Correlative GC-TOF-MS-based metabolite profiling and LC-MS-based protein profiling reveal time-related systemic regulation of metabolite-protein networks and improve pattern recognition for multiple biomarker selection

Metabolomics

Volumn 1, Issue 2, 2005, Pages 109-121

  Morgenthal, Katja ^a   Wienkoop, Stefanie ^a   Scholz, Matthias ^a   Selbig, Joachim ^a   Weckwerth, Wolfram ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Diurnal rhythm; ICA; Metabolomics; Multivariate data analysis; PCA; Proteomics; Shotgun proteomics; Systems biology; Unsupervised methods

Indexed keywords

AMINO ACID; BIOLOGICAL MARKER; CARBOHYDRATE; CARBON; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GLYCERIC ACID; GLYCINE; ISOPROTEIN; NITROGEN; PHOSPHOGLUCOMUTASE; STARCH; UREA;

ARABIDOPSIS; ARTICLE; CARBON PARTITIONING; CARBON UTILIZATION; CHLOROPLAST; CIRCADIAN RHYTHM; CONTROLLED STUDY; CORRELATION ANALYSIS; CYTOSOL; ENZYME ACTIVITY; GAS CHROMATOGRAPHY; GENE MUTATION; GROWTH INHIBITION; INDEPENDENT COMPONENT ANALYSIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLITE; MULTIVARIATE ANALYSIS; NITROGEN PARTITIONING; NONHUMAN; PATTERN RECOGNITION; PHOTORESPIRATION; PLANT METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PROTEIN ANALYSIS; PROTEIN DEGRADATION; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TIME; TIME OF FLIGHT MASS SPECTROMETRY; UREA CYCLE; WILD TYPE;

ARABIDOPSIS THALIANA;

EID: 20344392462     PISSN: 15733882     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11306-005-4430-9     Document Type: Article

References (57)

1. T. Blaschke and L. Wiskott 2004 CuBICA: Independent component analysis by simultaneous third- and fourth-order cumulant diagonalization IEEE Trans. Signal Process. 52 1250-1256 10.1109/TSP.2004.826173 MR2061981
2. D.C. Boyes A.M. Zayed R. Ascenzi A.J. McCaskill N.E. Hoffman K.R. Davis and J. Gorlach 2001 Growth stage-based phenotypic analysis of arabidopsis: A model for high throughput functional genomics in plants Plant Cell 13 1499-1510 10.1105/tpc.13.7.1499 1:CAS:528:DC%2BD3MXlsFKltrk%3D 11449047
3. Camacho, D., Fuente, A.D.L. and Mendes, P. (2005). The origin of correlations in metabolomics data. Metabolomics (in press).
4. Y. Cao D.D. Williams and N.E. Williams 1999 Data transformation and standardization in the multivariate analysis of river water quality Ecol. Appl. 9 669-677
5. T. Caspar S.C. Huber and C. Somerville 1985 Alterations in growth, photosynthesis, and respiration in a starchless mutant of Arabidopsis thaliana (L) deficient in chloroplast phosphoglucomutase activity Plant Physiol. 79 11-17 1:CAS:528:DyaL2MXlvFehs74%3D
6. J.O. Castrillo and S.G. Oliver 2004 Yeast as a touchstone in post-genomic research: Strategies for integrative analysis in functional genomics J. Biochem. Mol. Biol. 37 93-106 1:CAS:528:DC%2BD2cXhtlWgt7w%3D 14761307
7. Cichocki, A. and Amari, S. (2002). Adaptive Blind Signal and Image Processing: Learning Algorithms and Applications. Wiley
8. J.W. Collister G. Rieley B. Stern G. Eglinton and B. Fry 1994 Compound-specific delta-C-13 analyses of leaf lipids from plants with differing carbon-dioxide metabolisms Organic Geochem. 21 619-627 10.1016/ 0146-6380(94)90008-6 1:CAS:528:DyaK2cXlslGhtr4%3D
9. M. Cooper S. Chapman D. Podlich and G. Hammer 2002 The GP problem: quantifying gene-to-phenotype relationships In Silico Biol. 2 151-164 1:CAS:528:DC%2BD38XlsFWitbk%3D 12066839
10. K. Diamantaras and S. Kung 1996 Principal Component Neural Networks Wiley New York
11. O. Fiehn 2002 Metabolomics - the link between genotypes and phenotypes Plant Mol. Biol. 48 155-171 10.1023/A:1013713905833 1:CAS:528:DC%2BD38Xht1Kqtr0%3D 11860207
12. O. Fiehn J. Kopka P. Dormann T. Altmann R.N. Trethewey and L. Willmitzer 2000 Metabolite profiling for plant functional genomics Nat. Biotechnol. 18 1157-1161 10.1038/81137 1:CAS:528:DC%2BD3cXotVSmtL0%3D 11062433
13. D.R. Geiger and J.C. Servaites 1994 Diurnal regulation of photosynthetic carbon metabolism in C-3 plants Ann. Rev. Plant Physiol.- Plant Mol. Biol. 45 235-256 10.1146/annurev.pp.45.060194.001315
14. R. Gerhardt M. Stitt and H.W. Heldt 1987 Subcellular metabolite levels in spinach leaves - regulation of sucrose synthesis during diurnal alterations in photosynthetic partitioning Plant Physiol. 83 399-407 1:CAS:528:DyaL2sXhsleisL0%3D
15. Y. Gibon O. Blaesing J. Hannemann P. Carillo M. Hohne J. Hendriks N. Palacios J. Cross J. Selbig and M. Stitt 2004a A Robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness Plant Cell 16 3304-3325 10.1105/tpc.104.025973 1:CAS:528:DC%2BD2MXhtVKlsQ%3D%3D
16. Y. Gibon O.E. Blasing N. Palacios-Rojas D. Pankovic J.H.M. Hendriks J. Fisahn M. Hohne M. Gunther and M. Stitt 2004b Adjustment of diurnal starch turnover to short days: Depletion of sugar during the night leads to a temporary inhibition of carbohydrate utilization, accumulation of sugars and post-translational activation of ADP-glucose pyrophosphorylase in the following light period Plant J. 39 847-862 10.1111/j.1365-313X.2004.02173.x 1:CAS:528:DC%2BD2cXpt1GntLo%3D
17. M. Glinski T. Romeis C. Witte S. Wienkoop and W. Weckwerth 2003 Stable isotope labeling of phosphopeptides for multiparallel kinase target analysis and identification of phosphorylation sites Rapid Commun. Mass Spectrom. 17 1579-1584 10.1002/rcm.1093 1:CAS:528:DC%2BD3sXlsFGmurY%3D 12845583
18. R. Goodacre 2003 Explanatory analysis of spectroscopic data using machine learning of simple, interpretable rules Vibrat. Spectroscopy 32 33-45 10.1016/S0924-2031(03)00045-6 1:CAS:528:DC%2BD3sXls1alsb4%3D
19. R. Goodacre S. Vaidyanathan W.B. Dunn G.G. Harrigan and D.B. Kell 2004 Metabolomics by numbers: Acquiring and understanding global metabolite data Trends Biotechnol. 22 245-252 10.1016/j.tibtech.2004.03.007 1:CAS:528:DC%2BD2cXjtl2lt7k%3D 15109811
20. J.M. Halket A. Przyborowska S.E. Stein W.G. Mallard S. Down and R.A. Chalmers 1999 Deconvolution gas chromatography mass spectrometry of urinary organic acids - potential for pattern recognition and automated identification of metabolic disorders Rapid Commun. Mass Spectrom. 13 279-284 10.1002/ (SICI)1097-0231(19990228)13:4<279::AID-RCM478>3.0.CO;2-I 1:CAS:528:DyaK1MXhtlKntrw%3D 10097403
21. Hyvärinen, A., Karhunen, J. and Oja, E. (2001). Independent Component Analysis. J. Wiley
22. J. Ihmels R. Levy and N. Barkai 2004 Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae Nat. Biotechnol. 22 86-92 10.1038/nbt918 1:CAS:528:DC%2BD2cXls1ar 14647306
23. D.B. Kell 2002 Metabolomics and machine learning: Explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules Mol. Biol. Rep. 29 237-241 10.1023/A:1020342216314 1:CAS:528:DC%2BD38Xnt1agur8%3D 12241064
24. D. Kell and P. Mendes 2000 Snapshots of systems: Metabolic control analysis and biotechnology in the postgenomic era in A.J. Cornish-Bowden M.L. Cardenas (Eds.) Technological and Medical Implications of Metabolic Control Analysis Kluwer Academic Publishers Netherland 2-25
25. E. Kovats 1958 Gas-Chromatographische Charakterisierung Organischer Verbindungen. 1. Retentionsindices Aliphatischer Halogenide, Alkohole, Aldehyde Und Ketone Helv. Chim. Acta 41 1915-1932 10.1002/ hlca.19580410703
26. C. Leonard and R. Sacks 1999 Tunable-column selectivity and time-of-flight detection for high-speed GC/MS Anal. Chem. 71 5177-5184 10.1021/ac990631f 1:CAS:528:DyaK1MXmsVensLk%3D
27. J. Lippincott and I. Apostol 1999 Carbamylation of cysteine: A potential artifact in peptide mapping of hemoglobins in the presence of urea Anal. Biochem. 267 57-64 10.1006/abio.1998.2970 1:CAS:528:DyaK1MXotlGqtw%3D%3D 9918655
28. J.K. Nicholson J. Connelly J.C. Lindon and E. Holmes 2002 Metabonomics: a platform for studying drug toxicity and gene function Nat. Rev. Drug Discovery 1 153-161 10.1038/nrd728 1:CAS:528:DC%2BD38Xhs1aksbw%3D
29. J.K. Nicholson J.C. Lindon and E. Holmes 1999 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Xenobiotica 29 1181-1189 10.1080/ 004982599238047 1:CAS:528:DyaK1MXns12ms7k%3D 10598751
30. K.H. Ott N. Aranibar B.J. Singh and G.W. Stockton 2003 Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts Phytochemistry 62 971-985 10.1016/S0031-9422(02)00717-3 1:CAS:528:DC%2BD3sXhtVeltrY%3D 12590124
31. J. Peng J.E. Elias C.C. Thoreen L.J. Licklider and S.P. Gygi 2003 Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome J. Proteome Res. 2 43-50 10.1021/pr025556v 1:CAS:528:DC%2BD38XnvVOitro%3D 12643542
32. U. Roessner C. Wagner J. Kopka R.N. Trethewey and L. Willmitzer 2000 Simultaneous analysis of metabolites in potato tuber by gas chromatography - mass spectrometry Plant J. 23 131-142 10.1046/ j.1365-313x.2000.00774.x 1:CAS:528:DC%2BD3cXlvFWnsrc%3D 10929108
33. U. Roessner-Tunali E. Urbanczyk-Wochniak T. Czechowski A. Kolbe L. Willmitzer and A.R. Fernie 2003 De novo amino acid biosynthesis in potato tubers is regulated by sucrose levels Plant Physiol. 133 683-692 10.1104/pp.103.024802 1:CAS:528:DC%2BD3sXosVaqtLo%3D 14512520
34. Roweis, S.T. and Saul, L.K. (2000). Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323-2326
35. H. Sauter M. Lauer and H. Fritsch 1991 Metabolic profiling of plants - a new diagnostic-technique Acs Symp. Series 443 288-299 1:CAS:528:DyaK3MXhsFyqu7Y%3D
36. M. Scholz S. Gatzek A. Sterling O. Fiehn and J. Selbig 2004 Metabolite fingerprinting: Detecting biological features by independent component analysis Bioinformatics 20 2447-2454 10.1093/bioinformatics/bth270 1:CAS:528:DC%2BD2cXos1GisLs%3D 15087312
37. Scholz, M. and Vigário, R. (2002). Nonlinear PCA: A new hierarchical approach. Proc. ESANN. 439-444
38. R. Steuer J. Kurths O. Fiehn and W. Weckwerth 2003 Observing and interpreting correlations in metabolomic networks Bioinformatics 19 1019-1026 10.1093/bioinformatics/btg120 1:CAS:528:DC%2BD3sXktVCgs7g%3D 12761066
39. L.W. Sumner P. Mendes and R.A. Dixon 2003 Plant metabolomics: large-scale phytochemistry in the functional genomics era Phytochemistry 62 817-836 10.1016/S0031-9422(02)00708-2 1:CAS:528:DC%2BD3sXhtVeltr0%3D 12590110
40. D.L. Tabb W.H. McDonald and J.R. Yates 2002 DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics J. Proteome Res. 1 21-26 10.1021/pr015504q 1:CAS:528:DC%2BD38XhsFektro%3D 12643522
41. B.H. ter Kuile and H.V. Westerhoff 2001 Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway FEBS Lett. 500 169-171 10.1016/S0014-5793(01)02613-8 1:CAS:528:DC%2BD3MXkvVelsL4%3D 11445079
42. O. Thimm O. Blasing Y. Gibon A. Nagel S. Meyer P. Kruger J. Selbig L.A. Muller S.Y. Rhee and M. Stitt 2004 MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes Plant J. 37 914-939 10.1111/ j.1365-313X.2004.02016.x 1:CAS:528:DC%2BD2cXjtFChu78%3D 14996223
43. R.N. Trethewey A.J. Krotzky and L. Willmitzer 1999 Metabolic profiling: a Rosetta Stone for genomics? Curr. Opin. Plant Biol. 2 83-85 10.1016/ S1369-5266(99)80017-X 1:STN:280:DyaK1M3lslCqug%3D%3D 10322197
44. E. Urbanczyk-Wochniak A. Luedemann J. Kopka J. Selbig U. Roessner-Tunali L. Willmitzer and A.R. Fernie 2003 Parallel analysis of transcript and metabolic profiles: A new approach in systems biology EMBO Rep. 4 989-993 10.1038/sj.embor.embor944 1:CAS:528:DC%2BD3sXnslaqt7g%3D 12973302
45. T. Veriotti and R. Sacks 2001 High-speed GC and GC/time-of-flight MS of lemon and lime oil samples Anal. Chem. 73 4395-4402 10.1021/ac010239d 1:CAS:528:DC%2BD3MXlslyqt7o%3D 11575784
46. M.R. Viant 2003 Improved methods for the acquisition and interpretation of NMR metabolomic data Biochem. Biophys. Res. Commun. 310 943-948 10.1016/j.bbrc.2003.09.092 1:CAS:528:DC%2BD3sXnvVylurY%3D 14550295
47. A. Wagner 1997 Causality in complex systems Biol. Philos. 14 83-101 10.1023/A:1006580900476
48. J.T. Watson G.A. Schultz R.E. Tecklenburg and J. Allison 1990 Renaissance of Gas-chromatography time-of-flight mass-spectrometry - meeting the challenge of capillary columns with a beam deflection instrument and time array detection J. Chromatogr. 518 283-295 10.1016/S0021-9673(01)93190-5 1:CAS:528:DyaK3cXmt1ertL0%3D 2254386
49. Webb, J.W., Gates, S.C., Comiskey, J.P. and Weber, D.F. (1986). Metabolic profiling of corn plants using HPLC and GC/MS. Abstracts of Papers of the American Chemical Society 191, 70-ANYL
50. W. Weckwerth 2003 Metabolomics in systems biology Ann. Rev. Plant Biol. 54 669-689 10.1146/annurev.arplant.54.031902.135014 1:CAS:528:DC%2BD3sXntFSns78%3D
51. W. Weckwerth and O. Fiehn 2002 Can we discover novel pathways using metabolomic analysis? Curr. Opin. Biotechnol. 13 156-160 10.1016/ S0958-1669(02)00299-9 1:CAS:528:DC%2BD38Xis1CltL0%3D 11950569
52. W. Weckwerth M.E. Loureiro K. Wenzel and O. Fiehn 2004a Differential metabolic networks unravel the effects of silent plant phenotypes Proc. Natl. Acad. Sci. USA 101 7809-7814 10.1073/pnas.0303415101 1:CAS:528:DC%2BD2cXktlOksr0%3D
53. Weckwerth, W., Tolstikov, V. and Fiehn, O. (2001). Metabolomic characterization of transgenic potato plants using GC/TOF and LC-MS analysis reveals silent metabolic phenotypes. Proceedings of the 49th ASMS Conference on Mass spectrometry and Allied Topics, American Society of Mass Spectrometry, Chicago, pp. 1-2
54. W. Weckwerth K. Wenzel and O. Fiehn 2004b Process for the integrated extraction identification, and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks Proteomics 4 78-83 10.1002/pmic.200200500 1:CAS:528:DC%2BD2cXhtVamur4%3D
55. S. Wienkoop M. Glinski N. Tanaka V. Tolstikov O. Fiehn and W. Weckwerth 2004a Linking protein fractionation with multidimensional monolithic RP peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins Rapid Commun. Mass Spectrom. 18 643-650 10.1002/rcm.1376 1:CAS:528:DC%2BD2cXivVCgsLc%3D
56. S. Wienkoop D. Zoeller B. Ebert U. Simon-Rosin J. Fisahn M. Glinski and W. Weckwerth 2004b Cell-specific protein profiling in Arabidopsis thaliana trichomes: Identification of trichome-located proteins involved in sulfur metabolism and detoxification Phytochemistry 65 1641-1649 10.1016/j.phytochem.2004.03.026 1:CAS:528:DC%2BD2cXmtVCjs7o%3D
57. H. Winter and S.C. Huber 2000 Regulation of sucrose metabolism in higher plants: Localization and regulation of activity of key enzymes Crit. Rev. Biochem. Mol. Biol. 35 253-289 1:CAS:528:DC%2BD3cXntFajtrk%3D 11005202