메뉴 건너뛰기




Volumn 6, Issue MAY, 2015, Pages

Beyond the Western front: Targeted proteomics and organelle abundance profiling

Author keywords

Arabidopsis; Immunoblotting; Multiple reaction monitoring (MRM); Organelle abundance; Proteomics; Quantitative proteomics

Indexed keywords

ARABIDOPSIS;

EID: 84934877492     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00301     Document Type: Article
Times cited : (8)

References (39)
  • 1
    • 84884368148 scopus 로고    scopus 로고
    • Western blots versus selected reaction monitoring assays: Time to turn the tables?
    • Aebersold, R., Burlingame, A. L., and Bradshaw, R. A. (2013). Western blots versus selected reaction monitoring assays: time to turn the tables? Mol. Cell. Proteomics 12, 2381-2382. doi: 10. 1074/mcp. E113. 031658.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 2381-2382
    • Aebersold, R.1    Burlingame, A.L.2    Bradshaw, R.A.3
  • 2
    • 33947541574 scopus 로고    scopus 로고
    • Achieving in-depth proteomics profiling by mass spectrometry
    • Ahn, N. G., Shabb, J. B., Old, W. M., and Resing, K. A. (2007). Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem. Biol. 2, 39-52. doi: 10. 1021/cb600357d.
    • (2007) ACS Chem. Biol , vol.2 , pp. 39-52
    • Ahn, N.G.1    Shabb, J.B.2    Old, W.M.3    Resing, K.A.4
  • 3
    • 0037048707 scopus 로고    scopus 로고
    • A simple method for isolating import-competent Arabidopsischloroplasts
    • Aronsson, H., and Jarvis, P. (2002). A simple method for isolating import-competent Arabidopsischloroplasts. FEBS Lett. 529, 215-220. doi: 10. 1016/S0014-5793(02)03342-2.
    • (2002) FEBS Lett , vol.529 , pp. 215-220
    • Aronsson, H.1    Jarvis, P.2
  • 4
    • 0346668199 scopus 로고    scopus 로고
    • Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards
    • Barnidge, D. R., Dratz, E. A., Martin, T., Bonilla, L. E., Moran, L. B., and Lindall, A. (2003). Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 75, 445-451. doi: 10. 1021/ac026154+.
    • (2003) Anal. Chem , vol.75 , pp. 445-451
    • Barnidge, D.R.1    Dratz, E.A.2    Martin, T.3    Bonilla, L.E.4    Moran, L.B.5    Lindall, A.6
  • 5
    • 23144442824 scopus 로고    scopus 로고
    • Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides
    • Beynon, R. J., Doherty, M. K., Pratt, J. M., and Gaskell, S. J. (2005). Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2, 587-589. doi: 10. 1038/nmeth774.
    • (2005) Nat. Methods , vol.2 , pp. 587-589
    • Beynon, R.J.1    Doherty, M.K.2    Pratt, J.M.3    Gaskell, S.J.4
  • 6
    • 79960436501 scopus 로고    scopus 로고
    • Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
    • Brownridge, P., Holman, S. W., Gaskell, S. J., Grant, C. M., Harman, V. M., Hubbard, S. J., et al. (2011). Global absolute quantification of a proteome: challenges in the deployment of a QconCAT strategy. Proteomics 11, 2957-2970. doi: 10. 1002/pmic. 201100039.
    • (2011) Proteomics , vol.11 , pp. 2957-2970
    • Brownridge, P.1    Holman, S.W.2    Gaskell, S.J.3    Grant, C.M.4    Harman, V.M.5    Hubbard, S.J.6
  • 7
    • 0019551730 scopus 로고
    • Western blotting: Electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A
    • Burnette, W. N. (1981). "Western blotting": electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal. Biochem. 112, 195-203. doi: 10. 1016/0003-2697(81)90281-5.
    • (1981) Anal. Biochem , vol.112 , pp. 195-203
    • Burnette, W.N.1
  • 8
    • 40749153546 scopus 로고    scopus 로고
    • Peroxisome proliferation, wound-activated responses and expression of peroxisome-associated genes are cross-regulated but uncoupled in Arabidopsis thaliana
    • Castillo, M. C., Sandalio, L. M., Del Río, L. A., and León, J. (2008). Peroxisome proliferation, wound-activated responses and expression of peroxisome-associated genes are cross-regulated but uncoupled in Arabidopsis thaliana. Plant Cell Environ. 31, 492-505. doi: 10. 1111/j. 1365-3040. 2008. 01780. x.
    • (2008) Plant Cell Environ , vol.31 , pp. 492-505
    • Castillo, M.C.1    Sandalio, L.M.2    Del Río, L.A.3    León, J.4
  • 9
    • 0010506429 scopus 로고
    • Isolation and oxidative properties of intact mitochondria isolated from spinach leaves
    • Douce, R., Moore, A. L., and Neuburger, M. (1977). Isolation and oxidative properties of intact mitochondria isolated from spinach leaves. Plant Physiol. 60, 625-628. doi: 10. 1104/pp. 60. 4. 625.
    • (1977) Plant Physiol , vol.60 , pp. 625-628
    • Douce, R.1    Moore, A.L.2    Neuburger, M.3
  • 11
    • 35448934538 scopus 로고    scopus 로고
    • Free-flow electrophoresis for purification of plant mitochondria by surface charge
    • Eubel, H., Lee, C. P., Kuo, J., Meyer, E. H., Taylor, N. L., and Millar, A. H. (2007). Free-flow electrophoresis for purification of plant mitochondria by surface charge. Plant J. 52, 583-594. doi: 10. 1111/j. 1365-313X. 2007. 03253. x.
    • (2007) Plant J , vol.52 , pp. 583-594
    • Eubel, H.1    Lee, C.P.2    Kuo, J.3    Meyer, E.H.4    Taylor, N.L.5    Millar, A.H.6
  • 12
    • 84888312487 scopus 로고    scopus 로고
    • MRMaid: The SRM assay design tool for Arabidopsis and other species
    • Fan, J., Mohareb, F., Jones, A. M. E., and Bessant, C. (2012). MRMaid: the SRM assay design tool for Arabidopsis and other species. Front. Plant Sci. 3: 164. doi: 10. 3389/fpls. 2012. 00164.
    • (2012) Front. Plant Sci , vol.3
    • Fan, J.1    Mohareb, F.2    Jones, A.M.E.3    Bessant, C.4
  • 13
    • 0017366022 scopus 로고
    • The isolation of plasma membrane from protoplasts of soybean suspension cultures
    • Galbraith, D. W., and Northcote, D. H. (1977). The isolation of plasma membrane from protoplasts of soybean suspension cultures. J. Cell Sci. 24, 295-310.
    • (1977) J. Cell Sci , vol.24 , pp. 295-310
    • Galbraith, D.W.1    Northcote, D.H.2
  • 14
    • 0037795741 scopus 로고    scopus 로고
    • Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
    • Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U. S. A. 100, 6940-6945. doi: 10. 1073/pnas. 0832254100.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 6940-6945
    • Gerber, S.A.1    Rush, J.2    Stemman, O.3    Kirschner, M.W.4    Gygi, S.P.5
  • 15
    • 84856585935 scopus 로고    scopus 로고
    • Phytozome: A comparative platform for green plant genomics
    • Goodstein, D. M., Shu, S. Q., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., et al. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178-D1186. doi: 10. 1093/Nar/Gkr944.
    • (2012) Nucleic Acids Res , vol.40 , pp. D1178-D1186
    • Goodstein, D.M.1    Shu, S.Q.2    Howson, R.3    Neupane, R.4    Hayes, R.D.5    Fazo, J.6
  • 16
    • 84893841383 scopus 로고    scopus 로고
    • Identification of trans-Golgi network proteins in Arabidopsis thaliana root tissue
    • Groen, A. J., Sancho-Andres, G., Breckels, L. M., Gatto, L., Aniento, F., and Lilley, K. S. (2014). Identification of trans-Golgi network proteins in Arabidopsis thaliana root tissue. J. Proteome Res. 13, 763-776. doi: 10. 1021/pr4008464.
    • (2014) J. Proteome Res , vol.13 , pp. 763-776
    • Groen, A.J.1    Sancho-Andres, G.2    Breckels, L.M.3    Gatto, L.4    Aniento, F.5    Lilley, K.S.6
  • 17
    • 0342349777 scopus 로고
    • Characterization of monoclonal antibodies to protoplast membranes of Nicotiana tabacum identified by an enzyme-linked immunosorbent assay
    • Hahn, M. G., Lerner, D. R., Fitter, M. S., Norman, P. M., and Lamb, C. J. (1987). Characterization of monoclonal antibodies to protoplast membranes of Nicotiana tabacum identified by an enzyme-linked immunosorbent assay. Planta 171, 453-465. doi: 10. 1007/BF00392292.
    • (1987) Planta , vol.171 , pp. 453-465
    • Hahn, M.G.1    Lerner, D.R.2    Fitter, M.S.3    Norman, P.M.4    Lamb, C.J.5
  • 18
    • 0001331640 scopus 로고
    • Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex-mixtures
    • Kondrat, R. W., Mcclusky, G. A., and Cooks, R. G. (1978). Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex-mixtures. Anal. Chem. 50, 2017-2021. doi: 10. 1021/Ac50036a020.
    • (1978) Anal. Chem , vol.50 , pp. 2017-2021
    • Kondrat, R.W.1    McClusky, G.A.2    Cooks, R.G.3
  • 19
    • 51249117296 scopus 로고    scopus 로고
    • If the antibody fails-a mass Western approach
    • Lehmann, U., Wienkoop, S., Tschoep, H., and Weckwerth, W. (2008). If the antibody fails-a mass Western approach. Plant J. 55, 1039-1046. doi: 10. 1111/j. 1365-313X. 2008. 03554. x.
    • (2008) Plant J , vol.55 , pp. 1039-1046
    • Lehmann, U.1    Wienkoop, S.2    Tschoep, H.3    Weckwerth, W.4
  • 20
    • 84862173529 scopus 로고    scopus 로고
    • Targeted proteome investigation via selected reaction monitoring mass spectrometry
    • Maiolica, A., Jünger, M. A., Ezkurdia, I., and Aebersold, R. (2012). Targeted proteome investigation via selected reaction monitoring mass spectrometry. J. Proteomics 75, 3495-3513. doi: 10. 1016/j. jprot. 2012. 04. 048.
    • (2012) J. Proteomics , vol.75 , pp. 3495-3513
    • Maiolica, A.1    Jünger, M.A.2    Ezkurdia, I.3    Aebersold, R.4
  • 21
    • 0003785597 scopus 로고
    • Isolation and partial characterization of vacuoles from tobacco protoplasts
    • Mettler, I. J., and Leonard, R. T. (1979). Isolation and partial characterization of vacuoles from tobacco protoplasts. Plant Physiol. 64, 1114-1120. doi: 10. 1104/Pp. 64. 6. 1114.
    • (1979) Plant Physiol , vol.64 , pp. 1114-1120
    • Mettler, I.J.1    Leonard, R.T.2
  • 22
    • 0023711801 scopus 로고
    • Isolation and characterization of monoclonal antibodies directed against plant plasma membrane and cell wall epitopes: Identification of a monoclonal antibody that recognizes extensin and analysis of the process of epitope biosynthesis in plant tissues and cell cultures
    • Meyer, D. J., Alfonso, C. L., and Galbraith, D. W. (1988). Isolation and characterization of monoclonal antibodies directed against plant plasma membrane and cell wall epitopes: identification of a monoclonal antibody that recognizes extensin and analysis of the process of epitope biosynthesis in plant tissues and cell cultures. J. Cell Biol. 107, 163-175. doi: 10. 1083/jcb. 107. 1. 163.
    • (1988) J. Cell Biol , vol.107 , pp. 163-175
    • Meyer, D.J.1    Alfonso, C.L.2    Galbraith, D.W.3
  • 23
    • 84901032836 scopus 로고    scopus 로고
    • Subcellular proteomics-where cell biology meets protein chemistry
    • Millar, A. H., and Taylor, N. L. (2014). Subcellular proteomics-where cell biology meets protein chemistry. Front. Plant Sci. 5: 55. doi: 10. 3389/fpls. 2014. 00055.
    • (2014) Front. Plant Sci , vol.5
    • Millar, A.H.1    Taylor, N.L.2
  • 24
    • 84867114092 scopus 로고    scopus 로고
    • Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics
    • Nikolovski, N., Rubtsov, D., Segura, M. P., Miles, G. P., Stevens, T. J., Dunkley, T. P., et al. (2012). Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol. 160, 1037-1051. doi: 10. 1104/pp. 112. 204263.
    • (2012) Plant Physiol , vol.160 , pp. 1037-1051
    • Nikolovski, N.1    Rubtsov, D.2    Segura, M.P.3    Miles, G.P.4    Stevens, T.J.5    Dunkley, T.P.6
  • 25
    • 0001395793 scopus 로고
    • Monoclonal-antibodies to plant plasma-membrane antigens
    • Norman, P. M., Wingate, V. P. M., Fitter, M. S., and Lamb, C. J. (1986). Monoclonal-antibodies to plant plasma-membrane antigens. Planta 167, 452-459. doi: 10. 1007/Bf00391220.
    • (1986) Planta , vol.167 , pp. 452-459
    • Norman, P.M.1    Wingate, V.P.M.2    Fitter, M.S.3    Lamb, C.J.4
  • 26
    • 84910956178 scopus 로고
    • Ion transport in chloroplasts and plant mitochondria
    • Packer, L., Murakami, S., and Mehard, C. W. (1970). Ion transport in chloroplasts and plant mitochondria. Annu. Rev. Plant Physiol. 21, 271-302. doi: 10. 1146/annurev. pp. 21. 060170. 001415.
    • (1970) Annu. Rev. Plant Physiol , vol.21 , pp. 271-302
    • Packer, L.1    Murakami, S.2    Mehard, C.W.3
  • 27
    • 84860573550 scopus 로고    scopus 로고
    • Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis
    • Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A., Ito, J., Batth, T. S., et al. (2012). Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 159, 12-26. doi: 10. 1104/pp. 111. 193151.
    • (2012) Plant Physiol , vol.159 , pp. 12-26
    • Parsons, H.T.1    Christiansen, K.2    Knierim, B.3    Carroll, A.4    Ito, J.5    Batth, T.S.6
  • 28
    • 84872000473 scopus 로고    scopus 로고
    • Proteomics meets the scientific method
    • Picotti, P., Bodenmiller, B., and Aebersold, R. (2013). Proteomics meets the scientific method. Nat. Methods 10, 24-27. doi: 10. 1038/nmeth. 2291.
    • (2013) Nat. Methods , vol.10 , pp. 24-27
    • Picotti, P.1    Bodenmiller, B.2    Aebersold, R.3
  • 29
    • 74049131716 scopus 로고    scopus 로고
    • High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    • Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., et al. (2010). High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46. doi: 10. 1038/nmeth. 1408.
    • (2010) Nat. Methods , vol.7 , pp. 43-46
    • Picotti, P.1    Rinner, O.2    Stallmach, R.3    Dautel, F.4    Farrah, T.5    Domon, B.6
  • 30
    • 84908388827 scopus 로고    scopus 로고
    • Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass Western approach
    • Recuenco-Munoz, L., Offre, P., Valledor, L., Lyon, D., Weckwerth, W., and Wienkoop, S. (2015). Targeted quantitative analysis of a diurnal RuBisCO subunit expression and translation profile in Chlamydomonas reinhardtii introducing a novel Mass Western approach. J. Proteomics 113, 143-153. doi: 10. 1016/j. jprot. 2014. 09. 026.
    • (2015) J. Proteomics , vol.113 , pp. 143-153
    • Recuenco-Munoz, L.1    Offre, P.2    Valledor, L.3    Lyon, D.4    Weckwerth, W.5    Wienkoop, S.6
  • 31
    • 66149148256 scopus 로고    scopus 로고
    • In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes
    • Reumann, S., Quan, S., Aung, K., Yang, P., Manandhar-Shrestha, K., Holbrook, D., et al. (2009). In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes. Plant Physiol. 150, 125-143. doi: 10. 1104/pp. 109. 137703.
    • (2009) Plant Physiol , vol.150 , pp. 125-143
    • Reumann, S.1    Quan, S.2    Aung, K.3    Yang, P.4    Manandhar-Shrestha, K.5    Holbrook, D.6
  • 32
    • 0004745723 scopus 로고
    • Chloroplast isolation in non-aqueous media
    • Stocking, C. R. (1959). Chloroplast isolation in non-aqueous media. Plant Physiol. 34, 56-61. doi: 10. 1104/pp. 34. 1. 56.
    • (1959) Plant Physiol , vol.34 , pp. 56-61
    • Stocking, C.R.1
  • 33
    • 84876544295 scopus 로고    scopus 로고
    • SUBA3: A database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
    • Tanz, S. K., Castleden, I., Hooper, C. M., Vacher, M., Small, I., and Millar, H. A. (2013). SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res. 41, 24. doi: 10. 1093/nar/gks1151.
    • (2013) Nucleic Acids Res , vol.41
    • Tanz, S.K.1    Castleden, I.2    Hooper, C.M.3    Vacher, M.4    Small, I.5    Millar, H.A.6
  • 34
    • 84893460952 scopus 로고    scopus 로고
    • Selected reaction monitoring to determine protein abundance in Arabidopsis using the Arabidopsisproteotypic predictor
    • Taylor, N. L., Fenske, R., Castleden, I., Tomaz, T., Nelson, C. J., and Millar, A. H. (2014). Selected reaction monitoring to determine protein abundance in Arabidopsis using the Arabidopsisproteotypic predictor. Plant Physiol. 164, 525-536. doi: 10. 1104/pp. 113. 225524.
    • (2014) Plant Physiol , vol.164 , pp. 525-536
    • Taylor, N.L.1    Fenske, R.2    Castleden, I.3    Tomaz, T.4    Nelson, C.J.5    Millar, A.H.6
  • 35
    • 0009482260 scopus 로고
    • Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications
    • Towbin, H., Staehelin, T., and Gordon, J. (1979). Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc. Natl Acad. Sci. U. S. A. 76, 4350-4354. doi: 10. 1073/pnas. 76. 9. 4350.
    • (1979) Proc. Natl Acad. Sci. U.S.A , vol.76 , pp. 4350-4354
    • Towbin, H.1    Staehelin, T.2    Gordon, J.3
  • 36
    • 84874762979 scopus 로고    scopus 로고
    • The Proteomics Identifications (PRIDE) database and associated tools: Status in 2013
    • Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., et al. (2013). The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069. doi: 10. 1093/Nar/Gks1262.
    • (2013) Nucleic Acids Res , vol.41 , pp. D1063-D1069
    • Vizcaino, J.A.1    Cote, R.G.2    Csordas, A.3    Dianes, J.A.4    Fabregat, A.5    Foster, J.M.6
  • 37
    • 33646251130 scopus 로고    scopus 로고
    • Relative and absolute quantitative shotgun proteomics: Targeting low-abundance proteins in Arabidopsis thaliana
    • Wienkoop, S., and Weckwerth, W. (2006). Relative and absolute quantitative shotgun proteomics: targeting low-abundance proteins in Arabidopsis thaliana. J. Exp. Bot. 57, 1529-1535. doi: 10. 1093/jxb/erj157.
    • (2006) J. Exp. Bot , vol.57 , pp. 1529-1535
    • Wienkoop, S.1    Weckwerth, W.2
  • 38
    • 22044444453 scopus 로고    scopus 로고
    • The control of peroxisome number and size during division and proliferation
    • Yan, M., Rayapuram, N., and Subramani, S. (2005). The control of peroxisome number and size during division and proliferation. Curr. Opin. Cell Biol. 17, 376-383. doi: 10. 1016/j. ceb. 2005. 06. 003.
    • (2005) Curr. Opin. Cell Biol , vol.17 , pp. 376-383
    • Yan, M.1    Rayapuram, N.2    Subramani, S.3
  • 39
    • 71649085644 scopus 로고    scopus 로고
    • Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies)
    • Zulak, K. G., Lippert, D. N., Kuzyk, M. A., Domanski, D., Chou, T., Borchers, C. H., et al. (2009). Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies). Plant J. 60, 1015-1030. doi: 10. 1111/j. 1365-313X. 2009. 04020. x.
    • (2009) Plant J , vol.60 , pp. 1015-1030
    • Zulak, K.G.1    Lippert, D.N.2    Kuzyk, M.A.3    Domanski, D.4    Chou, T.5    Borchers, C.H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.