
  77. Gatlin, C. L., Kleemann, G. R., Hays, L. G., Link, A. J., & Yates, J. R., 3rd. (1998). Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. / Analytical Biochemistry, 263, 93-01.
  78. Martin, S. E., Shabanowitz, J., Hunt, D. F., & Marto, J. A. (2000). Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry. / Analytical Chemistry, 72, 4266-274.
  79. Domon, B., & Aebersold, R. (2006). Mass spectrometry and protein analysis. / Science, 312, 212-17.
  80. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., & Kuster, B. (2007). Quantitative mass spectrometry in proteomics: A critical review. / Analytical and Bioanalytical Chemistry, 389, 1017-031.
  81. America, A. H., & Cordewener, J. H. (2008). Comparative LC-MS: A landscape of peaks and valleys. / Proteomics, 8, 731-49.
  82. Gevaert, K., Impens, F., Ghesquiere, B., Van Damme, P., Lambrechts, A., & Vandekerckhove, J. (2008). Stable isotopic labeling in proteomics. / Proteomics, 8, 4873-885.
  83. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., & Chait, B. T. (1999). Accurate quantitation of protein expression and site-specific phosphorylation. / Proceedings of the National Academy of Sciences of the United States of America, 96, 6591-596.
  84. Ong, S. E., Blagoev, B., Kratchmarova, I., et al. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. / Molecular & Cellular Proteomics, 1, 376-86.
  85. Bendall, S. C., Hughes, C., Stewart, M. H., Doble, B., Bhatia, M., & Lajoie, G. A. (2008). Prevention of amino acid conversion in SILAC experiments with embryonic stem cells. / Molecular & Cellular Proteomics, 7, 1587-597.
  86. Prokhorova, T. A., Rigbolt, K. T., Johansen, P. T., et al. (2009). Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells. / Molecular & Cellular Proteomics, 8, 959-70.
  87. Graumann, J., Hubner, N. C., Kim, J. B., et al. (2008). Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins. / Molecular & Cellular Proteomics, 7, 672-83.
  88. Steiniger, S. C., Coppinger, J. A., Kruger, J. A., Yates, J., 3rd, & Janda, K. D. (2008). Quantitative mass spectrometry identifies drug targets in cancer stem cell-containing side population. / Stem Cells, 26, 3037-046.
  89. Orlando, R., Lim, J. M., Atwood, J. A., 3rd, et al. (2009). IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells. / Journal of Proteome Research, 8, 3816-823.
  90. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. / Nature Biotechnology, 17, 994-99.
  91. Schmidt, A., Kellermann, J., & Lottspeich, F. (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. / Proteomics, 5, 4-5.
  92. Ramus, C., Gonzalez de Peredo, A., Dahout, C., Gallagher, M., & Garin, J. (2006). An optimized strategy for ICAT quantification of membrane proteins. / Molecular & Cellular Proteomics, 5, 68-8.
  93. Tian, Q., Stepaniants, S. B., Mao, M., et al. (2004). Integrated genomic and proteomic analyses of gene expression in Mammalian cells. / Molecular & Cellular Proteomics, 3, 960-69.
  94. Prahalad, A. K., & Hock, J. M. (2009). Proteomic characteristics of ex vivo-enriched adult human bone marrow mononuclear cells in continuous perfusion cultures. / Journal of Proteome Research, 8, 2079-089.
  95. Ross, P. L., Huang, Y. N., Marchese, J. N., et al. (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. / Molecular & Cellular Proteomics, 3, 1154-169.
  96. Ow, S. Y., Salim, M., Noirel, J., Evans, C., Rehman, I., & Wright, P. C. (2009). iTRAQ underestimation in simple and complex mixtures: “The good, the bad and the ugly- / Journal of Proteome Research, 8, 5347-355.
  97. Richardson, K., Denny, R., Hughes, C., et al. (2010). A probabilistic framework for peptide and protein quantification. / submitted for publication.
  98. Thompson, A., Schafer, J., Kuhn, K., et al. (2003). Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. / Analytical Chemistry, 75, 1895-904.
  99. Unwin, R. D., Smith, D. L., Blinco, D., et al. (2006). Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. / Blood, 107, 4687-694.
  100. Griffiths, S. D., Burthem, J., Unwin, R. D., et al. (2007). The use of isobaric tag peptide labeling (iTRAQ) and mass spectrometry to examine rare, primitive hematopoietic cells from patients with chronic myeloid leukemia. / Molecular Biotechnology, 36, 81-9.
  101. Lund, T. C., Anderson, L. B., McCullar, V., et al. (2007). iTRAQ is a useful method to screen for membrane-bound proteins differentially expressed in human natural killer cell types. / Journal of Proteome Research, 6, 644-53.
  102. Seshi, B. (2006). An integrated approach to mapping the proteome of the human bone marrow stromal cell. / Proteomics, 6, 5169-182.
  103. Salim, K., Kehoe, L., Minkoff, M. S., Bilsland, J. G., Munoz-Sanjuan, I., & Guest, P. C. (2006). Identification of differentiating neural progenitor cell markers using shotgun isobaric tagging mass spectrometry. / Stem Cells and Development, 15, 461-70.
  104. Bondarenko, P. V., Chelius, D., & Shaler, T. A. (2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. / Analytical Chemistry, 74, 4741-749.
  105. Chelius, D., & Bondarenko, P. V. (2002). Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. / Journal of Proteome Research, 1, 317-23.
  106. Wang, W., Zhou, H., Lin, H., et al. (2003). Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. / Analytical Chemistry, 75, 4818-826.
  107. Silva, J. C., Denny, R., Dorschel, C. A., et al. (2005). Quantitative proteomic analysis by accurate mass retention time pairs. / Analytical Chemistry, 77, 2187-200.
  108. Ishihama, Y., Oda, Y., Tabata, T., et al. (2005). Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. / Molecular & Cellular Proteomics, 4, 1265-272.
  109. Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007). Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. / Nature Biotechnology, 25, 117-24.
  110. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P., & Geromanos, S. J. (2006). Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. / Molecular & Cellular Proteomics, 5, 144-56.
  111. Vissers, J. P., Langridge, J. I., & Aerts, J. M. (2007). Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. / Molecular & Cellular Proteomics, 6, 755-66.
  112. Rower, C., Vissers, J. P., Koy, C., et al. (2009). Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue. / Analytical and Bioanalytical Chemistry, 395, 2443-456.
  113. Malmstrom, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., & Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. / Nature, 460, 762-65.
  114. Van Hoof, D., Passier, R., Ward-Van Oostwaard, D., et al. (2006). A quest for human and mouse embryonic stem cell-specific proteins. / Molecular & Cellular Proteomics, 5, 1261-273.
  115. Chambery, A., Vissers, J. P., Langridge, J. I., et al. (2009). Qualitative and quantitative proteomic profiling of cripto(?? embryonic stem cells by means of accurate mass LC-MS analysis. / Journal of Proteome Research, 8, 1047-058.
  116. Anderson, L., & Hunter, C. L. (2006). Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. / Molecular & Cellular Proteomics, 5, 573-88.
  117. Keshishian, H., Addona, T., Burgess, M., Kuhn, E., & Carr, S. A. (2007). Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. / Molecular & Cellular Proteomics, 6, 2212-229.
  118. Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W., & Guild, B. (2004). Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. / Proteomics, 4, 1175-186.
  119. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. / Proceedings of the National Academy of Sciences of the United States of America, 100, 6940-945.
  120. Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., & Beynon, R. J. (2006). Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. / Nature Protocols, 1, 1029-043.
  121. Anderson, N. L., Jackson, A., Smith, D., Hardie, D., Borchers, C., & Pearson, T. W. (2009). SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. / Molecular & Cellular Proteomics, 8, 995-005.
  122. Duncan, M. W., Yergey, A. L., & Patterson, S. D. (2009). Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem. / Proteomics, 9, 1124-127.
  123. Sherman, J., McKay, M. J., Ashman, K., & Molloy, M. P. (2009). How specific is my SRM? The issue of precursor and product ion redundancy. / Proteomics, 9, 1120-123.
  124. Hoopmann, M. R., Finney, G. L., & MacCoss, M. J. (2007). High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. / Analytical Chemistry, 79, 5620-632.
  125. Luethy, R., Kessner, D. E., Katz, J. E., et al. (2008). Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. / Journal of Proteome Research, 7, 4031-039.
  126. Geromanos, S. J., Vissers, J. P., Silva, J. C., et al. (2009). The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. / Proteomics, 9, 1683-695.
  127. Limentani, G. B., Ringo, M. C., Ye, F., Berquist, M. L., & McSorley, E. O. (2005). Beyond the t-test: Statistical equivalence testing. / Analytical Chemistry, 77, 221A-26A.
  
• 作者单位：Luca Colucci-D’Amato (1) (2)
  Annarita Farina (3)
  Johannes P. C. Vissers (4)
  Angela Chambery (1)
  
  1. Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100, Caserta, Italy
  2. Istituto di Genetica e Biofisica “A. Buzzati-Traverso- Consiglio Nazionale delle Ricerche, 80131, Napoli, Italy
  3. Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Faculty of Medicine, Geneva University, CH-1211, Geneva, Switzerland
  4. Waters Corporation, Atlas Park, Simonsway, Manchester, M22 5PP, UK
  

文摘

Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience (“neuroproteomics- are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.