Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis

Methods

Volumn 61, Issue 3, 2013, Pages 260-268

  Rauniyar, Navin ^a   McClatchy, Daniel B ^a   Yates, John R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Census; Mass spectrometry; Metabolic labeling; Neurodevelopment; Quantitative proteomics

Indexed keywords

NITROGEN 15; STABLE ISOTOPE; TRYPSIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; BRAIN TISSUE; CONTROLLED STUDY; FEEDING BEHAVIOR; FEMALE; IN VIVO STUDY; ISOTOPE LABELING; LIMIT OF QUANTITATION; MALE; NERVE CELL DIFFERENTIATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN RESTRICTION; PROTEOMICS; QUANTITATIVE ANALYSIS; RAT; SPIRULINA; STANDARD;

ANIMALS; ANIMALS, NEWBORN; BRAIN; BRAIN CHEMISTRY; DIET; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; ISOTOPE LABELING; NERVE TISSUE PROTEINS; NITROGEN ISOTOPES; PEPTIDE FRAGMENTS; PROTEOMICS; RATS; SPIRULINA; TANDEM MASS SPECTROMETRY;

MAMMALIA; RATTUS; RODENTIA; SPIRULINA;

EID: 84879570027     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.03.008     Document Type: Article

References (29)

1. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Nat. Biotechnol. 1999, 17:994-999.
2. Hsu J.L., Huang S.Y., Chow N.H., Chen S.H. Anal. Chem. 2003, 75:6843-6852.
3. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., Neumann T., Johnstone R., Mohammed A.K., Hamon C. Anal. Chem. 2003, 75:1895-1904.
4. 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., Pappin D.J. Mol. Cell. Proteomics 2004, 3:1154-1169.
5. Johnson K.L., Muddiman D.C. J. Am. Soc. Mass Spectrom. 2004, 15:437-445.
6. Washburn M.P., Ulaszek R., Deciu C., Schieltz D.M., Yates J.R. Anal. Chem. 2002, 74:1650-1657.
7. Krijgsveld J., Ketting R.F., Mahmoudi T., Johansen J., Artal-Sanz M., Verrijzer C.P., Plasterk R.H., Heck A.J. Nat. Biotechnol. 2003, 21:927-931.
8. Nelson C.J., Huttlin E.L., Hegeman A.D., Harms A.C., Sussman M.R. Proteomics 2007, 7:1279-1292.
9. Wu C.C., MacCoss M.J., Howell K.E., Matthews D.E., Yates J.R. Anal. Chem. 2004, 76:4951-4959.
10. Huttlin E.L., Chen X., Barrett-Wilt G.A., Hegeman A.D., Halberg R.B., Harms A.C., Newton M.A., Dove W.F., Sussman M.R. Proc. Natl. Acad. Sci. USA 2009, 106:17235-17240.
11. Rose J.C., Epperson L.E., Carey H.V., Martin S.L. Comp. Biochem. Physiol., Part D: Genomics Proteomics 2011, 6:163-170.
12. Liao L.J., McClatchy D.B., Park S.K., Xu T., Lu B.W., Yates J.R. J. Proteome Res. 2008, 7:4743-4755.
13. Kline K.G., Sussman M.R. Annu. Rev. Biophys. 2010, 39:291-308.
14. McClatchy D.B., Dong M.Q., Wu C.C., Venable J.D., Yates J.R. J. Proteome Res. 2007, 6:2005-2010.
15. MacCoss M.J., Wu C.C., Liu H., Sadygov R., Yates J.R. Anal. Chem. 2003, 75:6912-6921.
16. McClatchy D.B., Liao L., Park S.K., Venable J.D., Yates J.R. Genome Res. 2007, 17:1378-1388.
17. Frank E., Kessler M.S., Filiou M.D., Zhang Y., Maccarrone G., Reckow S., Bunck M., Heumann H., Turck C.W., Landgraf R., Hambsch B. PloS One 2009, 4:e7821.
18. Zhang Y., Filiou M.D., Reckow S., Gormanns P., Maccarrone G., Kessler M.S., Frank E., Hambsch B., Holsboer F., Landgraf R., Turck C.W. Mol. Cell. Proteomics 2011, 10. M111.008110.
19. Park S.K., Venable J.D., Xu T., Yates J.R. Nat. Methods 2008, 5:319-322.
20. Washburn M.P., Wolters D., Yates J.R. Nat. Biotechnol. 2001, 19:242-247.
21. McDonald W.H., Tabb D.L., Sadygov R.G., MacCoss M.J., Venable J., Graumann J., Johnson J.R., Cociorva D., Yates J.R. Rapid Commun. Mass Spectrom. 2004, 18:2162-2168.
22. Xu T., Venable J.D., Park S.K., Cociorva D., Lu B., Liao L., Wohlschlegel J., Hewel J., Yates J.R. Mol. Cell. Proteomics 2006, 5:S174.
23. Eng J.K., McCormack A.L., Yates J.R. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
24. Venable J.D., Wohlschlegel J., McClatchy D.B., Park S.K., Yates J.R. Anal. Chem. 2007, 79:3056-3064.
25. MacCoss M.J., Wu C.C., Matthews D.E., Yates J.R. Anal. Chem. 2005, 77:7646-7653.
26. MacCoss M.J., Matthews D.E. Anal. Chem. 2005, 77:294A-302A.
27. Shimohama S., Fujimoto S., Sumida Y., Akagawa K., Shirao T., Matsuoka Y., Taniguchi T. Biochem. Biophys. Res. Commun. 1998, 251:394-398.
28. Tully T., Bourtchouladze R., Scott R., Tallman J. Nat. Rev. Drug Discovery 2003, 2:267-277.
29. Tau G.Z., Peterson B.S. Neuropsychopharmacology 2010, 35:147-168.