Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit

Proteomics

Volumn 13, Issue 12-13, 2013, Pages 2016-2030

  Mora, Leticia ^a   Bramley, Peter M ^a   Fraser, Paul D ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Food safety; Genetic modification; Label free quantitation; Plant proteomics; Tomato

Indexed keywords

PROTEOME;

ACCURACY; ARTICLE; CONTROLLED STUDY; NONHUMAN; NUTRIENT; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; TOMATO; WORKFLOW;

FOOD SAFETY; GENETIC MODIFICATION; LABEL-FREE QUANTITATION; PLANT PROTEOMICS; TOMATO;

AMINO ACID SEQUENCE; CHROMATOGRAPHY, REVERSE-PHASE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FRUIT; LINEAR MODELS; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; MULTIVARIATE ANALYSIS; PEPTIDE FRAGMENTS; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84880097658     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200480     Document Type: Article

References (40)

1. Fukao, Y., Ferjani, A., Tomioka, R., Nagasaki, N. et al., iTRAQ analysis reveals mechanisms of growth defects due to excess zinc in Arabidopsis. Plant Physiol. 2011, 155, 1893-1907.
2. Lan, P., Li, W. F., Wen, T. N., Shiau, J. Y. et al., iTRAQ protein profile analysis of Arabidopsis roots reveals new aspects critical for uron homeostasis. Plant Physiol. 2011, 155, 821-834.
3. Nogueira, F. C. S., Palmisano, G., Schwammle, V., Campos, F. A. P. et al., Performance of isobaric and isotopic labeling in quantitative plant proteomics. J. Proteome Res. 2012, 11, 3046-3052.
4. Fares, A., Rossignol, M., Peltier, J. B., Proteomics investigation of endogenous S-nitrosylation in Arabidopsis. Biochem. Biophys. Res. Commun. 2011, 416, 331-336.
5. Schutz, W., Hausmann, N., Krug, K., Hampp, R., Macek, B., Extending SILAC to proteomics of plant cell lines. Plant Cell 2011, 23, 1701-1705.
6. Colas, I., Koroleva, O., Shaw, P. J., Mass spectrometry in plant proteomic analysis. Plant Biosyst. 2010, 144, 703-714.
7. Nelson, C. J., Huttlin, E. L., Hegeman, A. D., Harms, A. C., Sussman M. R., Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana. Proteomics 2007, 7, 1279-1292.
8. Palmblad, M, Bindschedler, L.V., Cramer, R., Quantitative proteomics using uniform 15N-labeling, MASCOT, and the trans-proteomic pipeline. Proteomics 2007, 7, 3462-3469.
9. Rodrigues, S. P., Ventura, J. A., Aguilar, C., Nakayasu, E. S. et al., Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants. J. Proteomics 2012, 75, 3191-3198.
10. Zhu, W. H., Smith, J. W., Huang, C. M., Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2009, 2010, 840518.
11. Bindschedler, L., Palmblad, M., Cramer, R., Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study. Phytochemistry 2008, 69, 1962-1972.
12. Gammulla, C. G., Pascovici, D., Atwell, B. J., Haynes, P. A., Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress. Proteomics 2011, 11, 2839-2850.
13. Palmblad, M., Mills, D. J., Bindschedler, L. V., Heat-shock response in Arabidopsis thaliana explored by multiplexed quantitative proteomics using differential metabolic labeling. J. Proteome Res. 2008, 7, 780-785.
14. Elmore, J. M., Liu, J., Smith, B., Phinney, B., Coaker, G., Quantitative proteomics reveals dynamic changes in the plasma membrane during Arabidopsis immune signaling. Mol. Cell. Proteomics 2012, 11, M111.014555.
15. Han, B., Chen, S. X., Dai, S. J., Yang, N., Wang, T., Isobaric tags for relative and absolute quantification-based comparative proteomics reveals the features of plasma membrane-associated proteomes of pollen grains and pollen tubes from Lilium davidii. J. Integr. Plant Biol. 2010, 52, 1043-1058.
16. Pang, Q. Y., Chen, S. X., Dai, S. J., Chen, Y. Z. et al., Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila. J. Proteome Res. 2010, 9, 2584-2599.
17. Chen, S., Yuan, H. M., Liu, G. F., Li, H. Y., Jiang, J., A label-free differential quantitative proteomics analysis of a TaLEA-introduced transgenic Populus simonii x Populus nigra dwarf mutant. Mol. Biol. Rep. 2012, 39, 7657-7664.
18. Koga, H., Dohi, K., Nishiuchi, T., Kato, T. et al., Proteomic analysis of susceptible rice plants expressing the whole plant-specific resistance against Magnaporthe oryzae: involvement of a thaumatin-like protein. Physiol. Mol. Plant Path. 2012, 77, 60-66.
19. Satoh, R., Nakamura, R., Komatsu, A., Oshima, M., Teshima, R., Proteomic analysis of known and candidate rice allergens between non-transgenic and transgenic plants. Reg. Toxicol. Pharmacol. 2011, 59, 437-444.
20. Farr, D. R., Functional foods. Cancer Lett. 1997, 114, 59-63.
21. Enfissi, E. M. A., Barneche, F., Ahmed, I., Lichtle, C. et al., Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 down-regulated tomato fruit. Plant Cell 2010, 22, 1190-1215.
22. Bradford, M. M., Rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal. Biochem. 1976, 72, 248-54.
23. Laemmli, U. K., Cleavage of structural proteins during assembly of head of bacteriophage-T4. Nature 1970, 227, 680.
24. Meng, Y. Y., Liu, F., Pang, C. Y., Fan, S. L. et al., Label-free quantitative proteomics analysis of cotton leaf response to nitric oxide. J. Proteome Res. 2011, 10, 5416-5432.
25. Shen, Z., Li, P., Ni, R. J., Ritchie, M. et al., Label-free quantitative proteomics analysis of etiolated maize seedling leaves during greening. Mol. Cell. Proteomics 2009, 8, 2443-2460.
26. Wang, G., Wu, W. W., Zeng, W., Chou, C. L., Shen, R. F., Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes. J. Proteome Res. 2006, 5, 1214-1223.
27. Chelius, D., Zhang, T., Wang, G. H., Shen, R. F., Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. Anal. Chem. 2003, 75, 6658-6665.
28. Hughes, M. A., Silva, J. C., Geromanos, S. J., Townsend, C. A., Quantitative proteomic analysis of drug-induced changes in mycobacteria. J. Proteome Res. 2006, 5, 54-63.
29. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
30. Wang, W. X., Zhou, H. H., Lin, H., Roy, S. et al., Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 2003, 75, 4818-4826.
31. Silva, J. C, Gorenstein, M. V., Li, G. Z., Vissers, J. P. V., Geromanos, S. J. Absolute quantification of proteins by LCMS. A virtue of parallel MS acquisition. Mol. Cel. Proteomics 2006, 5, 144-156.
32. Ryu, S., Gallis, B., Goo, Y. A., Shaffer, S. A. et al., Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method. Cancer Inform. 2008, 6, 243-255.
33. Chen, J., Ryu, S., Gharib, S. A., Goodlett, D. R., Schnapp, L. M., Exploration of the normal human bronchoalveolar lavage fluid proteome. Proteomics Clin. Appl. 2008, 2, 585-595.
34. Colinge, J., Chiappe, D., Lagache, S., Moniatte, M., Bougueleret, L., Differential proteomics via probabilistic peptide identification scores. Anal. Chem. 2005, 77, 596-606.
35. Lundgren, D. H., Hwang, S.-I., Wu, L., Han, D. K., Role of spectral counting in quantitative proteomics. Exp. Rev. Proteomics 2010, 7, 39-53.
36. Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-53.
37. Kota, U., Goshe, M. B., Advances in qualitative and quantitative plant membrane proteomics. Phytochemistry 2011, 72, 1040-1060.
38. Matros, A., Kaspar, S., Witzel, K., Mock, H. P., Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. Phytochemistry 2011, 72, 963-974.
39. Brownridge, P., Beynon, R. J., The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 2011, 54, 351-360.
40. Robertson, R. P., Koistinen, K., Gerrish, C., Halket, J. M. et al., Proteome changes in tomato lines transformed with phytoene synthase-1 in the sense and antisense orientations. J. Exp. Bot. 2012, 63, 6035-6043.