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Mass Spectrometry for Metabolomics and Biomass Composition Analyses

  • Maria Esther Ricci-Silva
  • Boniek Gontijo Vaz
  • Géssica Adriana Vasconcelos
  • Wanderson Romão
  • Juliana A. Aricetti
  • Camila Caldana
  • Patrícia Verardi AbdelnurEmail author
Chapter

Abstract

Mass spectrometry (MS) is a versatile technique used to analyze a broad range of compounds originated from different species with high accuracy, resolution, sensibility, selectivity, and fast scan speed. MS has been widely used in various areas, from theoretical chemistry studies to the discovery of disease biomarkers. In this chapter, we will focus on the use of MS in bioenergy, describing new developed technologies that can perform a full metabolite characterization of a biological system. The chapter is presented in three topics: (1) Mass spectrometry; (2) Mass spectrometry-based metabolomics; and (3) Mass spectrometry for biomass composition analyses. The first topic (Section 1), is about the fundamentals of MS, including some advanced applications in instrumentation that greatly contribute to chemical compound identification and characterization. The next two other topics describe the applications of MS in two important areas related to metabolite characterization that are used in the bioenergy scenario. A general description of metabolomics principles and approaches, such as targeted and untargeted analyses, was discussed, including some applications in the system biology (Section 2). Finally, an overview of agricultural biomass composition for biofuel and chemicals production, based on MS approaches, is presented in Section 3.

Keywords

Metabolomics for bioenergy Metabolomics-assisted synthetic biology Metabolite characterization Biomass characterization 

References

  1. Abdelnur PV, Vaz BG, Rocha JD, Almeida MBB, Teixeira MAG, Pereira RCL (2013) Characterization of bio-oils from different pyrolysis process steps and biomass using high-resolution mass spectrometry. Energy Fuels 27:6646–6654CrossRefGoogle Scholar
  2. Abdelnur PV, Caldana C, Martins MCM (2014) Metabolomics applied in bioenergy. Chemical and Biological Technologies in Agriculture 1(22):1–9Google Scholar
  3. Araújo P, Ferreira MS, de Oliveira DN, Pereira L, Sawaya AC, Catharino RR, Mazzafera P (2014) Mass spectrometry imaging: an expeditious and powerful technique for fast in situ lignin assessment in Eucalyptus. Anal Chem 86(7):3415–3419CrossRefGoogle Scholar
  4. Ardey RE (2003) Liquid chromatography–mass spectrometry: an introduction. John Wiley & Sons, New YorkCrossRefGoogle Scholar
  5. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89CrossRefGoogle Scholar
  6. Baker JM, Hawkins ND, Ward JL, Lovegrove A, Napier JA, Shewry PR, Beale MH (2006) A metabolomic study of substantial equivalence of field-grown genetically modified wheat. Plant Biotech J 4(4):381–392CrossRefGoogle Scholar
  7. Banoub J, Delmas G-H Jr, Joly N, Mackenzie G, Cachet N, Benjelloun-Mlayah B, Delmas M (2015) A critique on the structural analysis of lignins and application of novel tandem mass spectrometric strategies to determine lignin sequencing. J Mass Spectrom 50:5–48CrossRefGoogle Scholar
  8. Bauer S (2012) Mass spectrometry for characterizing plant cell wall polysaccharides. Front Plant Sci 3:1–6CrossRefGoogle Scholar
  9. Bergdahl B, Heer D, Sauer U, Hahn-Hagerdal B, van Niel EW (2012) Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. Biotechnol for Biofuels 5:34CrossRefGoogle Scholar
  10. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Sci 9:418–425CrossRefGoogle Scholar
  11. Bleakney W (1930) The ionization of hydrogen by single electron impact. Physical Review 35:1180–1186CrossRefGoogle Scholar
  12. Bruins AP (1991) Mass spectrometry with ion sources operating at atmospheric pressure. Mass Spectrom Rev 10:53–77CrossRefGoogle Scholar
  13. Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA (2011) High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. The Plant J 67:869–884CrossRefGoogle Scholar
  14. Campbell MM, Sederoff RR (1996) Variation in lignin content and composition. Plant Physiol 110:3–13CrossRefGoogle Scholar
  15. Cherubini F, Stromman AH (2011) Principles of biorefining. Academic, In Biofuels – Alternative feedstocks and conversion processesCrossRefGoogle Scholar
  16. Covey TR, Huang EC, Henion JD (1991) Structural characterization of protein tryptic peptides via liquid chromatography/mass spectrometry and collision–induced dissociation of their doubly charged molecular ions. Anal Chem 63:1193–2000CrossRefGoogle Scholar
  17. Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Pena-Cortes H, Willmitzer L, Hannah MA (2009) TargetSearch – a bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. Bmc Bioinformatics 10:12CrossRefGoogle Scholar
  18. Dawson JHJ, Guilhaus M (1989) Orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 3(5):155–159CrossRefGoogle Scholar
  19. Dettmer K, Aronov PA, Hammock BD (2007) Mass spectrometry-based metabolomics. Mass Spectrom Reviews 26:51–78CrossRefGoogle Scholar
  20. Deutschmann R, Dekker RF (2012) From plant biomass to bio-based chemicals: latest developments in xylan research. Biotechnol Adv 30(6):1627–1640CrossRefGoogle Scholar
  21. Ellis DI, Goodacre R (2012) Metabolomics-assisted synthetic biology. Current Opinion in Biotechnol 23:22–28CrossRefGoogle Scholar
  22. Ernst M, Silva DB, Silva RR, Vencio RZN, Lopes NP (2014) Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing. Nat Product Reports 31:784–806CrossRefGoogle Scholar
  23. Fernández LEM, Obel N, Scheller HV, Roepstorff P (2003) Characterization of plant oligosaccharides by matrix–assisted laser desorption/ionization and electrospray mass spectrometry. J Mass Spectrom 38:427–437CrossRefGoogle Scholar
  24. Fernie AR, Aharoni A, Willmitzer L, Stitt M, Tohge T, Kopka J, Carroll AJ, Saito K, Fraser PD, DeLuca V (2011) Recommendations for reporting metabolite data. The Plant Cell 23:2477–2482CrossRefGoogle Scholar
  25. Fiehn O (2002) Metabolomics – the link between genotypes and phenotypes. Plant Mol Biol 48:155–171CrossRefGoogle Scholar
  26. Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner L, Goodacre R, Hardy N, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon J, Sansone S-A (2007) The metabolomics standards initiative (MSI). Metabolomics 3:175–178CrossRefGoogle Scholar
  27. Frei M (2013) Lignin: characterization of a multifaceted crop component. Sci World J 2013:1–25CrossRefGoogle Scholar
  28. Freudenberg K, Lautsch W (1939) The constitution of pine lignin. Naturwissenschaften 27:227–228CrossRefGoogle Scholar
  29. Fukushima A, Kusano M (2013) Recent progress in the development of metabolome databases for plant systems biology. Front in Plant Sci 4:73CrossRefGoogle Scholar
  30. Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, Trethewey R, Stitt M (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol 7(8):R76CrossRefGoogle Scholar
  31. Griffiths WJ, Koal T, Wang Y, Kohl M, Enot DP, Deigner HP (2010) Targeted metabolomics for biomarker discovery. Angew Chem Int Ed 49:5426–5445CrossRefGoogle Scholar
  32. Gu W-Y, Li N, Leung EL-H, Zhou H, Luo G-A, Liu L, Wu J-L (2015) Metabolites software-assisted flavonoid hunting in plants using ultra-high performance liquid chromatography-quadrupole-time of flight mass spectrometry. Molecules 20:3955–3971CrossRefGoogle Scholar
  33. Guy C, Kaplan F, Kopka J, Selbig J, Hincha DK (2008) Metabolomics of temperature stress. Physiologia Plantarum 132(2):220–235Google Scholar
  34. Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytologist 169:453–468CrossRefGoogle Scholar
  35. Hanold KA, Fischer SM, Cormia PH, Miller CE, Syage JA (2004) Atmospheric pressure photoionization: general properties for LC/MS. Anal Chem 76:2842–2851CrossRefGoogle Scholar
  36. Hasunuma T, Kondo A (2012) Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol Advances 30:1207–1218CrossRefGoogle Scholar
  37. Hasunuma T, Sanda T, Yamada R, Yoshimura K, Ishii J, Kondo A (2011) Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Microbial Cell Factories 10(1):2CrossRefGoogle Scholar
  38. Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155–1160CrossRefGoogle Scholar
  39. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J of Biol Chem 280(27):25590–25595CrossRefGoogle Scholar
  40. Hoffmann E, Stroobant V (2007) Mass spectrometry: principles and applications. Wiley, LondonGoogle Scholar
  41. Hoffmann T, Krug D, Huttel S, Muller R (2014) Improving natural products identification through targeted LC–MS/MS in an untargeted secondary metabolomics workflow. Anal Chem 86:10780–10788CrossRefGoogle Scholar
  42. Hu Q, Noll RJ, Li H, Makarov A, Hardmanc M, Cooks RG (2005) The Orbitrap: a new mass spectrometer. J of Mass Spectrom 40:430–443CrossRefGoogle Scholar
  43. Jalali HT, Petronilho S, Villaverde JJ, Coimbra MA, Domingues MRM, Ebrahimian ZJ, Silvestre AJD, Rocha SM (2013) Assessment of the sesquiterpenic profile of Ferula gummosa óleo–gum–resin (galbanum) from Iran. Contributes to its valuation as a potential source of sesquiterpenic compounds. Ind Crops Prod 44:185–191CrossRefGoogle Scholar
  44. Johnson CH, Ivanisevic J, Benton HP, Siuzdak G (2015) Bioinformatics: the next frontier of metabolomics. Anal Chem 87:147–156CrossRefGoogle Scholar
  45. Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C (2015) Mass spectrometry-based plant metabolomics: metabolite responses to abiotic stress. Mass Spectrom Reviews PMID:25589422. doi: 10.1002/mas.21449 Google Scholar
  46. Joyce BL, Stewart CN Jr (2012) Designing the perfect plant feedstock for biofuel production:using the whole buffalo to diversity fuels and products. Biotech Advances 30:1011–1022CrossRefGoogle Scholar
  47. Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L (2010) Metabolomic and transcriptomic stress response of Escherichia coli. Mol Sys Biol 6(364):1–16Google Scholar
  48. Jung JY, Kim TY, Ng CY, Oh MK (2012) Characterization of GCY1 in Saccharomyces cerevisiae by metabolic profiling. J of Appl Microbiol 113(6):1468–1478CrossRefGoogle Scholar
  49. Kaplan F, Kopka J, Sung DY, Zhao W, Popp M, Porat R, Guy CL (2007) Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J 50(6):967–981CrossRefGoogle Scholar
  50. Kebarle PA (2000) A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. J of Mass Spectrom 35:804–817CrossRefGoogle Scholar
  51. Keurentjes JJB, Fu J, de Vos CHR, Lommen A, Hall RD, Bino RJ, van der Plas LHW, Jansen RC, Vreugdenhil D, Koornneef M (2006) The genetics of plant metabolism. Nat Genet 38:842–849CrossRefGoogle Scholar
  52. Kiyota E, Mazzafera P, Sawaya ACHF (2012) Analysis of soluble lignin in sugarcane by ultrahigh performance liquid chromatography–tandem mass spectrometry with a do–it–youself oligomer database. Anal Chem 84:7015–7020CrossRefGoogle Scholar
  53. Koek MM, Jellema RH, Greef J, Tas AC, Hankemeier T (2011) Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives. Metabolomics 7:307–328CrossRefGoogle Scholar
  54. Kopka J, Walther D, Allwood JW, Goodacre R (2011) Progress in chemometrics and biostatistics for plant applications, or: a good red wine is a bad white wine. In: Hall RD (ed) Annual plant reviews, vol 43. Wiley-Blackwell, Oxford, pp 317–342Google Scholar
  55. Krastanov A (2010) Metabolomics – the state of art. Biotechnology & Biotechnological Equipment 24:1537–1543CrossRefGoogle Scholar
  56. Kusano M, Fukushima A, Kobayashi M, Hayashi N, Jonsson P, Moritz T, Ebana K, Saito K (2007) Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. J Chromatogr B Analyt Technol Biomed Life Sci 855:71–79CrossRefGoogle Scholar
  57. Kusano M, Redestig H, Hirai T, Oikawa A, Matsuda F, Fukushima A, Arita M, Watanabe S, Yano M, Hiwasa-Tanase K, Ezura H, Saito K (2011) Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. Plos One 6(2)Google Scholar
  58. Lei ZT, Huhman DV, Sumner LW (2011) Mass spectrometry strategies in metabolomics. J of Biolog Chem 286:25435–25442CrossRefGoogle Scholar
  59. Leijdekkers AG, Sanders MG, Schols HA, Gruppen H (2011) Characterizing plant cell wall derivative oligosaccharides using hydrophobic interaction chromatography with mass spectrometry detection. J Chromatogr A 1218(51):9227–9235CrossRefGoogle Scholar
  60. Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR (2006) Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols 1:387–396CrossRefGoogle Scholar
  61. Lisec J, Meyer RC, Steinfath M, Redestig H, Becher M, Witucka-Wall H, Fiehn O, Torjek O, Selbig J, Altmann T, Willmitzer L (2008) Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant J 53:960–972CrossRefGoogle Scholar
  62. Lisec J, Romisch-Margl L, Nikoloski Z, Piepho HP, Giavalisco P, Selbig J, Gierl A, Willmitzer L (2012) Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns. Plant J 68:326–336CrossRefGoogle Scholar
  63. Lommen A (2009) MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81:3079–3086CrossRefGoogle Scholar
  64. Luedemann A, Malotky L, Erban A, Kopka J (2012) TagFinder: preprocessing software for the fingerprinting and the profiling of gas chromatography–mass spectrometry based metabolome analyses. In: Hardy NW (ed) Plant metabolomics. Humana, Louisville, KY, pp 255–286Google Scholar
  65. Lupoi JS, Singh S, Parthasarathi R, Simmons BA, Henry RJ (2015) Recent innovations in analytical methods for the qualitative and quantitative assessment of lignin. Renewable Sustainable Energy Review 49:871–906CrossRefGoogle Scholar
  66. March RE, Hughes RJ (1989) Quadrupole storage mass spectrometry. John Wiley & Sons, New YorkGoogle Scholar
  67. Marshall AG, Hendrickson CL, Ernmetta MR, Rodgers RP, Blakney GT, Nilsson CL (2007) Fourier transform ion cyclotron resonance: state of the art. Eur J of Mass Spectrom 13(1):57–59CrossRefGoogle Scholar
  68. Mass Spectrometry Data Center (2014) NIST/EPA/NIH mass spectral database. Mass Spectrometry Data Center, Gaithersburg, MD, http://chemdata.nist.gov/dokuwiki/doku.php?id = chemdata:start. Accessed 12 Jun 2015Google Scholar
  69. McNeely K, Xu Y, Bennette N, Bryant DA, Dismukes GC (2010) Redirecting reductant flux into hydrogen production via metabolic engineering of fermentative carbon metabolism in a cyanobacterium. Appl and Environ Microbio 76(15):5032–5038CrossRefGoogle Scholar
  70. Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H, Torjek O, Fiehn O, Eckardt A, Willmitzer L, Selbig J, Altmann T (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proceedings of the Natl Acad of Sci USA 104:4759–4764CrossRefGoogle Scholar
  71. Miller PE, Denton MB (1986) The quadrupole mass filter: basic operating concepts. J of Chemical Education 63:617–622CrossRefGoogle Scholar
  72. Mol HGJ, Van Dam RCJ, Zomer P, Mulder PPJ (2011) Screening of plant toxins in food, feed and botanicals using full-scan high-resolution (Orbitrap) mass spectrometry. Food Addit Contam Part A 28:1405–1423CrossRefGoogle Scholar
  73. Moore JP, Nguema-Ona E, Fangel JU, Williats WGT, Hugo A, Vivier MA (2014) Profiling the main cell wall polysaccharides of grapevine leaves using high-throughput ans fractionation methods. Carbohydr Polymers 99:190–198CrossRefGoogle Scholar
  74. Morreel K, Kim H, Lu F, Dima O, Akiyama T, Vanholme R, Niculaes C, Goeminne G, Inzé D, Messens E, Ralph J, Boerjan W (2010) Mass spectrometry-based fragmentation as an identification tool in lignomics. Anal Chem 82:8095–8105CrossRefGoogle Scholar
  75. Nguyen Q-T, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E (2012) Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Letters 586:2177–2183CrossRefGoogle Scholar
  76. Nielsen J, Pronk JT (2012) Metabolic engineering, synthetic biology and systems biology. Fems Yeast Research 12:103CrossRefGoogle Scholar
  77. Nováková L, Vlčková H (2009) A review of current trends and advances in modern bio-analytical methods: chromatography and sample preparation. Anal Chimica Acta 656(1-2):8–35CrossRefGoogle Scholar
  78. Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends in Biotechn 16:373–378CrossRefGoogle Scholar
  79. Owen CB, Haupert LJ, Jarrell TM, Marcum CL, Parsell TH, Abu-Omar MM, Bozell JJ, Black SK, Kenttamaa HI (2012) High-performance liquid chromatography/high-resolution multiple stage tandem mass spectrometry using negative-ion mode hydroxide-doped electrospray ionization for the characterization of lignin degradation products. Anal Chem 84:6000–6007CrossRefGoogle Scholar
  80. Park C, Yun S, Lee S, Park K, Lee J (2012) Metabolic profiling of Klebsiella oxytoca: evaluation of methods for extraction of intracellular metabolites using UPLC/Q-TOF-MS. Appl Biochem and Biotechnol 167(3):425–438CrossRefGoogle Scholar
  81. Parveen I, Threadgill MD, Hauck B, Donnison I, Winters A (2011) Isolation, identification and quantitation of hydroxycinnamic acid conjugates, potential platform chemicals, in the leaves and stems of Miscanthus × giganteus using LC-ESI-MSn. Phytochem 72(18):2376–2384CrossRefGoogle Scholar
  82. Patti GJ, Yanes O, Siuzdak G (2012) Metabolomics: the apogee of the omic triology. Nature reviews - Molecular Cell Biol 13:263–269CrossRefGoogle Scholar
  83. Peng F, Peng P, Xu F, Sun R-C (2012) Fractional purification and bioconversion of hemicelluloses. Biotech Advances 30:879–903CrossRefGoogle Scholar
  84. Perry RH, Cooks RG, Noll RJ (2008) Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom Reviews 27:661–699CrossRefGoogle Scholar
  85. Plancot B, Vanier G, Maire F, Bardor M, Lerouge P, Farrant MJ, Driouich A, Vicré-Gibouin M, Afonso C, Loutilier-Bourhis C (2014) Structural characterization of arabinoxylans from two African species Eragrostis nindensis and Eragrostis tef using various mass spectrometric methods. Rapid Mass Spectrom 28:908–916CrossRefGoogle Scholar
  86. Quéméner B, Vigouroux J, Rathahao E, Tabet JC, Dimitrijevic A, Lahaye M (2015) Negative electrospray ionization mass spectrometry: a method for sequencing and determining linkage position in oligosaccharides from branched hemicelluloses. J Mass Spectrom 50:247–264CrossRefGoogle Scholar
  87. Ragauskas AJ, Beckham GT, Biddy MJ, Chandra R, Chen F, Davis MF, Davison BH, Dixon RA, Gilna P, Keller M, Langan P, Naskar AK, Saddler JN, Tschaplinski TJ, Tuskan GA, Wyman CE (2014) Lignin valorization: improving lignin processing in the biorefinery. Science 344:1246843-1–1246843-7CrossRefGoogle Scholar
  88. Raterink RJ, Lindenburg PW, Vreeken RJ, Ramautar R, Hankemeier T (2014) Recent developments in sample-pretreatment techniques for mass spectrometry-based metabolomics. TrAC Trends in Anal Chem 61:157–167CrossRefGoogle Scholar
  89. Reale S, Tullio A, Spreti N, De Angelis F (2004) Mass spectrometry in the biosynthetic and structural investigation of lignins. Mass Spectrom Rev 23:87–126CrossRefGoogle Scholar
  90. Rencoret J, Ralph J, Marques G, Gutiérrez A, Martínez AT, Del Río JC (2013) Structural characterization of lignin isolated from coconut (Cocos nucifera) coir fibers. J Agric Food Chem 61:2434–2445CrossRefGoogle Scholar
  91. Roberts LD, Souza AL, Gerszten RE, Clish CB (2012) Targeted metabolomics. In: Ausubel FM (ed) Current protocols in molecular biology, vol 30. John Willey, New York, NY, pp 30.2.1–30.2.24Google Scholar
  92. Saito K, Watanabe Y, Shirakawa M, Matsushita Y, Imai T, Koike T, Sano FR, Fukazawa K, Fukushima K (2012) Direct mapping of morphological distribution of syringyl and guaiacyl lignin in the xylem of maple by time-of-flight secondary ion mass spectrometry. Plant J 69(3):542–552CrossRefGoogle Scholar
  93. Shulaev V (2006) Metabolomics technology and bioinformatics. Briefings in Bioinformatics 7(2):128–139CrossRefGoogle Scholar
  94. Silverstein RM, Webster FX, Kiemle DJ (2005) Spectrometric identification of organic compounds. John Wiley & Sons, DanversGoogle Scholar
  95. 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 78:779–787CrossRefGoogle Scholar
  96. Sugimoto M, Kawakami M, Robert M, Soga T, Tomita M (2012) Bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis. Curr Bioinform 7:96–108CrossRefGoogle Scholar
  97. Sulpice R, Pyl ET, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Piques MC, Von Korff M, Steinhauser MC, Keurentjes JJB, Guenther M, Hoehne M, Selbig J, Fernie AR, Altmann T, Stitt M (2009) Starch as a major integrator in the regulation of plant growth. Proceedings of the Natl Acad of Sci USA 106:10348–10353CrossRefGoogle Scholar
  98. Taiz L, Zeiger E (2010) Plant physiology. Sunderland, MassachusettsGoogle Scholar
  99. Takats Z, Wiseman JM, Cooks RG (2006) Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology. J of Mass Spectrom 40:1261–1275CrossRefGoogle Scholar
  100. Tian Q, Giusti MM, Stoner GD, Schwartz SJ (2005) Screening for anthocyanins using high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry with precursor-ion analysis, product-ion analysis, common-neutral-loss analysis, and selected reaction monitoring. J Chromatogr A 1091(1-2):72–82CrossRefGoogle Scholar
  101. Tomás-Pejó E, Alvira P, Ballesteros M, Negro MJ (2011) Pretreatment technologies for lignocellulose-to-bioethanol conversion. In: Pandey A (ed) Biofuels – alternative feedstocks and conversion processes, 1st edn. Academic, San Diego, pp 149–176Google Scholar
  102. Toya Y, Shimizu H (2013) Flux analysis and metabolomics for systematic metabolic engineering of microorganisms. Biotechnol Advances 31:818–826CrossRefGoogle Scholar
  103. Vaidyanathan S, Gaskell S, Goodacre R (2006) Matrix-suppressed laser desorption/ionization mass spectrometry and its suitability for metabolome analyses. Rapid Commun Mass Spectrom 20:1192–1198CrossRefGoogle Scholar
  104. Van Bramer SE (1998) An introduction to mass spectrometry. Widener University, Chester, PA, http://science.widener.edu/svb/massspec/massspec.pdf. Accessed 31 May 2015Google Scholar
  105. van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7:142CrossRefGoogle Scholar
  106. Vanholme R, Morreel K, Darrah C, Oyarce P, Grabber JH, Ralph J, Boerjan W (2012a) Metabolic engineering of novel lignin in biomass crops – review. New Phytologist 196:978–1000CrossRefGoogle Scholar
  107. Vanholme R, Storme V, Vanholme B, Sundin L, Christensen JH, Goeminne G, Halpin C, Rohde A, Morreel K, Boerjan W (2012b) A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. The Plant Cell 24:3506–3529CrossRefGoogle Scholar
  108. Vismeh R, Humpula JF, Chundawat SPS, Balan V, Dale BE, Jones AD (2013) Profiling of soluble neutral oligosaccharides from treated biomass using solid phase extraction and LC–TOF MS. Carbohydr Polym 94:791–799CrossRefGoogle Scholar
  109. Watanabe M, Kusano M, Oikawa A, Fukushima A, Noji M, Saito K (2008) Physiological roles of the beta-substituted alanine synthase gene family in arabidopsis. Plant Physiol 146:310–320CrossRefGoogle Scholar
  110. Wehren R (2011) Chemometrics with R – multivariate data analysis in the natural sciences and life sciences. Springer, HeidelbergGoogle Scholar
  111. Williams JP, Scrivens JH (2005) Rapid accurate mass desorpition electrospray ionization tandem mass spectrometry of pharmaceutical samples. Rapid Commun Mass Spectrom 19:3643–3650CrossRefGoogle Scholar
  112. Xia J, Sinelnikov IV, Han B, Wishart DS (2015) MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Research 43:1–7CrossRefGoogle Scholar
  113. Yanes O, Tautenhahn R, Patti GJ, Siuzdak G (2011) Expanding coverage of the metabolome for global metabolite profiling. Anal Chem 83:2152–2161CrossRefGoogle Scholar
  114. Yang J, Gilmore I (2015) Application of secondary ion mass spectrometry to biomaterials, proteins and cells: a concise review. Materials Sci and Technol 31(2):131–136CrossRefGoogle Scholar
  115. Yoshida R, Tamura T, Takaoka C, Harada K, Kobayashi A, Mukai Y, Fukusaki E (2010) Metabolomics-based systematic prediction of yeast lifespan and its application for semi-rational screening of ageing-related mutants. Aging Cell 9(4):616–625CrossRefGoogle Scholar
  116. Zaia J (2010) Mass spectrometry and glycomics. OMICS 14(4):401–418CrossRefGoogle Scholar
  117. Zamboni N, Saghatelian A, Patti GJ (2015) Defining the metabolome: size, flux, and regulation. Mol Cell 58:699–706CrossRefGoogle Scholar
  118. Zhang J, Carey V, Gentleman R (2003) An extensible application for assembling annotation for genomic data. Bioinformatics 19:155–156CrossRefGoogle Scholar
  119. Ziebell AL, Barb JG, Sandhu S, Moyers BT, Sykes RW, Doeppke D, Gracom KL, Carlile M, Marek LF, Davis MF, Knapp SJ, Burke JM (2013) Sunflower as a biofuels crop: an analysis of lignocellulosic chemical properties. Biomass and Bioenergy 59:1–10CrossRefGoogle Scholar

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© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Maria Esther Ricci-Silva
    • 1
  • Boniek Gontijo Vaz
    • 2
  • Géssica Adriana Vasconcelos
    • 2
  • Wanderson Romão
    • 3
  • Juliana A. Aricetti
    • 4
  • Camila Caldana
    • 4
    • 5
  • Patrícia Verardi Abdelnur
    • 1
    • 2
    Email author
  1. 1.EMBRAPA Agroenergy, Brazilian Agricultural Research CorporationNational Center for Agroenergy ResearchBrasíliaBrazil
  2. 2.Institute of Chemistry, Mass Spectrometry and Chromatography LaboratoryFederal University of GoiásGoiâniaBrazil
  3. 3.Department of Chemistry, Petroleomic and Forensic LaboratoryFederal University of Espírito SantoVitoriaBrazil
  4. 4.Brazilian Bioethanol Science and Technology Laboratory at Brazilian Center for Research in Energy and MaterialsCampinasBrazil
  5. 5.Max Planck Partner Group at Brazilian Bioethanol Science and Technology Laboratory/CNPEMCampinasBrazil

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