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A non-directed approach to the differential analysis of multiple LC–MS-derived metabolic profiles

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An essential element of any strategy for non-targeted metabolomics analysis of complex biological extracts is the capacity to perform comparisons between large numbers of samples. As the most widely used technologies are all based on mass spectrometry (e.g. GCMS, LCMS), this entails that we must be able to compare reliably and (semi)automatically large series of chromatographic mass spectra from which compositional differences are to be extracted in a statistically justifiable manner. In this paper we describe a novel approach for the extraction of relevant information from multiple full-scan metabolic profiles derived from LC–MS analyses. Specifically-designed software has made it possible to combine all mass peaks on the basis of retention time and m/z values only, without prior identification, to produce a data matrix output which can then be used for multivariate statistical analysis. To demonstrate the capacity of this approach, aqueous methanol extracts from potato tuber tissues of eight contrasting genotypes, harvested at two developmental stages have been used. Our results showed that it is possible to discover reproducibly discriminatory mass peaks related both to the genetic origin of the material as well as the developmental stage at which it was harvested. In addition the limitations of the approach are explored by a careful evaluation of the alignment quality.

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References

  • A. Aharoni O. Vorst (2002) ArticleTitleDNA microarrays for functional plant genomics Plant Mol. Biol. 48 99–118 Occurrence Handle10.1023/A:1013734019946 Occurrence Handle1:CAS:528:DC%2BD38Xht1Kqsbc%3D Occurrence Handle11860216

    Article  CAS  PubMed  Google Scholar 

  • R.J. Bino R.D. Hall O. Fiehn et al. (2004) ArticleTitlePotential of metabolomics as a functional genomics tool Trends Plant Sci. 9 418–425 Occurrence Handle10.1016/j.tplants.2004.07.004 Occurrence Handle1:CAS:528:DC%2BD2cXntVOjt7w%3D Occurrence Handle15337491

    Article  CAS  PubMed  Google Scholar 

  • F.M. Cánovas E. Dumas-Gaudot G. Recorbet J. Jorrin H.P. Mock M Rossignol (2004) ArticleTitlePlant proteome analysis Proteomics 4 285–298 Occurrence Handle10.1002/pmic.200300602 Occurrence Handle14760698

    Article  PubMed  Google Scholar 

  • Celis Gamboa, B.C. (2002) The life cycle of the potato(Solanum tuberosum L.): from physiology to genetics. Ph.D. thesis, Wageningen, 186 pp

  • A.R. Fernie R.N. Trethewey A.J. Krotzky L. Willmitzer (2004) ArticleTitleMetabolite profiling: from diagnostics to systems biology Nat. Rev. Mol. Cell Biol. 5 763–769 Occurrence Handle10.1038/nrm1451 Occurrence Handle1:CAS:528:DC%2BD2cXntFCms7s%3D Occurrence Handle15340383

    Article  CAS  PubMed  Google Scholar 

  • O. Fiehn (2002) ArticleTitleMetabolomics – the link between genotypes and phenotypes Plant Mol. Biol. 48 155–171 Occurrence Handle10.1023/A:1013713905833 Occurrence Handle1:CAS:528:DC%2BD38Xht1Kqtr0%3D Occurrence Handle11860207

    Article  CAS  PubMed  Google Scholar 

  • O. Fiehn J. Kopka P. Dörmann T. Altmann R.N. Trethewey L. Willmitzer (2000) ArticleTitleMetabolite profiling for plant functional genomics Nat. Biotechnol. 18 1157–1161 Occurrence Handle10.1038/81137 Occurrence Handle1:CAS:528:DC%2BD3cXotVSmtL0%3D Occurrence Handle11062433

    Article  CAS  PubMed  Google Scholar 

  • K. Gallardo C. Job S.P. Groot et al. (2002) ArticleTitleProteomics of Arabidopsis seed germination. A comparative study of wild-type and gibberellin-deficient seeds Plant Physiol. 129 823–837 Occurrence Handle10.1104/pp.002816 Occurrence Handle1:CAS:528:DC%2BD38XkvV2jt7c%3D Occurrence Handle12068122

    Article  CAS  PubMed  Google Scholar 

  • A. Goossens S.T. Hakkinen I. Laakso et al. (2003) ArticleTitleA functional genomics approach toward the understanding of secondary metabolism in plant cells Proc. Natl Acad. Sci. USA 100 8595–8600 Occurrence Handle10.1073/pnas.1032967100 Occurrence Handle1:CAS:528:DC%2BD3sXlsFGnu7g%3D Occurrence Handle12826618

    Article  CAS  PubMed  Google Scholar 

  • R. Hall M. Beale O. Fiehn N. Hardy L. Sumner R. Bino (2002) ArticleTitlePlant metabolomics: the missing link in functional genomics strategies Plant Cell 14 1437–1440 Occurrence Handle10.1105/tpc.140720 Occurrence Handle1:CAS:528:DC%2BD38XlvV2rsLs%3D Occurrence Handle12119365

    Article  CAS  PubMed  Google Scholar 

  • M.Y. Hirai M. Yano D.B. Goodenowe et al. (2004) ArticleTitleIntegration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana Proc. Natl Acad. Sci. USA 101 10205–10210 Occurrence Handle10.1073/pnas.0403218101 Occurrence Handle1:CAS:528:DC%2BD2cXlvFOhsbw%3D Occurrence Handle15199185

    Article  CAS  PubMed  Google Scholar 

  • A. Lommen J.M. Weseman G.O. Smith H.P.J.M Noteborn (1998) ArticleTitleOn the detection of environmental effects on complex matrices combining off-line liquid chromatography and 1H-NMR Biodegradation 9 513–525 Occurrence Handle10.1023/A:1008398321079 Occurrence Handle1:CAS:528:DyaK1MXltVKis7Y%3D

    Article  CAS  Google Scholar 

  • B.C. Meyers D.W. Galbraith T. Nelson V. Agrawal (2004) ArticleTitleMethods for transcriptional profiling in plants. Be fruitful and replicate Plant Physiol. 135 637–652 Occurrence Handle10.1104/pp.104.040840 Occurrence Handle1:CAS:528:DC%2BD2cXltlKjtbo%3D Occurrence Handle15173570

    Article  CAS  PubMed  Google Scholar 

  • H.P.J.M. Noteborn A. Lommen R.C. Jagt Particlevan der J.M. Weseman (2000) ArticleTitleChemical fingerprinting for the evaluation of unintended secondary metabolic changes in transgenic food crops J. Biotechnol. 77 103–114 Occurrence Handle10.1016/S0168-1656(99)00210-2 Occurrence Handle1:CAS:528:DC%2BD3cXhtlyitbw%3D Occurrence Handle10674217

    Article  CAS  PubMed  Google Scholar 

  • U. Roessner A. Luedemann D. Brust et al. (2001) ArticleTitleMetabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems Plant Cell 13 11–29 Occurrence Handle1:CAS:528:DC%2BD3MXjslCrtr4%3D Occurrence Handle11158526

    CAS  PubMed  Google Scholar 

  • U. Roessner C. Wagner J. Kopka R.N. Trethewey L. Willmitzer (2000) ArticleTitleTechnical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry Plant J. 23 131–142 Occurrence Handle10.1046/j.1365-313x.2000.00774.x Occurrence Handle1:CAS:528:DC%2BD3cXlvFWnsrc%3D Occurrence Handle10929108

    Article  CAS  PubMed  Google Scholar 

  • U. Roessner L. Willmitzer A.R. Fernie (2001) ArticleTitleHigh-resolution metabolomic phenotyping of genetically and environmentally diverse potato tuber systems. Identification of phenocopies Plant Physiol. 127 749–764 Occurrence Handle10.1104/pp.127.3.749 Occurrence Handle1:CAS:528:DC%2BD3MXos1Kntb4%3D Occurrence Handle11706160

    Article  CAS  PubMed  Google Scholar 

  • P.S. Schnable F. Hochholdinger M. Nakazono (2004) ArticleTitleGlobal expression profiling applied to plant development Curr. Opin. Plant Biol. 7 50–56 Occurrence Handle10.1016/j.pbi.2003.11.001 Occurrence Handle1:CAS:528:DC%2BD2cXltFWqtw%3D%3D Occurrence Handle14732441

    Article  CAS  PubMed  Google Scholar 

  • T. Soga Y. Ueno H. Naraoka K. Matsuda M. Tomita T. Nishioka (2002) ArticleTitlePressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions Anal. Chem. 74 6224–6229 Occurrence Handle10.1021/ac0202684 Occurrence Handle1:CAS:528:DC%2BD38XosFyitb0%3D Occurrence Handle12510742

    Article  CAS  PubMed  Google Scholar 

  • L.W. Sumner P. Mendes R.A. Dixon (2003) ArticleTitlePlant metabolomics: large-scale phytochemistry in the functional genomics era Phytochemistry 62 817–836 Occurrence Handle10.1016/S0031-9422(02)00708-2 Occurrence Handle1:CAS:528:DC%2BD3sXhtVeltr0%3D Occurrence Handle12590110

    Article  CAS  PubMed  Google Scholar 

  • V.V. Tolstikov O. Fiehn (2002) ArticleTitleAnalysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry Anal. Biochem. 301 298–307 Occurrence Handle10.1006/abio.2001.5513 Occurrence Handle1:CAS:528:DC%2BD38Xns1KgtQ%3D%3D Occurrence Handle11814300

    Article  CAS  PubMed  Google Scholar 

  • V.V. Tolstikov A. Lommen K. Nakanishi N. Tanaka O. Fiehn (2003) ArticleTitleMonolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics Anal. Chem. 75 6737–6740 Occurrence Handle1:CAS:528:DC%2BD3sXosVSmsLY%3D Occurrence Handle14640754

    CAS  PubMed  Google Scholar 

  • E. Von Roepenack-Lahaye T. Degenkolb M. Zerjeski et al. (2004) ArticleTitleProfiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry Plant Physiol. 134 548–559 Occurrence Handle10.1104/pp.103.032714 Occurrence Handle1:CAS:528:DC%2BD2cXhs1CnsLc%3D Occurrence Handle14966245

    Article  CAS  PubMed  Google Scholar 

  • C. Wagner M. Sefkow J. Kopka (2003) ArticleTitleConstruction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles Phytochemistry 62 887–900 Occurrence Handle10.1016/S0031-9422(02)00703-3 Occurrence Handle1:CAS:528:DC%2BD3sXhtVelsbc%3D Occurrence Handle12590116

    Article  CAS  PubMed  Google Scholar 

  • B.S. Watson V.S. Asirvatham L. Wang L.W. Sumner (2003) ArticleTitleMapping the proteome of barrel medic (Medicago truncatula) Plant Physiol. 131 1104–1123 Occurrence Handle10.1104/pp.102.019034 Occurrence Handle12644662

    Article  PubMed  Google Scholar 

  • W. Weckwerth (2003) ArticleTitleMetabolomics in systems biology Annu. Rev. Plant Biol. 54 669–689 Occurrence Handle10.1146/annurev.arplant.54.031902.135014 Occurrence Handle1:CAS:528:DC%2BD3sXntFSns78%3D Occurrence Handle14503007

    Article  CAS  PubMed  Google Scholar 

  • W. Weckwerth K. Wenzel O. Fiehn (2004) ArticleTitleProcess for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks Proteomics 4 78–83 Occurrence Handle10.1002/pmic.200200500 Occurrence Handle1:CAS:528:DC%2BD2cXhtVamur4%3D Occurrence Handle14730673

    Article  CAS  PubMed  Google Scholar 

  • J.-C. Wolff C. Eckers A.B. Sage K. Giles R. Bateman (2001) ArticleTitleAccurate mass liquid chromatography/mass spectrometry on quadrupole orthogonal acceleration time-of-flight mass analyzers using switching between separate sample and reference sprays. 2. Applications using the dual-electrospray ion source Anal. Chem. 73 2605–2612 Occurrence Handle10.1021/ac001419a Occurrence Handle1:CAS:528:DC%2BD3MXjt1Sgtr4%3D Occurrence Handle11403306

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Plant Research International, PO Box 16, 6700 AA, Wageningen, The Netherlands

    O. Vorst, C. H. R. de Vos, A. Lommen, R. V. Staps, R. J. Bino & R. D. Hall

  2. Laboratory of Plant Breeding, PO Box 386, 6700 AJ, Wageningen, The Netherlands

    R. G. F. Visser

  3. Laboratory of Plant Physiology, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, The Netherlands

    R. J. Bino

  4. RIKILT-Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands

    A. Lommen

  5. Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB, Wageningen, The Netherlands

    R. D. Hall

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  1. O. Vorst
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  2. C. H. R. de Vos
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  3. A. Lommen
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  4. R. V. Staps
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  5. R. G. F. Visser
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  6. R. J. Bino
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Correspondence to O. Vorst.

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Vorst, O., Vos, C.H.R.d., Lommen, A. et al. A non-directed approach to the differential analysis of multiple LC–MS-derived metabolic profiles. Metabolomics 1, 169–180 (2005). https://doi.org/10.1007/s11306-005-4432-7

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  • DOI: https://doi.org/10.1007/s11306-005-4432-7

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