Popeye strikes again: The deep proteome of spinach leaves

Journal of Proteomics

Volumn 74, Issue 1, 2011, Pages 127-136

  Fasoli, Elisa ^a   D'Amato, Alfonsina ^a   Kravchuk, Alexander V ^a   Boschetti, Egisto ^b   Bachi, Angela ^c   Righetti, Pier Giorgio ^a  

^a POLITECNICO DI MILANO   (Italy)

^b Bio Rad   (France)

^c SAN RAFFAELE HOSPITAL   (Italy)

Author keywords

Combinatorial peptide libraries; Dynamic range; Low abundance proteins; Proteomics; Spinach leaves

Indexed keywords

GENE PRODUCT; PEPTIDE LIBRARY; PROTEOME;

ARTICLE; CONTROLLED STUDY; CYTOPLASM; ELUTION; ENZYME REGULATION; GENE IDENTIFICATION; NONHUMAN; PH; PLANT LEAF; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN RENATURATION; SPECIES; SPINACH;

CYTOPLASM; HYDROGEN-ION CONCENTRATION; LIGANDS; PEPTIDE LIBRARY; PLANT LEAVES; PROTEOME; PROTEOMICS; SPINACIA OLERACEA;

SPINACIA OLERACEA;

EID: 78649831385     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2010.10.009     Document Type: Article

References (43)

1. Omenn G.S. Exploring the Human Plasma Proteome. Wiley-VCH, Weinheim, 2005, 2006, pp. 1-372.
2. de Godoy L.M.F., Olsen J.V., de Souza G.A., Li G. Status of complete proteome analysis by mass spectrometry: SILAC-labelled yeast as a model system. Genome Biol 2006, 7:R50.
3. Canovas F.M., Dumas-Gaudot E., Recorbet G., Jorrín J., Mock H.P., Rossignol M. Plant proteome analysis. Proteomics 2004, 4:285-298.
4. Rossignol M., Peltier J.B., Mock H.P., Matros A., Maldonado A.M., Jorrín J.V. Plant proteome analysis: a 2004-2006 update. Proteomics 2006, 6:5529-5548.
5. Jorrín J.V., Maldonado A.M., Castillejo M.A. Plant proteome analysis: a 2006 update. Proteomics 2007, 7:2947-2962.
6. Jorrín-Novo J.V., Maldonado A.M., Echevarría-Zomeño S., Valledor L., Castillejo M.A., Curto M., et al. Plant proteomics update (2007-2008): second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009, 72:285-314.
7. http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html#C_SEQ.
8. Jorrín-Novo J.V. (Guest Editor) Plant Proteomics, J Proteomics 2009;72, issue No. 3, 291 pages.
9. Plant proteomics: technologies, strategies and applications 2008, 1-764. Wiley, Hoboken. G.K. Agrawal, R. Rakwal (Eds.).
10. Agrawal G.K., Jwa N.S., Rakwal R. Rice proteomics: ending phase I and the beginning of phase II. Proteomics 2009, 9:935-963.
11. Kersten B., Agrawal G.K., Durek P., Neigenfind J., Schulze W., Walther D., et al. Plant phosphoproteomics: an update. Proteomics 2009, 9:964-988.
12. Agrawal G.K., Jwa N.S., Lebrun M.H., Job D., Rakwal R. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 2010, 10:799-827.
13. Neilson K.A., Gammulla C.G., Mirzaei M., Imin N., Haynes P.A. Proteomic analysis of temperature stress in plants. Proteomics 2010, 10:828-845.
14. Rabilloud T. Solubilization of proteins for electrophoretic analyses. Electrophoresis 1996, 17:813-829.
15. Rose J.K., Bashir S., Giovannoni J.J., Jahn M.M., Saravanan R.S. Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J 2004, 39:715-733.
16. des Francs C.C., Thiellement H., de Vienne D. Analysis of leaf proteins by two-dimensional gel electrophoresis: protease action as exemplified by Ribulose bisphosphate carboxylase/oxygenase degradation and procedure to avoid proteolysis during extraction. Plant Physiol 1985, 78:178-182.
17. Gegenheimer P. Preparation of extracts from plants. Meth Enzymol 1990, 182:174-193.
18. McCabe M.S., Garratt L.C., Schepers F., Jordi W.J., Stoopen G.M., Davelaar E., et al. Effects of P(SAG12)-IPT gene expression on development and senescence in transgenic lettuce. Plant Physiol 2001, 127:505-516.
19. Giavalisco P., Nordhoff E., Kreitler T., Klöppel K.D., Lehrach H., Klose J., et al. Proteome analysis of Arabidopsis thaliana by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. Proteomics 2005, 5:1902-1913.
20. Khan M.M.K., Komatsu S. Rice proteomics: recent developments and analysis of nuclear proteins. Phytochemistry 2004, 65:1671-1681.
21. Hashimoto M., Komatsu S. Proteomic analysis of rice seedlings during cold stress. Proteomics 2007, 7:1293-1302.
22. Widjiaja I., Naumann K., Roth U., Wolf N., Mackey D., Dangl J.L., et al. Combining subproteome enrichment and Rubisco depletion enables identification of low-abundance proteins differentially regulated during plant defence. Proteomics 2009, 9:138-147.
23. Righetti P.G., Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom Rev 2008, 27:596-608.
24. Boschetti E., Righetti P.G. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 2009, 9:1492-1510.
25. Righetti P.G., Boschetti E., Zanella A., Fasoli E., Citterio A. Plucking, pillaging and plundering proteomes with combinatorial peptide ligand libraries. J Chromatogr A 2010, 1217:893-900.
26. Righetti P.G., Boschetti E., Kravchuk A.V., Fasoli E. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Expert Rev Proteomics 2010, 7:373-385.
27. Boschetti E., Bindschedler L.V., Tang C., Fasoli E., Righetti P.G. Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price. J Chromatogr A 2009, 1216:1215-1222.
28. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
29. Maere S., Heymans K., Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
30. Fasoli E., Farinazzo A., Sun C.J., Kravchuk A.V., Guerrier L., Fortis F., et al. Interaction among proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species. J Proteomics 2010, 73:733-742.
31. Candiano G., Dimuccio V., Bruschi M., Santucci L., Gusmano R., Boschetti E., et al. Combinatorial peptide ligand libraries for urine proteome analysis: investigation of different elution systems. Electrophoresis 2009, 30:2405-2411.
32. Olsen J.V., de Godoy L.M., Li G., Macek B., Mortensen P., Pesch R., et al. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005, 12:2010-2021.
33. Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
34. Carroll A.J., Heazlewood J.L., Ito J., Millar A.H. Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification. Mol Cell Prot 2008, 7:347-369.
35. Babujee L., Wurtz V., Ma C., Lueder F., Soni P., van Dorsselaer A., et al. The proteome map of spinach leaf peroxisomes indicates partial compartmentalization of phylloquinone (vitamin K1) biosynthesis in plant peroxisomes. J Exptl Bot 2010, 61:1441-1453.
36. Timperio A.M., D'Amici G.M., Barta C., Loreto F., Zolla L. Proteomic, pigment composition, and organization of thylakoid membranes in iron-deficient spinach leaves. J Exptl Bot 2007, 58:3695-3710.
37. Righetti P.G., Boschetti E., Zanella A., Fasoli E., Citterio A. Plucking, pillaging and plundering proteomes with combinatorial peptide ligand libraries. J Chromatogr A 2010, 1217:893-900.
38. Keidel E.M., Ribitsch D., Lottspeich F. Equalizer technology-equal rights for disparate beads. Proteomics 2010, 10:2089-2098.
39. Righetti P.G., Boschetti E., Fasoli E. Capturing and amplifying impurities from recombinant therapeutic proteins via combinatorial peptide libraries: a proteomic study. Curr. Pharm Biotech Rev 2011.
40. Sharma S., Sreenivasulu N., Harshavardhan V.T., Seiler C., Sharma S., Khalil Z.N., et al. Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses. BMC Plant Biol 2010, 10:134-145.
41. Fagioni M., Zolla L. Does the different proteomic profile found in apical and basal leaves of spinach reveal a strategy of this plant towards cadmium response?. J Prot Res 2009, 8:2519-2529.
42. Fagioni M., D'Amici G.M., Timperio A.M., Zolla L. Proteomic analysis of multiprotein complexes in the thylakoid membrane upon cadmium treatment. J Prot Res 2009, 8:310-326.
43. Byrne M.E. A role of the ribosome in development. Trends Plant Sci 2009, 14:512-519.