NanoUPLC-MSE proteomic data assessment of soybean seeds using the Uniprot database

BMC Biotechnology

Volumn 12, Issue , 2012, Pages

  Murad, Andre M ^a   Rech, Elibio L ^a  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

Author keywords

NanoUPLC MSE; Seed proteomics; Soybean; Uniprot database

Indexed keywords

COMPLEX MIXTURE; DATA ASSESSMENT; DATA BANK; DETECTION RANGE; GENE EXPRESSION PATTERNS; GENETICALLY MODIFIED ORGANISMS; GLYCININ; MASS MEASUREMENTS; NANOUPLC-MSE; PEPTIDE ANALYSIS; PI VALUES; PROTEIN ANALYSIS; PROTEIN CONTENTS; PROTEIN DATABASE; PROTEIN DIGESTION; PROTEIN IDENTIFICATION; PROTEOMIC PROFILES; PROTEOMICS; SEED PROTEIN; SOYBEAN; SOYBEAN SEEDS; TRANSGENIC SOYBEAN; TRYPTIC DIGESTION; UNIPROT;

DATABASE SYSTEMS; EXPERIMENTS; GENE EXPRESSION; GENETIC ENGINEERING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; OILSEEDS; TISSUE;

PEPTIDES;

GLYCININ; PEPTIDE; SOYBEAN PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; FRAGMENTATION REACTION; MOLECULAR WEIGHT; NONHUMAN; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEOMICS; SOYBEAN; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; FACTUAL DATABASE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; NANOTECHNOLOGY; PLANT SEED;

GLYCINE MAX;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DATABASES, FACTUAL; MASS SPECTROMETRY; NANOTECHNOLOGY; PEPTIDES; PROTEOMICS; SEEDS; SOYBEAN PROTEINS; SOYBEANS;

EID: 84868220534     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-12-82     Document Type: Article

References (38)

1. Soystats www.soystats.com.
2. BASF and Embrapa's Cultivance soybeans receive approval for commercial cultivation in Brazil http://www.basf.com/group/pressrelease/P-10-148.
3. Aluru MR, Rodermel SR, Reddy MB. Genetic modification of low phytic Acid 1-1 maize to enhance iron content and bioavailability. J Agric Food Chem 2011, 59(24):12954-12962. 10.1021/jf203485a, 22088162.
4. Drakakaki G, Marcel S, Glahn RP, Lund EK, Pariagh S, Fischer R, Christou P, Stoger E. Endosperm-specific co-expression of recombinant soybean ferritin and Aspergillus phytase in maize results in significant increases in the levels of bioavailable iron. Plant Mol Biol 2005, 59(6):869-880. 10.1007/s11103-005-1537-3, 16307363.
5. Herman EM, Helm RM, Jung R, Kinney AJ. Genetic modification removes an immunodominant allergen from soybean. Plant Physiol 2003, 132(1):36-43. 10.1104/pp.103.021865, 1540313, 12746509.
6. Cunha NB, Murad AM, Cipriano TM, Araujo ACG, Aragao FJL, Leite A, Vianna GR, McPhee TR, Souza GHMF, Waters MJ, et al. Expression of functional recombinant human growth hormone in transgenic soybean seeds. Transgenic Res 2010, 20(4):811-826.
7. Cunha NB, Murad AM, Ramos GL, Maranhao AQ, Bri{dotless}gido MM, Araujo ACG, Lacorte C, Aragao FJL, Covas DT, Fontes AM, et al. Accumulation of functional recombinant human coagulation factor IX in transgenic soybean seeds. Transgenic Res 2010, 20(4):841-855.
8. Boothe J, Nykiforuk C, Shen Y, Zaplachinski S, Szarka S, Kuhlman P, Murray E, Morck D, Moloney MM. Seed-based expression systems for plant molecular farming. Plant Biotechnol J 2010, 8:588-606. 10.1111/j.1467-7652.2010.00511.x, 20500681.
9. Cunha NB, Araújo ACG, Leite A, Murad AM, Vianna GR, Rech EL. Correct targeting of proinsulin in protein storage vacuoles of transgenic soybean seeds. Genet Mol Res 2010, 9(2):1163-1170.
10. Jolliffe NA, Craddock CP, Frigerio L. Pathways for protein transport to seed storage vacuoles. Biochem Soc Trans 2005, 33:1016-1018. 10.1042/BST20051016, 16246035.
11. Ma JK-C, Drake PMW, Christou P. The production of recombinant pharmaceutical proteins in plants. Nat Rev Genet 2003, 4:794-805.
12. Tremblay R, Wang D, Jevnikar AM, Ma S. Tobacco, a highly efficient green bioreactor for production of therapeutic proteins. Biotechnol Adv 2010, 28:214-221. 10.1016/j.biotechadv.2009.11.008, 19961918.
13. Kim Y-H, Choi SJ, Lee H-A, Moon TW. Quantitation of CP4 5-Enolpyruvylshikimate-3-Phosphate synthase in soybean by two-dimensional gel electrophoresis. J Microbiol Biotechnol 2006, 16(1):25-31.
14. Barbosa HS, Arruda SC, Azevedo RA, Arruda MA. New insights on proteomics of transgenic soybean seeds: evaluation of differential expressions of enzymes and proteins. Anal Bioanal Chem 2012, 402(1):299-314. 10.1007/s00216-011-5409-1, 21947011.
15. Natarajan SS, Xu C, Bae H, Caperna TJ, Garrett WM. Characterization of storage proteins in wild (Glycine soja) and cultivated (Glycine max) soybean seeds using proteomic analysis. J Agric Food Chem 2006, 54(8):3114-3120. 10.1021/jf052954k, 16608239.
16. Aghaei K, Ehsanpour AA, Shah AH, Komatsu S. Proteome analysis of soybean hypocotyl and root under salt stress. Amino Acids 2009, 36(1):91-98. 10.1007/s00726-008-0036-7, 18264660.
17. Komatsu S, Ahsan N. Soybean proteomics and its application to functional analysis. J Proteomics 2009, 72(3):325-336. 10.1016/j.jprot.2008.10.001, 19022415.
18. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 2006, 1(6):2856-2860.
19. Yang Y, Zhang S, Howe K, Wilson DB, Moser F, Irwin D, Thannhauser TW. A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics. J Biomol Tech 2007, 18:226-237. 2062563, 17916795.
20. Mooney BP, Krishnan HB, Thelen JJ. High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification. Phytochemistry 2004, 65(12):1733-1744. 10.1016/j.phytochem.2004.04.011, 15276434.
21. Nogueira SB, Labate CA, Gozzo FC, Pilau EJ, Lajolo FM, Oliveira do Nascimento JR. Proteomic analysis of papaya fruit ripening using 2DE-DIGE. J Proteomics 2012, 75(4):1428-1439. 10.1016/j.jprot.2011.11.015, 22134357.
22. Brandao AR, Barbosa HS, Arruda MA. Image analysis of two-dimensional gel electrophoresis for comparative proteomics of transgenic and non-transgenic soybean seeds. J Proteomics 2010, 73(8):1433-1440. 10.1016/j.jprot.2010.01.009, 20123049.
23. Murad AM, Souza GH, Garcia JS, Rech EL. Detection and expression analysis of recombinant proteins in plant-derived complex mixtures using nanoUPLC-MS(E). J Sep Sci 2011, 34(19):2618-2630. 10.1002/jssc.201100238, 21898799.
24. Shen Y, Zhao R, Berger SJ, Anderson GA, Rodriguez N, Smith RD. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem 2002, 74:4235-4249. 10.1021/ac0202280, 12199598.
25. Liu H, Finch JW, Lavallee MJ, Collamati RA, Benevides CC, Gebler JC. Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations. J Chromatogr A 2007, 1147(1):30-36. 10.1016/j.chroma.2007.02.016, 17320886.
26. Levin Y, Wang L, Ingudomnukul E, Schwarz E, Baron-Cohen S, Palotás A, Bahn S. Real-time evaluation of experimental variation in large-scale LC-MS/MS-based quantitative proteomics of complex samples. J Chromatogr B 2009, 877:1299-1305.
27. Geromanos SJ, Vissers JPC, Silva JC, Dorschel CA, Li G-Z, Gorenstein MV, Bateman RH, Langridge JI. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009, 9(6):1683-1695. 10.1002/pmic.200800562, 19294628.
28. Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2005, 5(1):144-156. 10.1074/mcp.M500230-MCP200, 16219938.
29. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al. The universal protein resource (UniProt). Nucleic Acids Res 2005, 33(Database issue):D154-D159. 540024, 15608167.
30. Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R. UniProt archive. Bioinformatics 2004, 20(17):3236-3237. 10.1093/bioinformatics/bth191, 15044231.
31. Li G-Z, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009, 9:1696-1719. 10.1002/pmic.200800564, 19294629.
32. Sakata K, Ohyanagi H, Nobori H, Nakamura T, Hashiguchi A, Nanjo Y, Mikami Y, Yunokawa H, Komatsu S. Soybean proteome database: a data resource for plant differential omics. J Proteome Res 2009, 8(7):3539-3548. 10.1021/pr900229k, 19489578.
33. Shutov AD, Kakhovskaya IA, Bastrygina AS, Bulmaga VP, Horstmann C, Muntz K. Limited proteolysis of beta-conglycinin and glycinin, the 7S and 11S storage globulins from soybean [Glycine max (L.) Merr.]. Structural and evolutionary implications. Eur J Biochem 1996, 241(1):221-228. 10.1111/j.1432-1033.1996.0221t.x, 8898910.
34. Lee KJ, Kim JB, Ha BK, Kim SH, Kang SY, Lee BM, Kim DS. Proteomic characterization of Kunitz trypsin inhibitor variants, Tia and Tib, in soybean [Glycine max (L.) Merrill]. Amino Acids 2011, 43(1):379-388.
35. Wang W, Vinocur B, Altman A. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 2003, 218(1):1-14. 10.1007/s00425-003-1105-5, 14513379.
36. Hill JE, Breidenbach RW. Proteins of soybean seeds: II. Accumulation of the major protein components during seed development and maturation. Plant Physiol 1974, 53(5):747-751. 10.1104/pp.53.5.747, 541438, 16658782.
37. Hsing YC, Tsou CH, Hsu TF, Chen ZY, Hsieh KL, Hsieh JS, Chow TY. Tissue- and stage-specific expression of a soybean (Glycine max L.) seed-maturation, biotinylated protein. Plant Mol Biol 1998, 38(3):481-490. 10.1023/A:1006079926339, 9747855.
38. Robic G, Farinas CS, Rech EL, Miranda EA. Transgenic soybean seed as protein expression system: aqueous extraction of recombinant beta-glucuronidase. Appl Biochem Biotechnol 2010, 160(4):1157-1167. 10.1007/s12010-009-8637-5, 19412577.