Affiliation: University of California
- LipidBlast in silico tandem mass spectrometry database for lipid identificationTobias 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. ..
- Qualitative analysis of algal secretions with multiple mass spectrometric platformsTobias 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)...
- Metabolite profiling of human colon carcinoma--deregulation of TCA cycle and amino acid turnoverCarsten 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...
- Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppmTobias 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...
- Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometryTobias 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...
- FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometryTobias Kind
University of California Davis, Genome Center, Davis, California 95616, USA
Anal Chem 81:10038-48. 2009....
- How large is the metabolome? A critical analysis of data exchange practices in chemistryTobias 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...
- Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometryDinesh 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...
- MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarityDinesh 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...
- Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolismJohn 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...
- Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometrySangeeta 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...
- The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reportsGert Wohlgemuth
University of California Davis, CA, Genome Center, USA
Bioinformatics 26:2647-8. 2010..Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed...
- MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectraYan Ma
UC Davis Genome Center Metabolomics, University of California, Davis, California 95616, United States
Anal Chem 86:10724-31. 2014..Use of this tool has been successfully demonstrated for complex lipids in microalgae...
- Extending biochemical databases by metabolomic surveysOliver 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...
- LipidBlast templates as flexible tools for creating new in-silico tandem mass spectral librariesTobias Kind
West Coast Metabolomics Center, University of California Davis, Davis, California 95616, United States
Anal Chem 86:11024-7. 2014..Such libraries allow for high-throughput annotations of previously unknown glycolipids. The publicly available LipidBlast templates are universally applicable for the development of MS/MS libraries for novel lipid classes...
- Role of squalene in the organization of monolayers derived from lipid extracts of Halobacterium salinarumSean 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. ..
- Quality control for plant metabolomics: reporting MSI-compliant studiesOliver 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...
- Software platform virtualization in chemistry research and university teachingTobias 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...
- A comprehensive urinary metabolomic approach for identifying kidney cancerrTobias 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...
- Metabolite profiling in blood plasmaOliver 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...
- Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumorsCarsten 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...
- Polychlorinated naphthalenes in sediments from the industrial region of BitterfeldWerner 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...