Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment

Journal of Proteome Research

Volumn 5, Issue 2, 2006, Pages 361-369

  Wang, Haixing ^a   Qian, Wei Jun ^a   Chin, Mark H ^b   Petyuk, Vladislav A ^a   Barry, Richard C ^a   Liu, Tao ^a   Gritsenko, Marina A ^a   Mottaz, Heather M ^a   Moore, Ronald J ^a   Camp II, David G ^a   Khan, Arshad H ^b   Smith, Desmond J ^b   Smith, Richard D ^a,c  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Cysteinyl peptide enrichment; Mass spectrometry; Mouse brain proteome; Protein categorization; Proteome coverage

Indexed keywords

BRAIN PEPTIDE; MEMBRANE PROTEIN; PROTEOME;

ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; CYSTEINYL PEPTIDE ENRICHMENT; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR WEIGHT; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEOMICS;

ANIMALS; BRAIN; CHROMATOGRAPHY, LIQUID; CYSTEINE; MASS SPECTROMETRY; MEMBRANE PROTEINS; MICE; PEPTIDES; PROTEOME;

ANIMALIA; MAMMALIA;

EID: 32344447939     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0503681     Document Type: Article

References (45)

1. Peterson, A. S. Pixelating the brain. Genome Res. 2002, 12 (2), 217-218.
2. Carson, J. P.; Thaller, C.; Eichele, G. A transcriptome atlas of the mouse brain at cellular resolution. Curr. Opin. Neurobiol. 2002, 12 (5), 562-565.
3. Allen Brain Atlas, www.brain-map.org.
4. Singh, R. P.; Smith, D. J. Genome scale mapping of brain gene expression. Biol. Psych. 2003, 53 (12), 1069-1074.
5. Stoeckli, M.; Chaurand, P.; Hallahan, D. E.; Caprioli, R. M. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 2001, 4, 7493-7496.
6. Fountoulakis, M. Application of proteomics technologies in the investigation of the brain. Mass Spectrom. Rev. 2004, 23 (4), 231-258.
7. Beranova-Giorgianni, S.; Pabst, M. J.; Russell, T. M.; Giorgianni, F.; Goldowitz, D.; Desiderio, D. M. Preliminary analysis of the mouse cerebellum proteome. Brain Res. Mol. Brain Res. 2002, 98, 135-140.
8. Nielsen, P. A.; Olsen, J. V.; Podtelejnikov, A. V.; Andersen, J. R.; Mann, M.; Wisniewski, J. R. Proteomic mapping of brain plasma membrane proteins. Mol. Cell Proteomics 2005, 4, 402-408.
9. Tsuji, T.; Shiozaki, A.; Kohno, R.; Yoshizato, K.; Shimohama, S. Proteomic profiling and neurodegeneration in Alzheimer's disease. Neurochem. Res. 2002, 27, 1245-1253.
10. Butterfield, D. A.; Boyd-Kimball, D.; Castegna, A. Proteomics in Alzheimer's disease: insights into potential mechanisms of neurodegeneration. J. Neurochem. 2003, 86, 1313-1327.
11. Zhang, J.; Goodlett, D. R. Proteomic approach to studying Parkinson's disease. Mol. Neurobiol. 2004, 29, 271-288.
12. Tribl, F.; Gerlach, M.; Marcus, K.; Asan, E.; Tatschner, T.; Arzberger, T.; Meyer, H. E.; Bringmann, G.; Riederer, P. "Sub-cellular Proteomics" of Neuromelanin Granules Isolated from the Human Brain. Mol. Cell Proteomics 2005, 4, 945-957.
13. Davidsson, P.; Sjogren, M. The use of proteomics in biomarker discovery in neurodegenerative diseases. Dis. Markers. 2005, 21, 81-92.
14. Boyd-Kimball, D.; Sultana, R.; Fai Poon, H.; Lynn, B. C.; Casamenti, F.; Pepeu, G.; Klein, J. B.; Butterfield, D. A. Proteomic identification of proteins specifically oxidized by intracerebral injection of amyloid beta-peptide (1-42) into rat brain: implications for Alzheimer's disease. Neuroscience 2005, 132, 313-324.
15. Lovell, M. A.; Xiong, S.; Markesbery, W. R.; Lynn, B. C. Quantitative proteomic analysis of mitochondria from primary neuron cultures treated with amyloid beta peptide. Neurochem. Res. 2005, 30, 113-122.
16. Lubec, G.; Krapfenbauer, K.; Fountoulakis, M. Proteomics in brain research: potentials and limitations. Prog. Neurobiol. 2003, 69, 193-211.
17. Gauss, C.; Kalkum, M.; Lowe, M.; Lehrach, H.; Klose, J. Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 1999, 20, (3), 575-600.
18. Klose, J.; Nock, C.; Herrmann, M.; Stuhler, K.; Marcus, K.; Bluggel, M.; Krause, E.; Schalkwyk, L. C.; Rastan, S.; Brown, S. D. M.; Bussow, K.; Himmelbauer, H.; Lehrach, H. Genetic analysis of the mouse brain proteome. Nat. Genet. 2002, 30, 385-393.
19. Krapfenbauer, K.; Fountoulakis, M.; Lubec, G. A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions. Electrophoresis 2003, 24 (11), 1847-1870.
20. Langen, H.; Berndt, P.; Roder, D.; Cairns, N.; Lubec, G.; Fountoulakis, M. Two-dimensional map of human brain proteins. Electrophoresis 1999, 20, 907-916.
21. Yu, L. R.; Conrads, T. P.; Uo, T.; Kinoshita, Y.; Morrison, R. S.; Lucas, D. A.; Chan, K. C.; Blonder, J.; Issaq, H. J.; Veenstra, T. D. Global analysis of the cortical neuron proteome. Mol. Cell Proteomics 2004, 3, 896-907.
22. Liu, T.; Qian, W. J.; Strittmatter, E. F.; Camp, D. G.; Anderson, G. A.; Thrall, B. D.; Smith, R. D. High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology, Anal. Chem. 2004, 76, 5345-5353.
23. Liu, T.; Qian, W. J.; Chen, W. U.; Jacobs, J. M.; Moore, R. J.; Anderson, D. J.; Gritsenko, M. A.; Monroe, M. E.; Thrall, B. D.; Camp, D. G.; Smith, R. D. Improved Proteome Coverage by Using High Efficiency Cysteinyl Peptide Enrichment; The Human Mammary Epithelial Cell Proteome. Proteomics 2005, 5 (5), 1263-1273.
24. Qian, W. J.; Liu, T.; Monroe, M. E.; Strittmatter, E. F.; Jacobs, J. M.; Kangas, L. J.; Petritis, K.; Camp, D. G.; Smith, R. D. Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome. J. Proteome Res. 2005, 4, 53-62.
25. Wallin, E.; von Heijne, G. Genome-wide Analysis of Integral Membrane Proteins from Eubacterial, Archaean, and Eukaryotic Organisms. Protein Sci. 1998, 7 (4), 1029-1038.
26. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry. Anal. Chem. 2003, 75 (17), 4646-4658.
27. Sonnhammer, E. L.; von Heijne, G.; Krogh, A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1998, 6, 175-182.
28. Schwartz, R.; Ting, C. S.; King, J. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome. Res. 2001, 11, 703-709.
29. Taylor, S. W.; Fahy, E.; Zhang, B.; Glenn, G. M.; Warnock, D. E.; Wiley: S.; Murphy, A. N.; Gaucher, S. P.; Capaldi, R. A.; Gibson, B. W.; Ghosh, S. S. Characterization of the human heart mitochondrial proteome. Nat Biotechnol 2003, 21 (3), 281-286.
30. Stevens, S. M., Jr.; Zharikova, A. D.; Prokai, L. Proteomic analysis of the synaptic plasma membrane fraction isolated from rat forebrain. Brain Res. Mol. Brain Res. 2003, 117 (2), 116-128.
31. Yoshimura, Y.; Yamauchi, Y.; Shinkawa, T.; Taoka, M.; Donai, H.; Takahashi, N.; Isobe, T.; Yamauchi, T. Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J Neurochem 2004, 88 (3), 759-768.
32. Li, K. W.; Hornshaw, M. P.; Van Der Schors, R. C.; Watson, R.; Tate, S.; Casetta, B.; Jimenez, C. R.; Gouwenbeig, Y.; Gundelfinger, E. D.; Smalla, K. H.; Smit, A. B. Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology. J. Biol. Chem. 2004, 279 (2), 987-1002.
33. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001, 305, 567-580.
34. Ahram, M.; Springer, D. L. Large-scale proteomic analysis of membrane proteins. Exp. Rev. Proteomics 2004, 1, 293-302.
35. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 2003, 21, 532-538.
36. Tucker, W. C.; Weber, T.; Chapman, E. R. Reconstitution of Ca2+-regulated membrane fusion by synaptotagmin and SNAREs. Science 2004, 304 (5669), 435-438.
37. Qian, W. J.; Jacobs, J. M.; Camp II, D. G.; Monroe, M. E.; Moore, R. J.; Gritsenko, M. A.; Calvano, S. E.; Lowry, S. F.; Xiao, W.; Moldawer, L. L.; Davis, R. W.; Tompkins, R. G.; Smith, R. D. Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics 2005, 5 (2), 572-584.
38. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-201.
39. Li, X.; Low, S. H.; Miura, M.; Weimbs, T. SNARE expression and localization in renal epithelial cells suggest mechanism for variability of trafficking phenotypes. Am. J. Physiol. Renal Physiol. 2002, 283 (5), F1111-1122.
40. Osborne, S. L.; Herreros, J.; Bastiaens, P. I.; Schiavo, G. Calcium-dependent oligomerization of synaptotagmins I and II. Synaptotagmins I and II are localized on the same synaptic vesicle and heterodimerize in the presence of calcium. J. Biol. Chem. 1999, 274 (1), 59-66.
41. Wisden, W.; Seeburg, P. H. A complex mosaic of high-affinity kainate receptors in rat brain. J. Neurosci. 1993, 13 (8), 3582-3598.
42. Feigenspan, A.; Wassle, H.; Bormann, J. Pharmacology of GABA receptor C1- channels in rat retinal bipolar cells. Nature 1993, 361 (6408), 159-162.
43. Wang, H.; Qian, W. J.; Mottaz, H. M.; Clauss, T. R. W.; Anderson, D. J.; Moore, R. J.; Camp, D. G.; Khan, A. H.; Sforza, D. M.; Pallavicini, M.; Smith, D. J.; Smith, R. D. Development and Evaluation of a Micro- and Nano-Scale Proteomic Sample Preparation Methodology. J. Proteome Res. In press.
44. Qian, W. J.; Monroe, M. E.; Liu, T.; Jacobs, J. M.; Anderson, G. A.; Shen, Y.; Moore, R. J.; Anderson, D. J.; Zhang, R.; Calvano, S. E.; Lowry, S. F.; Xiao, W.; Moldawer, L. L.; Davis, R. W.; Tompkins, R. G.; Camp, D. G.; Smith, R. D. Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach. Mol. Cell. Proteomics 2005, 4 (5), 700-709.
45. Qian, W. J.; Camp, D. G.; Smith, R. D. High Throughput Proteomics Using Fourier Transform Ion Cyclotron Resonance (FTICR) Mass Spectrometry. Exp. Rev. Proteomics 2004, 1 (1), 89-97.