Developmentally-dynamic murine brain proteomes and phosphoproteomes revealed by quantitative proteomics

Proteomes

Volumn 2, Issue 2, 2014, Pages 191-207

  Doubleday, Peter F ^a   Ballif, Bryan A ^a  

^a UNIVERSITY OF VERMONT   (United States)

Author keywords

Brain development; Phosphoproteomics; Phosphorylation; Quantitative mass spectrometry; Reductive amination

Indexed keywords

EID: 84915776031     PISSN: None     EISSN: 22277382     Source Type: Journal    
DOI: 10.3390/proteomes2020191     Document Type: Article

References (26)

1. Patterson, S.D.; Aebersold, R.H. Proteomics: The first decade and beyond. Nat. Genet. 2003, 33, 311-323
2. Goswami, T.; Ballif, B.A. Methods for the isolation of phosphoproteins and phosphopeptides for mass spectrometry analysis: Toward increased functional phosphoproteomics. In Sample Preparation in Biological Mass Spectrometry; Ivanov, A.R., Lazarev, A.V., Eds.; Springer: New York, NY, USA, 2011; pp. 627-655
3. Ballif, B.A.; Villen, J.; Beausoleil, S.A.; Schwartz, D.; Gygi, S.P. Phosphoproteomic analysis of the developing mouse brain. Mol. Cell. Proteomics 2004, 3, 1093-1101
4. Goswami, T.; Li, X.; Smith, A.M.; Luderowski, E.M.; Vincent, J.J.; Rush, J.; Ballif, B.A. Comparative phosphoproteomic analysis of neonatal and adult murine brain. Proteomics 2012, 12, 2185-2189
5. Ballif, B.A.; Carey, G.R.; Sunyaev, S.R.; Gygi, S.P. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J. Proteome Res. 2008, 7, 311-318
6. Huttlin, E.L.; Jedrychowski, M.P.; Elias, J.E.; Goswami, T.; Rad, R.; Beausoleil, S.A.; Villen, J.; Haas, W.; Sowa, M.E.; Gygi, S.P. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 2010, 143, 1174-1189
7. Dephoure, N.; Gygi, S.P. A solid phase extraction-based platform for rapid phosphoproteomic analysis. Methods 2011, 54, 379-386
8. Elias, J.E.; Gygi, S.P. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 2010, 604, 55-71
9. Matsuoka, S.; Ballif, B.A.; Smogorzewska, A.; McDonald, E.R., 3rd; Hurov, K.E.; Luo, J.; Bakalarski, C.E.; Zhao, Z.; Solimini, N.; Lerenthal, Y.; et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316, 1160-1166
10. Bakalarski, C.E.; Elias, J.E.; Villen, J.; Haas, W.; Gerber, S.A.; Everley, P.A.; Gygi, S.P. The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. J. Proteome Res. 2008, 7, 4756-4765
11. Beausoleil, S.A.; Villen, J.; Gerber, S.A.; Rush, J.; Gygi, S.P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292
12. Ballif, B.A.; Arnaud, L.; Cooper, J.A. Tyrosine phosphorylation of disabled-1 is essential for reelin-stimulated activation of Akt and Src family kinases. Brain Res. Mol. Brain Res. 2003, 117, 152-159
13. Huang, D.W.; Sherman, B.T.; Lempicki, R.A. Systematic and integrative analysis of large gene lists using david bioinformatics resources. Nat. Protoc. 2009, 4, 44-57
14. Huang, D.W.; Sherman, B.T.; Lempicki, R.A. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37, 1-13
15. Kanehisa, M.; Goto, S. Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28, 27-30
16. Kanehisa, M.; Goto, S.; Sato, Y.; Kawashima, M.; Furumichi, M.; Tanabe, M. Data, information, knowledge and principle: Back to metabolism in kegg. Nucleic Acids Res. 2014, 42, D199-D205
17. Khidekel, N.; Ficarro, S.B.; Clark, P.M.; Bryan, M.C.; Swaney, D.L.; Rexach, J.E.; Sun, Y.E.; Coon, J.J.; Peters, E.C.; Hsieh-Wilson, L.C. Probing the dynamics of o-glcnac glycosylation in the brain using quantitative proteomics. Nat. Chem. Biol. 2007, 3, 339-348
18. Ballif, B.A.; Arnaud, L.; Arthur, W.T.; Guris, D.; Imamoto, A.; Cooper, J.A. Activation of a dab1/crkl/c3g/rap1 pathway in reelin-stimulated neurons. Curr. Biol. 2004, 14, 606-610
19. Buel, G.R.; Rush, J.; Ballif, B.A. Fyn promotes phosphorylation of collapsin response mediator protein 1 at tyrosine 504, a novel, isoform-specific regulatory site. J. Cell. Biochem. 2010, 111, 20-28
20. Uchida, Y.; Ohshima, T.; Sasaki, Y.; Suzuki, H.; Yanai, S.; Yamashita, N.; Nakamura, F.; Takei, K.; Ihara, Y.; Mikoshiba, K.; et al. Semaphorin3a signalling is mediated via sequential cdk5 and gsk3beta phosphorylation of crmp2: Implication of common phosphorylating mechanism underlying axon guidance and Alzheimer's disease. Genes Cells 2005, 10, 165-179
21. Graham, M.E.; Ruma-Haynes, P.; Capes-Davis, A.G.; Dunn, J.M.; Tan, T.C.; Valova, V.A.; Robinson, P.J.; Jeffrey, P.L. Multisite phosphorylation of doublecortin by cyclin-dependent kinase 5. Biochem. J. 2004, 381, 471-481
22. Kettenbach, A.N.; Rush, J.; Gerber, S.A. Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat. Protoc. 2011, 6, 175-186
23. Hornbeck, P.V.; Kornhauser, J.M.; Tkachev, S.; Zhang, B.; Skrzypek, E.; Murray, B.; Latham, V.; Sullivan, M. Phosphositeplus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40, D261-D270
24. Sigrist, C.J.; de Castro, E.; Cerutti, L.; Cuche, B.A.; Hulo, N.; Bridge, A.; Bougueleret, L.; Xenarios, I. New and continuing developments at prosite. Nucleic Acids Res. 2013, 41, D344-D347
25. Lopez, A.J. Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 1998, 32, 279-305
26. Kalsotra, A.; Cooper, T.A. Functional consequences of developmentally regulated alternative splicing. Nat. Rev. Genet. 2011, 12, 715-729