Plant proteomics methods and protocols

Methods in Molecular Biology

Volumn 1072, Issue , 2014, Pages 3-13

  Jorrin Novo, Jesus V ^a  

^a UNIVERSITY OF CÓRDOBA   (Spain)

Author keywords

Comparative proteomics; Descriptive proteomics; Plant proteomics; Plant systems biology; Proteomics workflows

Indexed keywords

PROTEOME; VEGETABLE PROTEIN;

ARTICLE; DATA ANALYSIS; DATA MINING; EXPERIMENTAL DESIGN; GEL ELECTROPHORESIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PLANT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN PURIFICATION; PROTEOMICS; SEQUENCE ANALYSIS; WESTERN BLOTTING; WORKFLOW;

MASS SPECTROMETRY; PLANT PROTEINS; PLANTS; PROTEOMICS;

EID: 84934435475     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-631-3_1     Document Type: Article

References (31)

1. Bini L, Pallini V, Hochstrasser DF et al (2007) From genome to proteome: back to the future. Proteomics 7:1561-1563, Editorial
2. Renaut J, Jorrin-Novo J, Panis B, Svensson B, guest editors (2011) Plant proteomics in Europe. J Proteomics 74:1161-1164
3. Picotti P, Bodenmiller B, Aebersold R (2013) Proteomics meets the scientifi c method. Nat Methods 1:24-27
4. Thelen JJ, Miernyk JA (2012) The proteomic future: where mass spectrometry should be taking us. Biochem J 444:169-181
5. Uhrig G, Moorhead GB (2013) Plant proteomics: current status and future prospects. J Proteomics (On line advanced) doi:10.1016/j. jprot.2013.01.018
6. Marte B (2003) Introduction proteomics. Nature 422:191
7. Jungblut PR, Schluter H (2011) Towards the analysis of protein species: an overview about strategies and methods. Amino Acids 41:219-222
8. Petricka JJ, Schauer MA, Megraw M et al (2012) The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci USA 109:6811-6818
9. Agrawal GK, Pedreschi R, Barkla BJ et al (2012) Translational plant proteomics: a perspective. J Proteomics 75:4588-4601
10. Xu XM, Moller SG (2011) The value of Arabidopsis research in understanding human disease states. Curr Opin Biotechnol 22:300-307
11. Weckwerth W (2011) Green systems biology: from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics 75:284-305
12. Cánovas FM, Dumas-Gaudot E, Recorbet G (2004) Plant proteome analysis. Proteomics 4:285-298
13. Rossignol M, Peltier JB, Mock HP (2006) Plant proteome analysis: a 2004-2006 update. Proteomics 6:5529-5548
14. Jorrin JV, Rubiales D, Dumas-Gaudot E (2006) Proteomics: a promising approach to study biotic stresses in legumes. A review. Euphytica 147:37-47
15. Rispail N, Dita MA, González verdejo N et al (2007) Plant resistance to parasitic plants: molecular approaches to an old foe. New Phytol 173:703-712
16. Jorrin Novo J, Maldonado AM, Castillejo MA (2007) Plant proteome analysis: a 2006 update. Proteomics 7:2947-2962
17. Jorrin Novo J, Maldonado AM, Echevarria Zomeño S et al (2009) Plant proteomics update (2007-2008). Second generation proteomic techniques, an appropiate experimental design and data analysis to fulfi ll MIAPE standards, increase plant proteome coverage and biological knowledge. J Proteomics 72:285-314
18. Whitelegge JP, Komatsu S, Jorrin-Novo JV (2011) Diverse facets of plant proteomics. Phytochemistry 72:961-962, Editorial
19. Abril N, Gion J-M, Kerner R et al (2011) Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 72:1219-1242
20. Cox J, Heeren RMA, James P et al (2011) Facing challenges in proteomics today and in the coming decade: report of roundtable discussions at the 4th EuPA scientifi c meeting, Portugal, Estoril 2010. J Proteomics 75:4-17
21. Valledor L, Jorrin JV (2011) Back to the basics: maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses. J Proteomics 74:1-18
22. González-Fernández R, Jorrin-Novo JV (2012) Contribution of proteomics to the study of plant pathogenic fungi. J Proteome Res 11:3-16
23. Salamanca G, Rodriguez R, Quiralte J et al (2010) Pectin methylesterases of pollen tissue, a major allergen in olive tree. FEBS J 277:2729-2739
24. Liu CW, Hsu Y-K, Cheng Y-H et al (2012) Proteomic analysis of salt-responsive ubiquitinrelated proteins in rice roots. Rapid Commun Mass Spectrom 26:1649-1660
25. Bantscheff M, Lemeer S, Savitski MM et al (2012) Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 404:939-965
26. Cappadona S, Baker PR, Cutillas PR et al (2012) Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 43:1087-1108
27. Ghaemmaghami S, Huh W-K, Bower K et al (2003) Global analysis of protein expression in yeast. Nature 425:737-741
28. Zhang QC, Petrey D, Deng L et al (2012) Structure-based prediction of protein-protein. Nature. doi: 10.1038/nature11503
29. Kaundal R, Saini R, Zhao PX (2010) Combining machine learning and homologybased approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol 154:36-54
30. Tran JC, Zamdborg L, Ahlf DR (2011) Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480:254-258
31. Wu C, Tran JC, Zamdborg L (2012) A protease for "middle-down" proteomics. Nat Methods 9:822