4 – Proteome and metabolome analyses for food authentication

[1]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[2]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[3]  A. Davies,et al.  Study of the Use of Molecular Spectroscopy for the Authentication of Extra Virgin Olive Oils. Part I: Fourier Transform Raman Spectroscopy , 2000 .

[4]  K Chapman,et al.  The ProteinChip Biomarker System from Ciphergen Biosystems: a novel proteomics platform for rapid biomarker discovery and validation. , 2001, Biochemical Society transactions.

[5]  Tommy J Phelps,et al.  Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. , 2002, Current opinion in biotechnology.

[6]  F. Chaplen,et al.  Developments in metabolic engineering. , 1997, Current opinion in biotechnology.

[7]  H. Boucherie,et al.  Identification by mass spectrometry of two‐dimensional gel electrophoresis‐separated proteins extracted from lager brewing yeast , 2001, Electrophoresis.

[8]  Philip J. Dale,et al.  Potential for the environmental impact of transgenic crops , 2002, Nature Biotechnology.

[9]  Beat Mollet,et al.  Functional foods: at the frontier between food and pharma. , 2002, Current opinion in biotechnology.

[10]  H. Noteborn,et al.  Chemical fingerprinting for the evaluation of unintended secondary metabolic changes in transgenic food crops. , 2000, Journal of biotechnology.

[11]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[12]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[13]  S. N. Davey,et al.  The rapid identification of intact microorganisms using mass spectrometry , 1996, Nature Biotechnology.

[14]  P. Andrews,et al.  Virtual 2-D gel electrophoresis: visualization and analysis of the E. coli proteome by mass spectrometry. , 2001, Analytical chemistry.

[15]  W. Wiechert,et al.  Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy , 1999, Archives of Microbiology.

[16]  Shaoyi Liu,et al.  Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells , 2002, Nature Biotechnology.

[17]  P. Legrain Protein domain networking , 2002, Nature Biotechnology.

[18]  J. Lay,et al.  MALDI-TOF mass spectrometry of bacteria. , 2001, Mass spectrometry reviews.

[19]  D. Eisenberg,et al.  Protein function in the post-genomic era , 2000, Nature.

[20]  C. Gray,et al.  Two‐dimensional map of the proteome of Haemophilus influenzae , 2000, Electrophoresis.

[21]  A Bairoch,et al.  High-throughput mass spectrometric discovery of protein post-translational modifications. , 1999, Journal of molecular biology.

[22]  E. Li-Chan,et al.  The applications of Raman spectroscopy in food science , 1996 .

[23]  Dieter Stoll,et al.  Protein microarray technology. , 2002, Frontiers in bioscience : a journal and virtual library.

[24]  Thomas P Conrads,et al.  The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. , 2002, Biochemical and biophysical research communications.

[25]  Yuqin Dai,et al.  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. , 1999, Rapid communications in mass spectrometry : RCM.

[26]  T. Kuhara,et al.  Gas chromatographic‐mass spectrometric metabolic profiling of patients with fatal infantile mitochondrial myopathy with de Toni‐Fanconi‐Debré syndrome , 1996, Acta paediatrica Japonica : Overseas edition.

[27]  George G. Khachatourians,et al.  Liabilities and economics of transgenic crops , 2002, Nature Biotechnology.

[28]  S. Gygi,et al.  Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Andrew Emili,et al.  De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging , 2002, Nature Biotechnology.

[30]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[31]  M. Emmett,et al.  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. , 1999, Analytical chemistry.

[32]  M. Gerstein,et al.  Analysis of yeast protein kinases using protein chips , 2000, Nature Genetics.

[33]  Gerard Downey,et al.  Food and food ingredient authentication by mid-infrared spectroscopy and chemometrics , 1998 .

[34]  J. Nielsen,et al.  Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. , 1999, Journal of biotechnology.

[35]  S. Weinberger,et al.  Recent advancements in surface‐enhanced laser desorption/ionization‐time of flight‐mass spectrometry , 2000, Electrophoresis.

[36]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[37]  D B Kell,et al.  Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy. , 2000, Analytical chemistry.

[38]  B. Blagoev,et al.  Microarrays go live--new prospects for proteomics. , 2001, Trends in biochemical sciences.

[39]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[40]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[41]  S. Patterson,et al.  Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. , 2001, Journal of chromatography. B, Biomedical sciences and applications.

[42]  D. Kell,et al.  Pyrolysis mass spectrometry and its applications in biotechnology. , 1996, Current opinion in biotechnology.

[43]  Gary D Bader,et al.  Analyzing yeast protein–protein interaction data obtained from different sources , 2002, Nature Biotechnology.

[44]  T. Kuhara,et al.  A new chemical diagnostic method for inborn errors of metabolism by mass spectrometry-rapid, practical, and simultaneous urinary metabolites analysis. , 1996, Mass spectrometry reviews.

[45]  Douglas B. Kell,et al.  Characterisation of intact microorganisms using electrospray ionisation mass spectrometry , 1999 .

[46]  D. Kell,et al.  Rapid and Quantitative Detection of the Microbial Spoilage of Meat by Fourier Transform Infrared Spectroscopy and Machine Learning , 2002, Applied and Environmental Microbiology.

[47]  R. Trethewey,et al.  Gene discovery via metabolic profiling. , 2001, Current opinion in biotechnology.

[48]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[49]  Gillian M. Greenway,et al.  Sample manipulation in micro total analytical systems , 2002 .

[50]  Royston Goodacre,et al.  Progress toward the Rapid Nondestructive Assessment of the Floral Origin of European Honey Using Dispersive Raman Spectroscopy , 2002 .

[51]  H. Westerhoff,et al.  Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway , 2001, FEBS letters.

[52]  K. Voorhees,et al.  Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells. , 1999, Analytical chemistry.

[53]  A. Madonna,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. , 2000, Rapid communications in mass spectrometry : RCM.

[54]  I. Raskin,et al.  Plants and human health in the twenty-first century. , 2002, Trends in biotechnology.

[55]  D. Chelius,et al.  Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. , 2002, Analytical chemistry.

[56]  C. Watanabe,et al.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Oliver Fiehn,et al.  Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks , 2001, Comparative and functional genomics.

[58]  Uwe Claussen,et al.  Mass spectrometry meets chip technology: A new proteomic tool in cancer research? , 2001, Electrophoresis.

[59]  P. Demirev,et al.  Characterization of intact microorganisms by MALDI mass spectrometry. , 2001, Mass spectrometry reviews.

[60]  D. Kell,et al.  Metabolic profiling using direct infusion electrospray ionisation mass spectrometry for the characterisation of olive oils. , 2002, The Analyst.

[61]  J. Lüthy,et al.  Detection strategies for food authenticity and genetically modified foods , 1999 .

[62]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[63]  Douglas B. Kell,et al.  Metabolomics and Machine Learning: Explanatory Analysis of Complex Metabolome Data Using Genetic Programming to Produce Simple, Robust Rules , 2004, Molecular Biology Reports.

[64]  Bert Popping,et al.  The application of biotechnological methods in authenticity testing. , 2002, Journal of biotechnology.

[65]  P. Mitchell A perspective on protein microarrays , 2002, Nature Biotechnology.

[66]  M E Belov,et al.  High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. , 2001, Analytical chemistry.

[67]  N. Ahn,et al.  Monitoring post-translational modification of proteins with allosteric ribozymes , 2002, Nature Biotechnology.

[68]  Erik Millstone,et al.  Beyond ‘substantial equivalence’ , 1999, Nature.

[69]  F. Pineda,et al.  Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori. , 2001, Analytical chemistry.

[70]  D B Kell,et al.  Discrimination of aerobic endospore-forming bacteria via electrospray-lonization mass spectrometry of whole cell suspensions. , 2001, Analytical chemistry.

[71]  Marta Cascante,et al.  Metabolic profiling of cell growth and death in cancer: applications in drug discovery. , 2002, Drug discovery today.

[72]  Gary Hardiman,et al.  Protein microarrays: challenges and promises. , 2002, Pharmacogenomics.

[73]  C. Fenselau,et al.  Profiling of bacteria by fast atom bombardment mass spectrometry. , 1987, Analytical chemistry.

[74]  H. Williams,et al.  Metabolic profiling of genetic disorders: a multitissue (1)H nuclear magnetic resonance spectroscopic and pattern recognition study into dystrophic tissue. , 2001, Analytical biochemistry.

[75]  D. Kell,et al.  RAPID COMMUNICATIONS IN MASS SPECTROMETRY Rapid Commun. Mass Spectrom. 2002; 16: 1276±1286 , 2022 .

[76]  Sterner,et al.  Signal suppression in electrospray ionization Fourier transform mass spectrometry of multi-component samples , 2000, Journal of mass spectrometry : JMS.

[77]  R. Aebersold,et al.  Peptide electroextraction for direct coupling of in-gel digests with capillary LC-MS/MS for protein identification and sequencing. , 2000, Analytical chemistry.

[78]  F Baganz,et al.  Systematic functional analysis of the yeast genome. , 1998, Trends in biotechnology.

[79]  R. Goodacre,et al.  Fourier transform infrared spectroscopy and chemometrics as a tool for the rapid detection of other vegetable fats mixed in cocoa butter , 2001 .

[80]  Hanno Steen,et al.  Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. , 2002, Trends in biotechnology.

[81]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[82]  Thomas Szyperski,et al.  Intracellular Carbon Fluxes in Riboflavin-Producing Bacillussubtilis during Growth on Two-Carbon Substrate Mixtures , 2002, Applied and Environmental Microbiology.

[83]  C. Barbas,et al.  Development and validation of a capillary electrophoresis method for direct measurement of isocitric, citric, tartaric and malic acids as adulteration markers in orange juice. , 2000, Journal of chromatography. A.

[84]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[85]  D. Krizman,et al.  Picoliter‐Scale Protein Microarrays by Laser Direct Write , 2002, Biotechnology progress.

[86]  B. V. Baar Characterisation of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry. , 2000 .

[87]  Dirk Wolters,et al.  Proteomic survey of metabolic pathways in rice , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  M. Mann,et al.  Analysis of proteins and proteomes by mass spectrometry. , 2001, Annual review of biochemistry.

[89]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[90]  Barry Schweitzer,et al.  Measuring proteins on microarrays. , 2002, Current opinion in biotechnology.

[91]  Koji Otsuka,et al.  Capillary electrophoretic techniques toward the metabolome analysis , 2001 .

[92]  Milan Mrksich,et al.  Selective immobilization of proteins to self-assembled monolayers presenting active site-directed capture ligands , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[93]  Gordon A Anderson,et al.  Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[94]  S. Oliver Proteomics: Guilt-by-association goes global , 2000, Nature.

[95]  C. Fenselau,et al.  Characterization of the protein subset desorbed by MALDI from whole bacterial cells. , 2001, Analytical Chemistry.

[96]  D. Schubert A different perspective on GM food , 2002, Nature Biotechnology.

[97]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[98]  D. Hochstrasser,et al.  From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Arnino Acid Analysis , 1996, Bio/Technology.

[99]  S. Oliver Functional genomics: lessons from yeast. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[100]  B. Futcher,et al.  A Sampling of the Yeast Proteome , 1999, Molecular and Cellular Biology.

[101]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[102]  Jochen Förster,et al.  A functional genomics approach using metabolomics and in silico pathway analysis. , 2002, Biotechnology and bioengineering.

[103]  Sam F. Y. Li,et al.  Protein Microarrays on ITO Surfaces by a Direct Covalent Attachment Scheme , 2002 .

[104]  S. Kingsmore,et al.  Multiplexed protein profiling on microarrays by rolling-circle amplification , 2002, Nature Biotechnology.

[105]  G. Siuzdak,et al.  Probing viruses with mass spectrometry. , 1998, Journal of mass spectrometry : JMS.

[106]  H. Kuiper,et al.  Assessment of the food safety issues related to genetically modified foods. , 2001, The Plant journal : for cell and molecular biology.

[107]  P. Kearns,et al.  Substantial equivalence is a useful tool , 1999, Nature.

[108]  F. Reniero,et al.  Use of pyrolysis–mass spectrometry in food analysis: applications in the food analysis laboratory of the European Commissions’ Joint Research Centre , 1999 .

[109]  J. Ramírez,et al.  Tandem mass spectrometry of intact proteins for characterization of biomarkers from Bacillus cereus T spores. , 2001, Analytical chemistry.

[110]  J. Lindon,et al.  Metabonomics: a platform for studying drug toxicity and gene function , 2002, Nature Reviews Drug Discovery.

[111]  O. Fiehn Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[112]  Allison A. Snow,et al.  Transgenic crops—why gene flow matters , 2002, Nature Biotechnology.

[113]  R. Atkinson,et al.  Overexpression of Polygalacturonase in Transgenic Apple Trees Leads to a Range of Novel Phenotypes Involving Changes in Cell Adhesion1 , 2002, Plant Physiology.

[114]  H. Miller Substantial equivalence: Its uses and abuses , 1999, Nature Biotechnology.

[115]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[116]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[117]  P Berndt,et al.  Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography , 1999, Electrophoresis.

[118]  Royston Goodacre,et al.  Rapid and quantitative detection of the microbial spoilage of muscle foods: current status and future trends. , 2001 .

[119]  T. Ferenci,et al.  Effect of Slow Growth on Metabolism of Escherichia coli, as Revealed by Global Metabolite Pool (“Metabolome”) Analysis , 1998, Journal of bacteriology.

[120]  Philip J. Dale,et al.  Potential for the environmental impact of transgenic crops , 2002, Nature Biotechnology.

[121]  T. Veenstra,et al.  Characterization of microorganisms and biomarker development from global ESI-MS/MS analyses of cell lysates. , 2000, Analytical chemistry.

[122]  J. Yates,et al.  MASS SPECTRAL INVESTIGATIONS ON MICROORGANISMS , 2000 .

[123]  D. Kell,et al.  Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification , 2002, Journal of the American Society for Mass Spectrometry.

[124]  Nikola Tolić,et al.  Mass spectrometic detection for capillary isoelectric focusing separations of complex protein mixtures , 2000 .

[125]  Jean Rossier,et al.  Systematic identification of mitochondrial proteins by LC-MS/MS. , 2002, Analytical chemistry.

[126]  M. Gerstein,et al.  Subcellular localization of the yeast proteome. , 2002, Genes & development.