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Metabolome and Proteome Profiling for Microbial Characterization

Mass Spectrometric Applications

  • Chapter
Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis

Abstract

In the post-genomic era, there is greater emphasis in evaluating functional aspects of genes and gene products for cellular characterization. There is a better appreciation of the extent of microbial diversity, of how uncultured microorganisms might be grown, and a better understanding of how the metabolic potential of microorganisms can be maximized. This can be attributed to a paradigm shift from traditional biology to bioinformatics (Bull et al., 2000). Evaluation and assessment of cellular activities is evolving from the traditional approaches of biochemistry and molecular biology, where cellular processes are investigated individually and often independently of each other, to a more global approach in which cellular composition is analyzed in its entirety, in order to establish a more holistic picture. While the genetic make-up of a cell characterizes an organism to some extent, there are questions that will remain unanswered by analyzing at the genetic level alone. The physiological response of a cell to fluctuations in its environment is the most obvious case in point. In such instances, analysis of gene products, such as mRNAs, proteins and metabolites will be of greater relevance (Oliver, 2002) as we strive to understand, and even define, an organism’s phenotype.

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References

  • Bacher G, Korner R, Atrih A et al. Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus species. J Mass Spectrom 36: 124–139 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Black GE, Fox A. Liquid chromatography with electrospray ionization tandem mass spectrometry — profiling carbohydrates in whole bacterial cell hydrolysates. In Biochemical and Biotechnological Applications of Electrospray Ionization Mass Spectrometry. Vol. 619. Snyder PA (Ed) pp. 81–105, American Chemical Society, Washington, DC (1996).

    Chapter  Google Scholar 

  • Black GE, Snyder AP, Heroux KS. Chemotaxonomic differentiation between the Bacillus cereus group and Bacillus subtilis by phospholipid extracts analyzed with electrospray ionization tandem mass spectrometry. J Microbiol Meth 28: 187–199 (1997).

    Article  CAS  Google Scholar 

  • Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 17: 121–127 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Blagoev B, Pandey A. Microarrays go live — new prospects for proteomics. Trends Biochem Sci 26: 639–641 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Buchholz A, Takors R, Wandrey C. Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Anal Biochem 295: 129–137 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Bull AT, Ward AC, Goodfellow M. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev 64: 573–606 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Cameron DC, Chaplen FWR. Developments in metabolic engineering. Curr Opin Biotechnol 8: 175–180 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Christensen B, Nielsen J. Metabolic network analysis of Penicillium chrysogenum using C-13-labeled glucose. Biotechnol Bioeng 68: 652–659 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Claydon MA, Davey SN, Edwards JV, Gordon DB. The rapid identification of intact microorganisms using mass spectrometry. Nature Biotechnol 14: 1584–1586 (1996).

    Article  CAS  Google Scholar 

  • Cordwell SJ, Nouwens AS, Walsh BJ. Comparative proteomics of bacterial pathogens. Proteomics 1: 461–472 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Cotter RJ. Plasma desorption mass spectrometry - coming of age. Anal Chem 60: A781 (1988).

    Article  Google Scholar 

  • Dai Y, Li L, Roser DC, Long SR. Detection and identification of low-mass peptides and proteins from solvent suspensions of Escherichia coli by high performance liquid chromatography fractionation and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Comm Mass Spectrom 13: 73–78 (1999).

    Article  CAS  Google Scholar 

  • Dando M. Biological Warfare in the 21 st Century. Brassey’s Ltd, London (1994).

    Google Scholar 

  • Dauner M, Sauer U. GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol Prog 16: 642–649 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Dauner M, Sonderegger M, Hochuli M et al. Intracellular carbon fluxes in riboflavin- producing Bacillus subtilis during growth on two-carbon substrate mixtures. Appl Environ Microbiol 68: 1760–1771 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Davis MT, Beierle J, Bures ET et al. Automated LC-LC-MS-MS platform using binary ion-exchange and gradient re versed-phase chromatography for improved proteomic analyses. J Chromatogr 752: 281–291 (2001).

    Article  CAS  Google Scholar 

  • de Graaf AA, Striegel K, Wittig RM et al. Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by C-13- and P- 31-NMR spectroscopy. Arch Microbiol 171: 371–385 (1999).

    Article  PubMed  Google Scholar 

  • Delneri D, Brancia FL, Oliver SG. Towards a truly integrative biology through the functional genomics of yeast. Curr Opin Biotechnol 12: 87–91 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Demirev PA, Lin JS, Pineda FJ, Fenselau C. Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H-pylori. Anal Chem 73: 4566–4573 (2001a).

    Article  CAS  Google Scholar 

  • Demirev PA, Ramirez J, Fenselau C. Tandem mass spectrometry of intact proteins for characterization of biomarkers from Bacillus cereus T spores. Anal Chem 73: 5725–5731 (2001b).

    Article  PubMed  CAS  Google Scholar 

  • Drucker DB. Fast atom bombardment mass spectrometry of phospholipids for bacterial chemotaxonomy. In Mass Spectrometry for the Characterization of Microorganisms. Vol. 541. Fenselau C (Ed) pp. 18–35, American Chemical Society, Washington, DC (1994).

    Chapter  Google Scholar 

  • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature 405: 823–826 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Erhard M, von Dohren H, Jungblut P. Rapid typing and elucidation of new secondary metabolites of intact cyanobacteria using MALDI-TOF mass spectrometry. Nature Biotechnol 15: 906–909 (1997).

    Article  CAS  Google Scholar 

  • Fang J, Barcelona MJ. Structural determination and quantitative analysis of bacterial phospholipids using liquid chromatography electrospray ionization mass spectrometry. J Microbiol Meth 33: 23–35 (1998).

    Article  CAS  Google Scholar 

  • Fell DA. Beyond genomics. Trends Genet 17: 680–682 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Fenselau C, Demirev PA. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom Rev 20: 157–171 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Ficarro SB, McCleland ML, Stukenberg PT et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nature Biotechnol 20: 301–305 (2002).

    Article  CAS  Google Scholar 

  • Fiehn O, Kopka J, Dörmann P et al. Metabolite profiling for plant functional genomics. Nature Biotechnol 18: 1157–1161 (2000).

    Article  CAS  Google Scholar 

  • Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Compar Fund Genom 2: 155–168 (2001).

    Article  CAS  Google Scholar 

  • Fields S, Song OK. A novel genetic system to detect protein-protein interactions. Nature 340: 245–246 (1989).

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann RD, Adams, MD, White O et al. Whole-genome random sequencing and assembly of Haemophilus- influenzae Rd. Science 269: 496–512 (1995).

    Article  PubMed  CAS  Google Scholar 

  • Fountoulakis M, Takacs MF, Berndt P et al. Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography. Electrophoresis 20: 2181–2195 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Fraser CM, Eisen J, Fleischmann RD et al. Comparative genomics and understanding of microbial biology. Emerg Infect Dis 6: 505–512 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Futcher B, Latter GI, Monardo P et al. A sampling of the yeast proteome. Mol Cell Biol 19: 7357–7368 (1999).

    PubMed  CAS  Google Scholar 

  • Gavin AC, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Giaever G, Chu AM, Ni L et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387–391 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Gibson BW, Phillips NJ, John CM, Melaugh W. Lipooligosaccharides in pathogenic Haemophilus and Neisseria species — mass spectrometry techniques for identification and characterization. ACS Symposium Series 541: 185–202 (1994).

    Article  CAS  Google Scholar 

  • Godovac-Zimmermann J, Brown LR. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 20: 1–57 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Goodacre R, Heald JK, Kell DB. Characterisation of intact microorganisms using electrospray ionisation mass spectrometry. FEMS Microbiol Lett 176: 17–24 (1999).

    Article  CAS  Google Scholar 

  • Goodacre R, Kell DB. Correction of mass spectral drift using artificial neural networks. Anal Chem 68: 271–280 (1996a).

    Article  PubMed  CAS  Google Scholar 

  • Goodacre R, Kell DB. Pyrolysis mass spectrometry and its applications in biotechnology. Curr Opin Biotechnol 7: 20–28 (1996b).

    Article  PubMed  CAS  Google Scholar 

  • Goodacre R, Shann B, Gilbert RJ et al. Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy. Anal Chem 72: 119–127 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Goodacre R, Timmins ÉM, Jones A et al. On mass spectrometer instrument standardization and interlaboratory calibration transfer using neural networks. Anal Chim Acta 348: 511– 532 (1997).

    Article  CAS  Google Scholar 

  • Goodfellow M. Inter-strain comparison of pathogenic microorganisms by pyrolysis mass spectrometry. Binary Comp Microbiol 7: 54–60 (1995).

    Google Scholar 

  • Griffin TJ, Aebersoid R. Advances in proteome analysis by mass spectrometry. J Biol Chem 276:45497–45500 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol 17: 994–999 (1999a).

    Article  CAS  Google Scholar 

  • Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720–1730 (1999b).

    PubMed  CAS  Google Scholar 

  • Gygi SP, Corthals GL, Zhang Y et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97: 9390–9395 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Haas G, Karaali G, Ebermayer K et al. Immunoproteomics of Helicobacter pylori infection and relation to gastric disease. Proteomics 2: 313–324 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Hathout Y, Demirev PA, Ho YP et al. Identification of Bacillus spores by matrix-assisted laser desorption ionization-mass spectrometry. Appl Environ Microbiol 65: 4313–4319 (1999).

    PubMed  CAS  Google Scholar 

  • Heller DN, Cotter RJ, Fenselau C. Profiling of bacteria by fast atom bombardment mass spectrometry. Anal Chem 59: 2806–2809 (1987).

    Article  PubMed  CAS  Google Scholar 

  • Henzel WJ, Billed TM, Stults JT et al. Identifying proteins from 2-dimensional gels by molecular mass searching of peptide-fragments in protein-sequence databases. Proc Natl Acad Sci USA 90: 5011–5015 (1993).

    Article  PubMed  CAS  Google Scholar 

  • Higgs RE, Zahn JA, Gygi JD, Hilton MD. Rapid method to estimate the presence of secondary metabolites in microbial extracts. Appl Environ Microbiol 67: 371–376 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Ho Y, Gruhler A, Heilbut A et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Holland RD, Duffy CR, Rafii F et al. Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells. Anal Chem 71: 3226–3230 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929–934 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Jensen PK, Pasa-Tolic L, Peden KK et al. Mass spectrometic detection for capillary isoelectric focusing separations of complex protein mixtures. Electrophoresis 21: 1372–1380 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Joubert R, Strub JM, Zugmeyer S et al. Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast. Electrophoresis 22: 2969–2982 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Jungblut PR, Bumann D, Haas G et al. Comparative proteome analysis of Helicobacter pylori Mol Microbiol 36: 710–725 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Kirkpatrick C, Maurer LM, Oyelakin NE et al. Acetate and formate stress: opposite responses in the proteome of Escherichia coli. J Bacteriol 183: 6466–6477 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Krishnamurthy T, Davis MT, Stahl DC, Lee TD. Liquid chromatography/microspray mass spectrometry for bacterial investigations. Rapid Comm Mass Spectrom 13: 39–49 (1999).

    Article  CAS  Google Scholar 

  • Krishnamurthy T, Rajamani U, Ross PL et al. Mass spectral investigations on microorganisms. J Toxicol Toxin Rev 19: 95–117 (2000).

    CAS  Google Scholar 

  • Kumar A, Agarwal S, Heyman J A et al. Subcellular localization of the yeast proteome. Genes Dev 16:707–719(2002).

    Article  PubMed  CAS  Google Scholar 

  • Langen H, Takacs B, Evers S et al. Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 21: 411–429 (2000).

    Article  CAS  Google Scholar 

  • Lay JO. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev 20: 172–194 (2000).

    Article  CAS  Google Scholar 

  • Lay JO. MALDI-TOF mass spectrometry and bacterial taxonomy. Trends Anal Chem 19: 507–516 (2000).

    Article  CAS  Google Scholar 

  • Lee SW, Berger SJ, Martinovic S et al. Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc Natl Acad Sci USA 99: 5942–5947 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Leenders F, Stein TH, Kablitz B et al. Rapid typing of Bacillus subtilis strains by their secondary metabolites using matrix-assisted laser desorption ionization mass spectrometry of intact cells. Rapid Comm Mass Spectrom 13: 943–949 (1999).

    Article  CAS  Google Scholar 

  • Li J, Thibault P, Martin A et al. Development of an on-line preconcentration method for the analysis of pathogenic lipopolysaccharides using capillary electrophoresis-electrospray mass spectrometry — Application to small colony isolates. J Chromatogr 817: 325–336 (1998).

    Article  CAS  Google Scholar 

  • Li WQ, Hendrickson CL, Emmett MR, Marshall AG. Identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and LC ESI infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 71:4397–4402 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Link AJ, Eng J, Schieltz DM et al. Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol 17: 676–682 (1999).

    Article  CAS  Google Scholar 

  • Liu XQ, Ng C, Ferenci T. Global adaptations resulting from high population densities in Escherichia coli cultures. J Bacterial 182: 4158–4164 (2000).

    Article  CAS  Google Scholar 

  • Lock RA, Coombs GW, McWilliams TM et al. Proteome analysis of highly immunoreactive proteins of Helicobacter pylori. Helicobacter 7:175–182 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Loo RRO, Cavalcoli JD, Van Bogelen RA et al. Virtual 2-D gel electrophoresis: visualization and analysis of the E-coli proteome by mass spectrometry. Anal Chem 73: 4063–4070 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Madonna AJ, Basile F, Ferrer I et al. On-probe sample pretreatment for the detection of proteins above 15 KDa from whole cell bacteria by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. Rapid Comm Mass Spectrom 14: 2220–2229 (2000).

    Article  CAS  Google Scholar 

  • Magee JT. Whole-organism fingerprinting. In Handbook of New Bacterial Systematica. Goodfellow M, O’Donnell AG (Ed) pp. 383–427, Academic Press, London (1993).

    Google Scholar 

  • Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Ann Rev Biochem 70: 437–473 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Mann M, Ong SE, Gronborg M et al. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 20: 261–268 (2002).

    Article  PubMed  CAS  Google Scholar 

  • McAtee CP, Lim MY, Fung K et al. Characterization of a Helicobacter pylori vaccine candidate by proteome techniques. J Chromatogr 714: 325–333 (1998).

    Article  CAS  Google Scholar 

  • Meuzelaar HLC, Haverkamp J, Hileman FD. Pyrolysis Mass Spectrometry of Recent and Fossil Biomaterials. Elsevier, Amsterdam (1982).

    Google Scholar 

  • Nicholson JK, Lindon JC, Holmes E. ‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29: 1181–1189 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Nielsen J. Metabolic engineering. Appl Microbiol Biotechnol 55: 263–283 (2001).

    Article  PubMed  CAS  Google Scholar 

  • O’Connor CD, Adams P, Alefounder P et al. The analysis of microbial proteomes: strategies and data exploitation. Electrophoresis 21: 1178–1186 (2000).

    Article  PubMed  Google Scholar 

  • Oliver SG. Functional genomics: lessons from yeast. Philos Trans R Soc Lond Ser B 357: 17–23 (2002).

    Article  CAS  Google Scholar 

  • Oosthuizen MC, Steyn B, Theron J et al. Proteomic analysis reveals differential protein expression by Bacillus cereus during biofilm formation. Appl Environ Microbiol 68: 2770– 2780 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Perrot F, Hebraud M, Charlionet R et al. Protein patterns of gel-entrapped Escherichia coli cells differ from those of free-floating organisms. Electrophoresis 21: 645–653 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Pflieger D, Le Caer JP, Lemaire C et al. Systematic identification of mitochondrial proteins by LC-MS/MS. Anal Chem 74: 2400–2406 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Phelps TJ, Palumbo AV, Beliaev AS. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol 13: 20–24 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Pineda FJ, Lin JS, Fenselau C, Demirev PA. Testing the significance of microorganism identification by mass spectrometry and proteome database search. Anal Chem 72: 3739– 3744 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Raamsdonk LM, Teusink B, Broadhurst D et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnol 19: 45–50 (2001).

    Article  CAS  Google Scholar 

  • Rain JC, Selig L, De Reuse H et al. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211–215 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Rigaut G, Shevchenko A, Rutz B et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol 17: 1030–1032 (1999).

    Article  CAS  Google Scholar 

  • Roepstorff P. Mass spectrometry in protein studies from genome to function. Curr Opin Biotechnol 8: 6–13 (1997).

    Article  PubMed  CAS  Google Scholar 

  • Ryzhov V, Fenselau C. Characterization of the protein subset desorbed by MALDI from whole bacterial cells. Anal Chem 73: 746–750 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Schmidt K, Nielsen J, Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J Biotechnol 71: 175–189 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Schweitzer B, Kingsmore SF. Measuring proteins on microarrays. Curr Opin Biotechnol 13: 14–19 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Shen YF, Tolic N, Zhao R et al. High-throughput proteomics using high efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. Anal Chem 73: 3011–3021 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal Chem 68: 850–858 (1996).

    Article  PubMed  CAS  Google Scholar 

  • Siuzdak G. Probing viruses with mass spectrometry. J Mass Spectrom 33: 203–211 (1998).

    Article  PubMed  CAS  Google Scholar 

  • Smedsgaard J, Frisvad JC. Using direct electrospray mass spectrometry in taxonomy and secondary metabolite profiling of crude fungal extracts. J Microbiol Meth 25: 5–17 (1996).

    Article  CAS  Google Scholar 

  • Smith PBW, Snyder P, Harden CS. Characterization of bacterial phospholipids by electrospray-ionization tandem mass spectrometry. Anal Chem 67: 1824–1830 (1995).

    Article  PubMed  CAS  Google Scholar 

  • Stafford DE, Stephanopoulos G. Metabolic engineering as an integrating platform for strain development. Curr Opin Microbiol 4: 336–340 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Tas AC, van der Greef J. Mass spectrometric profiling and pattern recognition. Mass Spectrom Rev 13: 155–181(1994).

    Article  CAS  Google Scholar 

  • ter Kuile BH, Westerhoff HV. Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett 500: 169–171 (2001).

    Article  PubMed  Google Scholar 

  • Terabe S, Markuszewski MJ, Inoue N et al. Capillary electrophoretic techniques toward the metabolome analysis. Pure Appl Chem 73: 1563–1572 (2001).

    Article  CAS  Google Scholar 

  • Timperman AT, Aebersold R. Peptide electroextraction for direct coupling of in-gel digests with capillary LC-MS/MS for protein identification and sequencing. Anal Chem 72: 4115– 4121 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Tweeddale H, Notley-McRobb L, Ferenci T. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool (“metabolome”) analysis. J Bacteriol 180: 5109–5116 (1998).

    PubMed  CAS  Google Scholar 

  • Tweeddale H, Notley-McRobb L, Ferenci T. Assessing the effect of reactive oxygen species on Escherichia coli using a metabolome approach. Redox Rep 4: 237–241 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Vaidyanathan S, Rowland JJ, Kell DB, Goodacre R. Discrimination of aerobic endospore- forming bacteria via electrospray-ionization mass spectrometry of whole cell suspensions. Anal Chem 73: 4134–4144 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Vaidyanathan S, Kell DB, Goodacre R. Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification. J Am Soc Mass Spectrom 13: 118–128 (2002a).

    Article  PubMed  CAS  Google Scholar 

  • Vaidyanathan S, Winder CL, Wade SC et al. Sample preparation in matrix-assisted laser desoiption ionization mass spectrometry of whole bacterial cells and the detection of high mass (> 20 kDa) proteins. Rapid Comm Mass Spectrom 16: 1276–1286 (2002b).

    Article  CAS  Google Scholar 

  • van Baar BLM. Characterization of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry. FEMS Microbiol Rev 24: 193–219 (2000).

    Article  PubMed  Google Scholar 

  • Varma A, Boesch BW, Palsson BO. Biochemical production capabilities of Escherichia-coli. Biotechnol Bioeng 42: 59–73 (1993).

    Article  PubMed  CAS  Google Scholar 

  • Wang ZP, Dunlop K, Long SR, Li L. Mass spectrometric methods for generation of protein mass database used for bacterial identification. Anal Chem 74: 3174–3182 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol 19: 242–247 (2001).

    Article  CAS  Google Scholar 

  • Wilkins MR, Gasteiger E, Gooley AA et al. High-throughput mass spectrometric discovery of protein post- translational modifications. J Mol Biol 289: 645–657 (1999).

    Article  PubMed  CAS  Google Scholar 

  • Wilkins MR, Pasquali C, Appel RD et al. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14:61–65 (1996).

    Article  PubMed  CAS  Google Scholar 

  • Wittmann C, Heinzle E. Application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum — A novel approach for metabolic flux analysis. Eur J Biochem 268: 2441–2455 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Wunschel DS, Fox KF, Fox A et al. Quantitative analysis of neutral and acidic sugars in whole bacterial cell hydrolysates using high-performance anion-exchange liquid chromatography electrospray ionization tandem mass spectrometry. J Chromatogr 776: 205–219 (1997).

    Article  CAS  Google Scholar 

  • Xiang F, Anderson GA, Veenstra TD et al. Characterization of microorganisms and biomarker development from global ESI-MS/MS analysis of cell lysates. Anal Chem 72: 2475–2481 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Yates JR. Mass spectrometry — from genomics to proteomics. Trends Genet 16: 5–8 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Zhu H, Klemic JF, Chang S et al. Analysis of yeast protein kinases using protein chips. Nature Genet 26: 283–289 (2000).

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Biological Sciences, University of Wales, SY23 3DD, Aberystwyth, UK

    Seetharaman Vaidyanathan

  2. Department of Chemistry, University of Manchester Institute of Science and Technology, Sackville St., PO Box 88, M60 1QD, Manchester, UK

    Royston Goodacre

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  1. Pharmacia Corporation, Chesterfield, MO, 63198, USA

    George G. Harrigan

  2. Department of Chemistry, UMIST, PO Box 88, Manchester, M60 1QD, UK

    Royston Goodacre

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Vaidyanathan, S., Goodacre, R. (2003). Metabolome and Proteome Profiling for Microbial Characterization. In: Harrigan, G.G., Goodacre, R. (eds) Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-0333-0_2

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