Tobias Kind

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc LipidBlast in silico tandem mass spectrometry database for lipid identification
    Tobias Kind
    Metabolics Core, UC Davis Genome Center, University of California, Davis, Davis, California, USA
    Nat Methods 10:755-8. 2013
  2. pmc Qualitative analysis of algal secretions with multiple mass spectrometric platforms
    Tobias Kind
    UC Davis Genome Center Metabolomics, University of California, Davis, CA 95616, USA
    J Chromatogr A 1244:139-47. 2012
  3. pmc Metabolite profiling of human colon carcinoma--deregulation of TCA cycle and amino acid turnover
    Carsten Denkert
    Institute of Pathology, Charite University Hospital, 10117 Berlin, Germany
    Mol Cancer 7:72. 2008
  4. pmc Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm
    Tobias Kind
    University of California Davis, Genome Center, Davis, CA 95616, USA
    BMC Bioinformatics 7:234. 2006
  5. pmc Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
    Tobias Kind
    University of California Davis, Genome Center, Davis, CA 95616, USA
    BMC Bioinformatics 8:105. 2007
  6. pmc FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry
    Tobias Kind
    University of California Davis, Genome Center, Davis, California 95616, USA
    Anal Chem 81:10038-48. 2009
  7. pmc How large is the metabolome? A critical analysis of data exchange practices in chemistry
    Tobias Kind
    University of California Davis, Genome Center Metabolomics, Davis, CA, USA
    PLoS ONE 4:e5440. 2009
  8. pmc Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry
    Dinesh K Barupal
    Genome Center, University of California, Davis, USA
    BMC Biotechnol 10:40. 2010
  9. pmc MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
    Dinesh K Barupal
    UC Davis Genome Center, Metabolomics, Davis, CA 95616, USA
    BMC Bioinformatics 13:99. 2012
  10. pmc Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism
    John K Meissen
    University of California Davis Genome Center, University of California Davis, Davis, California, USA
    PLoS ONE 7:e46770. 2012

Collaborators

Detail Information

Publications21

  1. pmc LipidBlast in silico tandem mass spectrometry database for lipid identification
    Tobias Kind
    Metabolics Core, UC Davis Genome Center, University of California, Davis, Davis, California, USA
    Nat Methods 10:755-8. 2013
    ..We show platform independence by using tandem mass spectra from 40 different mass spectrometer types including low-resolution and high-resolution instruments. ..
  2. pmc Qualitative analysis of algal secretions with multiple mass spectrometric platforms
    Tobias Kind
    UC Davis Genome Center Metabolomics, University of California, Davis, CA 95616, USA
    J Chromatogr A 1244:139-47. 2012
    ..We observed a series of triacylglycerols (TG), sulfoquinovosyldiacylglycerols (SQDG), phosphatidylinositols and phosphatidylglycerols, as well as betaine lipids diacylglyceryl-N,N,N-trimethylhomoserines (DGTS)...
  3. pmc Metabolite profiling of human colon carcinoma--deregulation of TCA cycle and amino acid turnover
    Carsten Denkert
    Institute of Pathology, Charite University Hospital, 10117 Berlin, Germany
    Mol Cancer 7:72. 2008
    ..However, in contrast to genomics and proteomics, comprehensive metabolomic investigations of alterations in malignant tumors have rarely been conducted...
  4. pmc Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm
    Tobias Kind
    University of California Davis, Genome Center, Davis, CA 95616, USA
    BMC Bioinformatics 7:234. 2006
    ..This report demonstrates the necessity of isotope abundance information by mathematical confirmation of the concept...
  5. pmc Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
    Tobias Kind
    University of California Davis, Genome Center, Davis, CA 95616, USA
    BMC Bioinformatics 8:105. 2007
    ..In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas...
  6. pmc FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry
    Tobias Kind
    University of California Davis, Genome Center, Davis, California 95616, USA
    Anal Chem 81:10038-48. 2009
    ....
  7. pmc How large is the metabolome? A critical analysis of data exchange practices in chemistry
    Tobias Kind
    University of California Davis, Genome Center Metabolomics, Davis, CA, USA
    PLoS ONE 4:e5440. 2009
    ..We detail current obstacles to compile such a knowledge base of metabolites...
  8. pmc Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry
    Dinesh K Barupal
    Genome Center, University of California, Davis, USA
    BMC Biotechnol 10:40. 2010
    ..Biofuels derived from algae biomass and algae lipids might reduce dependence on fossil fuels. Existing analytical techniques need to facilitate rapid characterization of algal species by phenotyping hydrocarbon-related constituents...
  9. pmc MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
    Dinesh K Barupal
    UC Davis Genome Center, Metabolomics, Davis, CA 95616, USA
    BMC Bioinformatics 13:99. 2012
    ..Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites...
  10. pmc Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism
    John K Meissen
    University of California Davis Genome Center, University of California Davis, Davis, California, USA
    PLoS ONE 7:e46770. 2012
    ..The identified metabolomics signatures of iPSCs and ESCs may have important implications for functional regulation of maintenance and induction of pluripotency...
  11. pmc The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports
    Gert Wohlgemuth
    University of California Davis, CA, Genome Center, USA
    Bioinformatics 26:2647-8. 2010
    ..5 min. Structures are automatically displayed. Implementation: The software was implemented in Groovy and JAVA, the web frontend was implemented in GRAILS and the database used was PostgreSQL...
  12. pmc Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometry
    Sangeeta Kumari
    UC Davis Genome Center, University of California Davis, Davis, California 95616, United States
    Anal Chem 83:5895-902. 2011
    ..Using a mass error window of 10 ppm for fragment ions, 89% of all isomeric structures were removed and the correct structure was reported in 73% within the top-5 hits of the cases...
  13. pmc Extending biochemical databases by metabolomic surveys
    Oliver Fiehn
    University of California Davis Genome Center, Davis, California 95616, USA
    J Biol Chem 286:23637-43. 2011
    ..The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome...
  14. doi request reprint Role of squalene in the organization of monolayers derived from lipid extracts of Halobacterium salinarum
    Sean F Gilmore
    Department of Applied Science, University of California at Davis, Davis, California 95616, USA
    Langmuir 29:7922-30. 2013
    ..e., domain formation) in the membranes of archaea analogous to that of cholesterol in eukaryotic membranes. ..
  15. doi request reprint Quality control for plant metabolomics: reporting MSI-compliant studies
    Oliver Fiehn
    Davis Genome Center, University of California, Davis, CA 95616, USA
    Plant J 53:691-704. 2008
    ..Standardized data processing methods are proposed for consistent data storage and dissemination via databases...
  16. pmc Software platform virtualization in chemistry research and university teaching
    Tobias Kind
    UC Davis Genome Center, Metabolomics, 451 Health Sci Drive, Davis, California, 95616, USA
    J Cheminform 1:18. 2009
    ..Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories...
  17. ncbi request reprint A comprehensive urinary metabolomic approach for identifying kidney cancerr
    Tobias Kind
    Genome Center, University of California, Davis, CA 95616, USA
    Anal Biochem 363:185-95. 2007
    ..Such investigation will likely lead to clinically applicable assays for earlier diagnosis of RCC, as well as other malignancies, and thereby improved patient prognosis...
  18. ncbi request reprint Metabolite profiling in blood plasma
    Oliver Fiehn
    Genome Center, University of California Davis, USA
    Methods Mol Biol 358:3-17. 2007
    ..A major difference to profiling plant tissues is that no fractionation step is utilized, enabling the analysis of primary metabolites like sugars and amino acids concomitant with lipids such as sterols and free fatty acids...
  19. ncbi request reprint Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors
    Carsten Denkert
    Institute of Pathology and Department of Gynecology and Obstetrics, Charite University Hospital, Berlin, Germany
    Cancer Res 66:10795-804. 2006
    ..We conclude that metabolomics is a promising high-throughput, automated approach in addition to functional genomics and proteomics for analyses of molecular changes in malignant tumors...
  20. ncbi request reprint Polychlorinated naphthalenes in sediments from the industrial region of Bitterfeld
    Werner Brack
    Department of Chemical Ecotoxicology, UFZ Center for Environmental Research Leipzig Halle, Germany
    Environ Pollut 121:81-5. 2003
    ..Because of their toxicological relevance we suggest to include PCNs into monitoring and risk assessment programs of the rivers Mulde and Elbe downstream of Bitterfeld...