Evaluation of changes induced in rice metabolome by Cd and Cu exposure using LC-MS with XCMS and MCR-ALS data analysis strategies

Analytical and Bioanalytical Chemistry

Volumn 407, Issue 29, 2015, Pages 8835-8847

  Navarro Reig, Meritxell ^a   Jaumot, Joaquim ^a   García Reiriz, Alejandro ^a,b   Tauler, Romà ^a  

^a INSTITUTE OF ENVIRONMENTAL ASSESSMENT AND WATER RESEARCH   (Spain)

^b Universidad Nacional de Rosario   (Argentina)

Author keywords

Cd; Cu; LC MS; MCR ALS; Metabolomics; Rice; Sample discrimination; XCMS

Indexed keywords

BIOMOLECULES; CHROMATOGRAPHY; COPPER; DATA HANDLING; ENVIRONMENTAL CHAMBERS; ENVIRONMENTAL TESTING; INFORMATION ANALYSIS; MASS SPECTROMETRY; METABOLITES; TISSUE; TISSUE ENGINEERING;

CD; LC-MS; MCR-ALS; METABOLOMICS; RICE; XCMS;

METAL ANALYSIS;

CADMIUM; COPPER;

CHEMISTRY; GROWTH, DEVELOPMENT AND AGING; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LEAST SQUARE ANALYSIS; MASS SPECTROMETRY; METABOLISM; METABOLOME; MULTIVARIATE ANALYSIS; ORYZA;

CADMIUM; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COPPER; LEAST-SQUARES ANALYSIS; MASS SPECTROMETRY; METABOLOME; MULTIVARIATE ANALYSIS; ORYZA;

EID: 84947037595     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-015-9042-2     Document Type: Article

References (41)

1. Fukusaki E, Kobayashi A (2005) Plant metabolomics: potential for practical operation. J Biosci Bioeng 100(4):347-354
2. Xiao JF, Zhou B, Ressom HW (2012) Metabolite identification and quantitation in LC-MS/MS-based metabolomics. TrAC Trends Anal Chem 32:1-14
3. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13(1):11-29
4. Lommen A (2009) Metalign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81(8):3079-3086
5. Pluskal T, Castillo S, Villar-Briones A, Orešič M (2010) MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395
6. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78(3):779-787
7. Johnson CH, Ivanisevic J, Benton HP, Siuzdak G (2015) Bioinformatics: the next frontier of metabolomics. Anal Chem 87(1):147-156
8. Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G (2012) XCMS online: A web-based platform to process untargeted metabolomic data. Anal Chem 84(11):5035-5039
9. Jaumot J, de Juan A, Tauler R (2015) MCR-ALS GUI 2.0: new features and applications. Chemometr Intell Lab 140:1-12
10. Farrés M, Piña B, Tauler R (2014) Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC-MS. Metabolomics 11:210-224
11. Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163
12. D'Alessandro A, Taamalli M, Gevi F, Timperio AM, Zolla L, Ghnaya T (2013) Cadmium stress responses in Brassica juncea: hints from proteomics and metabolomics. J Proteome Res 12(11):4979-4997
13. Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C, Bourguignon J (2011) Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches. Proteomics 11(9):1650-1663
14. Järup L (2003) Hazards of heavy metal contamination. Brit Med Bull 68(1):167-182
15. Ahsan N, Nakamura T, Komatsu S (2012) Differential responses of microsomal proteins and metabolites in two contrasting cadmium (Cd)-accumulating soybean cultivars under Cd stress. Amino Acids 42(1):317-327
16. Antti H, Ebbels TMD, Keun HC, Bollard ME, Beckonert O, Lindon JC, Nicholson JK, Holmes E (2004) Statistical experimental design and partial least squares regression analysis of biofluid metabonomic NMR and clinical chemistry data for screening of adverse drug effects. Chemometr Intell Lab 73(1 SPEC. ISS):139-149
17. Johnson HE, Lloyd AJ, Mur LAJ, Smith AR, Causton DR (2007) The application of MANOVA to analyse Arabidopsis thaliana metabolomic data from factorially designed experiments. Metabolomics 3(4):517-530
18. Aina R, Labra M, Fumagalli P, Vannini C, Marsoni M, Cucchi U, Bracale M, Sgorbati S, Citterio S (2007) Thiol-peptide level and proteomic changes in response to cadmium toxicity in Oryza sativa L. roots. Environ Exp Bot 59(3):381-392
19. Roth U, Von Roepenack-Lahaye E, Clemens S (2006) Proteome changes in Arabidopsis thaliana roots upon exposure to Cd 2+. J Exp Bot 57(15):4003-4013
20. Huang SM, Toh W, Benke PI, Tan CS, Ong CN (2014). MetaboNexus: an interactive platform for integrated metabolomics analysis. Metabolomics 10:1084-1093
21. Prince JT, Marcotte EM (2006) Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem 78(17):6140-6152
22. Tautenhahn R, Bottcher C, Neumann S (2008) Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics 9:504
23. De Juan A, Jaumot J, Tauler R (2014) Multivariate Curve Resolution (MCR). Solving the mixture analysis problem. Anal Methods 6(14):4964-4976
24. de Juan A, Tauler R (2007) Factor analysis of hyphenated chromatographic data. Exploration, resolution and quantification of multicomponent systems. J Chromatogr A 1158(1-2):184-195
25. Ruckebusch C, Blanchet L (2013) Multivariate curve resolution: a review of advanced and tailored applications and challenges. Anal Chim Acta 765:28-36
26. Golub GH, Loan CFV (1996) Matrix computations, 3rd edn. Johns Hopkins University Press, Baltimore
27. Windig W, Guilment J (1991) Interactive self-modeling mixture analysis. Anal Chem 63(14):1425-1432
28. Tauler R, Maeder M, de Juan A (2010) Multiset data analysis: extended multivariate curve resolution. In: Brown SD, Tauler R, Walczak, B (ed) Comprehensive Chemometrics, vol 2. Elsevier B.V., Amsterdam, pp 473-505
29. Wold S, Esbensen K, Geladi P (1987) Principal component analysis. Chemometr Intell Lab 2(1-3):37-52
30. Barker M, Rayens W (2003) Partial least squares for discrimination. J Chemom 17(3):166-173
31. Jansen JJ, Hoefsloot HCJ, Van Der Greef J, Timmerman ME, Westerhuis JA, Smilde AK (2005) ASCA: analysis of multivariate data obtained from an experimental design. J Chemom 19(9):469-481
32. Kuhl C, Tautenhahn R, Böttcher C, Larson TR, Neumann S (2012) CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem 84(1):283-289
33. Ortiz-Villanueva E, Jaumot J, Benavente F, Piña B, Sanz-Nebot V, Tauler R (2015) Combination of CE-MS and advanced chemometric methods for high-throughput metabolic profiling. Electrophoresis 36:2324-2335
34. Schmidtke LM, Blackman JW, Clark AC, Grant-Preece P (2013) Wine metabolomics: objective measures of sensory properties of semillon from GC-MS profiles. J Agric Food Chem 61(49):11957-11967
35. Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45(7):703-714
36. Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G (2012) An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol 30(9):826-828
37. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, de Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythei I (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37(Suppl 1):D603-D610
38. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(D1):D109-D114
39. Sun X, Zhang J, Zhang H, Ni Y, Zhang Q, Chen J, Guan Y (2010) The responses of Arabidopsis thaliana to cadmium exposure explored via metabolite profiling. Chemosphere 78(7):840-845
40. Satterfield M, Brodbelt JS (2001) Structural characterization of flavonoid glycosides by collisionally activated dissociation of metal complexes. J Am Soc Mass Spectrom 12(5):537-549
41. Gyurcsik B, Nagy L (2000) Carbohydrates as ligands: coordination equilibria and structure of the metal complexes. Coordin Chem Rev 203(1):81-149