isotope labeling

Summary

Summary: Techniques for labeling a substance with a stable or radioactive isotope. It is not used for articles involving labeled substances unless the methods of labeling are substantively discussed. Tracers that may be labeled include chemical substances, cells, or microorganisms.

Top Publications

  1. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
  2. ncbi A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Protoc 4:698-705. 2009
  3. ncbi A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
    Shao En Ong
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Protoc 1:2650-60. 2006
  4. ncbi Quantitative mass spectrometry in proteomics: a critical review
    Marcus Bantscheff
    Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
    Anal Bioanal Chem 389:1017-31. 2007
  5. ncbi Mass spectrometry-based proteomics turns quantitative
    Shao En Ong
    The Broad Institute of MIT and Harvard, 320 Bent Street, Cambridge, Massachusetts 02141, USA
    Nat Chem Biol 1:252-62. 2005
  6. ncbi Functional and quantitative proteomics using SILAC
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Rev Mol Cell Biol 7:952-8. 2006
  7. pmc Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages
    Michael D Urbaniak
    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
    PLoS ONE 7:e36619. 2012
  8. ncbi SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
    Marcus Kruger
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    Cell 134:353-64. 2008
  9. ncbi Evolution of graphene growth on Ni and Cu by carbon isotope labeling
    Xuesong Li
    Department of Mechanical Engineering and the Texas Materials Institute, 1 University Station C2200, The University of Texas at Austin, Austin, Texas 78712 0292, USA
    Nano Lett 9:4268-72. 2009
  10. pmc A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage
    François Michel Boisvert
    The Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, MSI WTB JBC Complex, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
    Mol Cell Proteomics 9:457-70. 2010

Research Grants

Detail Information

Publications391 found, 100 shown here

  1. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
    ....
  2. ncbi A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Protoc 4:698-705. 2009
    ..This protocol explains step by step how to use MaxQuant on stable isotope labeling by amino acids in cell culture (SILAC) data obtained with double or triple labeling...
  3. ncbi A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
    Shao En Ong
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Protoc 1:2650-60. 2006
    Stable isotope labeling by amino acids in cell culture (SILAC) is a simple, robust, yet powerful approach in mass spectrometry (MS)-based quantitative proteomics...
  4. ncbi Quantitative mass spectrometry in proteomics: a critical review
    Marcus Bantscheff
    Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
    Anal Bioanal Chem 389:1017-31. 2007
    ..Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the ..
  5. ncbi Mass spectrometry-based proteomics turns quantitative
    Shao En Ong
    The Broad Institute of MIT and Harvard, 320 Bent Street, Cambridge, Massachusetts 02141, USA
    Nat Chem Biol 1:252-62. 2005
    ..This isotopic handle facilitates direct quantification from the mass spectra. Using these quantitative approaches, precise functional information as well as temporal changes in the proteome can be captured by MS...
  6. ncbi Functional and quantitative proteomics using SILAC
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Rev Mol Cell Biol 7:952-8. 2006
    ....
  7. pmc Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages
    Michael D Urbaniak
    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
    PLoS ONE 7:e36619. 2012
    ..optimized a procedure for growing Trypanosoma brucei procyclic form cells in conditions suitable for stable isotope labeling by amino acids in culture (SILAC) and report a comparative proteomic analysis of cultured procyclic form and ..
  8. ncbi SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
    Marcus Kruger
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    Cell 134:353-64. 2008
    Stable isotope labeling by amino acids in cell culture (SILAC) has become a versatile tool for quantitative, mass spectrometry (MS)-based proteomics...
  9. ncbi Evolution of graphene growth on Ni and Cu by carbon isotope labeling
    Xuesong Li
    Department of Mechanical Engineering and the Texas Materials Institute, 1 University Station C2200, The University of Texas at Austin, Austin, Texas 78712 0292, USA
    Nano Lett 9:4268-72. 2009
    ..Here we used carbon isotope labeling in conjunction with Raman spectroscopic mapping to track carbon during the growth process...
  10. pmc A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage
    François Michel Boisvert
    The Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, MSI WTB JBC Complex, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
    Mol Cell Proteomics 9:457-70. 2010
    ..DNA damage was found to cause dissociation of the proteasome from inhibitory proteins and assembly chaperones in the cytoplasm and relocation to associate with proteasome activators in the nucleus...
  11. ncbi Super-SILAC mix for quantitative proteomics of human tumor tissue
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 7:383-5. 2010
    We describe a method to accurately quantify human tumor proteomes by combining a mixture of five stable-isotope labeling by amino acids in cell culture (SILAC)-labeled cell lines with human carcinoma tissue...
  12. ncbi Can stable isotope ratios provide for community-wide measures of trophic structure?
    Craig A Layman
    Marine Science Program, Department of Biological Sciences, 3000 NE 151st Street, North Miami, Florida 33181, USA
    Ecology 88:42-8. 2007
    ..Building from extensive applications of stable isotope ratios by ecologists, the community-wide metrics may provide a new perspective on food web structure, function, and dynamics...
  13. ncbi Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products
    Oded Kleifeld
    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
    Nat Biotechnol 28:281-8. 2010
    ....
  14. ncbi (68)Ga-labeled multimeric RGD peptides for microPET imaging of integrin alpha(v)beta (3) expression
    Zi Bo Li
    Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305 5484, USA
    Eur J Nucl Med Mol Imaging 35:1100-8. 2008
    ..The goal of this study was to investigate the feasibility of (68)Ga-labeled RGD peptides for tumor imaging...
  15. ncbi Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes
    Chunaram Choudhary
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Mol Cell 36:326-39. 2009
    ..Thus, intracellular activation of RTKs by oncogenic mutations in the biosynthetic route may exploit cellular architecture to initiate aberrant signaling cascades, thus evading negative regulation...
  16. ncbi Global analysis of cellular protein translation by pulsed SILAC
    Björn Schwanhäusser
    Max Delbruck Center for Molecular Medicine, Berlin, Germany
    Proteomics 9:205-9. 2009
    ..Here, we developed pulsed stable isotope labeling by amino acids in cell culture (pSILAC) with two heavy isotope labels to directly quantify protein ..
  17. ncbi MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
    Peter Mortensen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Campusvej 55, DK 5230 Odense M, Denmark
    J Proteome Res 9:393-403. 2010
    ..g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net ...
  18. ncbi A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    Blagoy Blagoev
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Nat Biotechnol 21:315-8. 2003
    ..SILAC combined with modification-based affinity purification is a useful approach to detect specific and functional protein-protein interactions...
  19. pmc Stable-isotope labeling with amino acids in nematodes
    Mark Larance
    Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
    Nat Methods 8:849-51. 2011
    ..We adapted stable-isotope labeling with amino acids in cell culture (SILAC) for nematodes by feeding worms a heavy lysine- and heavy arginine-..
  20. ncbi Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
    Blagoy Blagoev
    Nat Biotechnol 22:1139-45. 2004
    ..Global activation profiles provide an informative perspective on cell signaling and will be crucial to modeling signaling networks in a systems biology approach...
  21. pmc Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells
    Christian M Metallo
    Department of Chemical Engineering, Massachusetts Institute of Technology, Building 56 Room 469C, 77 Massachusetts Ave, Cambridge, MA 02139, United States
    J Biotechnol 144:167-74. 2009
    ..These results provide valuable, quantitative information on the performance of (13)C-labeled substrates and can aid in the design of more informative MFA experiments in mammalian cell culture...
  22. ncbi Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology
    Pierre Barraud
    Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zurich, Switzerland
    J Biomol NMR 55:119-38. 2013
    ..In the present study, we have used NMR spectroscopy in combination with segmental isotope labeling techniques to carefully analyze the inter-RRM contacts present in solution and subsequently determine the ..
  23. pmc Analysis of proteome dynamics in the mouse brain
    John C Price
    Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 107:14508-13. 2010
    ..The developed methodology can be adapted to assess in vivo proteome homeostasis in any model organism that will tolerate a labeled diet and may be particularly useful in the analysis of neurodegenerative diseases in vivo...
  24. ncbi Identifying and quantifying in vivo methylation sites by heavy methyl SILAC
    Shao En Ong
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M 5230, Denmark
    Nat Methods 1:119-26. 2004
    ..We have previously described stable isotope labeling by amino acids in cell culture (SILAC) for quantitative comparison of proteomes...
  25. pmc Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle
    Chandar S Thakur
    Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences Bldg 296, College Park, MD 20742 3360, USA
    J Biomol NMR 48:179-92. 2010
    ..Even under conditions of slow tumbling, all the expected carbon correlations were observed, which indicates this approach of using nucleotides obtained from DL323 E. coli will be applicable to high molecular weight RNA systems...
  26. ncbi Mass spectrometric-based approaches in quantitative proteomics
    Shao En Ong
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, M 5230 Odense, Denmark
    Methods 29:124-30. 2003
    ..most commonly used protocols, focusing on a procedure now being used extensively in our laboratory, stable isotope labeling with amino acids in cell culture (SILAC)...
  27. ncbi Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    Hui Zhang
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 21:660-6. 2003
    ..It is based on the conjugation of glycoproteins to a solid support using hydrazide chemistry, stable isotope labeling of glycopeptides and the specific release of formerly N-linked glycosylated peptides via peptide- N-..
  28. ncbi Stable isotope assisted assignment of elemental compositions for metabolomics
    Adrian D Hegeman
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 79:6912-21. 2007
    ..These results demonstrate that metabolic labeling can be used to provide additional constraints for higher confidence formula assignments over an extended mass range...
  29. pmc Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions
    Maciek R Antoniewicz
    Department of Chemical Engineering, Bioinformatics and Metabolic Engineering Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Metab Eng 9:68-86. 2007
    ..An important limitation of MFA, as carried out via stable isotope labeling and GC/MS and nuclear magnetic resonance (NMR) measurements, is the large number of isotopomer or cumomer ..
  30. ncbi Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry
    Albrecht Gruhler
    Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 4:1697-709. 2005
    ..Stable isotope labeling by amino acids in cell culture (SILAC) has been successfully used in yeast and mammalian cells to measure ..
  31. ncbi Synthesis and evaluation of bombesin derivatives on the basis of pan-bombesin peptides labeled with indium-111, lutetium-177, and yttrium-90 for targeting bombesin receptor-expressing tumors
    Hanwen Zhang
    Division of Radiological Chemistry, Institute of Nuclear Medicine, Department of Radiology, University Hospital, Basel
    Cancer Res 64:6707-15. 2004
    ....
  32. ncbi Synthesis of 11C, 18F, 15O, and 13N radiolabels for positron emission tomography
    Philip W Miller
    Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
    Angew Chem Int Ed Engl 47:8998-9033. 2008
    ..This Review highlights key aspects of the synthesis of PET radiotracers with the short-lived positron-emitting radionuclides (11)C, (18)F, (15)O, and (13)N, with emphasis on the most recent strategies...
  33. ncbi Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling
    Richard Baran
    Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
    Anal Chem 82:9034-42. 2010
    ..Here we present an integrated workflow for metabolite identification using uniform stable isotope labeling. Metabolite profiling of cell and growth media extracts of unlabeled control, (15)N, and (13)C-labeled ..
  34. pmc Integrating stomach content and stable isotope analyses to quantify the diets of pygoscelid penguins
    Michael J Polito
    Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
    PLoS ONE 6:e26642. 2011
    ....
  35. ncbi Current trends in quantitative proteomics
    Monica H Elliott
    University of Victoria Genome BC Proteomics Centre, British Columbia, V8Z 7X8, Canada
    J Mass Spectrom 44:1637-60. 2009
    ..However, even though there is no perfect technique--and a better technique may be developed tomorrow--valuable information on biomarkers and pathways can be obtained using these currently available methods...
  36. ncbi Protein-based stable isotope probing
    Nico Jehmlich
    Department of Proteomics, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
    Nat Protoc 5:1957-66. 2010
    ..Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d...
  37. ncbi Isotope labeling and segmental labeling of larger RNAs for NMR structural studies
    Olivier Duss
    Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
    Adv Exp Med Biol 992:121-44. 2012
    ..Recent improvements in isotope labeling of RNA have strongly contributed to the high impact of NMR in RNA structure determination...
  38. ncbi Isotope labeling experiments in metabolomics and fluxomics
    Sebastian Klein
    Biochemical Engineering Institute, Saarland University, Saarbrucken, Germany
    Wiley Interdiscip Rev Syst Biol Med 4:261-72. 2012
    ..This includes the underlying principles, experimental and computational methods used, and examples of application...
  39. ncbi IsoCor: correcting MS data in isotope labeling experiments
    Pierre Millard
    Universite de Toulouse, 135 Avenue de Rangueil, Toulouse, France
    Bioinformatics 28:1294-6. 2012
    ..Its user-friendly interface makes isotope labeling experiments more accessible to a wider biological community.
  40. pmc Quantitative proteomics reveals regulation of karyopherin subunit alpha-2 (KPNA2) and its potential novel cargo proteins in nonsmall cell lung cancer
    Chun I Wang
    Graduate Institute of Biomedical Sciences, Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, and Department of Thoracic Medicine, Chang Gung Memorial Hospital, Tao Yuan, Taiwan
    Mol Cell Proteomics 11:1105-22. 2012
    ..In the current study, we applied gene knockdown, subcellular fractionation, and stable isotope labeling by amino acids in cell culture-based quantitative proteomic strategies to systematically analyze the KPNA2-..
  41. ncbi Elucidation of cellular metabolism via metabolomics and stable-isotope assisted metabolomics
    Karsten Hiller
    Massachusetts Institute of Technology, Department of Chemical Engineering, 77 Massachusetts Ave, 56 439, Cambridge, MA 02140, USA
    Curr Pharm Biotechnol 12:1075-86. 2011
    ....
  42. pmc Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation
    Ulrich auf dem Keller
    Department of Oral Biological and Medical Sciences, 4 401 Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Sci Signal 6:rs2. 2013
    ..Thus, our systems-level analysis of proteolysis dissected cleavage events associated with skin inflammation and demonstrated that loss of a single protease could perturb the proteolytic signaling network and enhance inflammation...
  43. pmc A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS
    Da Qi
    Institute of Integrative Biology, University of Liverpool, Merseyside, UK
    OMICS 16:489-95. 2012
    ..post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation...
  44. pmc Ontogenetic and among-individual variation in foraging strategies of northeast Pacific white sharks based on stable isotope analysis
    Sora L Kim
    Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, California, USA
    PLoS ONE 7:e45068. 2012
    ..Our data reveal substantial ontogenetic and individual dietary variation within a white shark population...
  45. pmc Population-level metrics of trophic structure based on stable isotopes and their application to invasion ecology
    Michelle C Jackson
    School of Biological and Chemical Sciences, Queen Mary University of London, London, England
    PLoS ONE 7:e31757. 2012
    ..Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications...
  46. pmc Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics
    Anna Prudova
    Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, 4 401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Mol Cell Proteomics 9:894-911. 2010
    ..Hence, N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases...
  47. pmc A fast, efficient and sequence-independent method for flexible multiple segmental isotope labeling of RNA using ribozyme and RNase H cleavage
    Olivier Duss
    Institute of Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
    Nucleic Acids Res 38:e188. 2010
    ..Segmental isotope labeling of RNA or ligation of a chemically synthesized RNA containing modified nucleotides with an unmodified RNA ..
  48. ncbi Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol
    Keith Vosseller
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
    Proteomics 5:388-98. 2005
    ..These results demonstate BEMAD is suitable for large-scale quantitative analysis of both protein expression and serine / threonine post-translational modifications...
  49. ncbi Activated MAO-B in the brain of Alzheimer patients, demonstrated by [11C]-L-deprenyl using whole hemisphere autoradiography
    Balazs Gulyas
    Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden
    Neurochem Int 58:60-8. 2011
    ....
  50. ncbi Radiolabeling of lipid-based nanoparticles for diagnostics and therapeutic applications: a comparison using different radiometals
    Anna Helbok
    Clinical Department of Nuclear Medicine, Medical University Innsbruck, Innsbruck, Austria
    J Liposome Res 20:219-27. 2010
    ..Overall, our study shows that PEGylated DTPA-NP are suitable for radiolabeling studies with a variety of radiometals, thereby achieving high SA suitable for targeting applications...
  51. ncbi Stationary versus non-stationary (13)C-MFA: a comparison using a consistent dataset
    Stephan Noack
    Institut fur Biotechnologie, Forschungszentrum Julich, Leo Brandt Straße, Julich, NRW, Germany
    J Biotechnol 154:179-90. 2011
    ..Taking further criteria on the experimental and computational part into consideration, the current limitations of both methods are demonstrated and possible pitfalls are concluded...
  52. ncbi Quantitative proteomics of complex mixtures
    Kevin M Coombs
    Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
    Expert Rev Proteomics 8:659-77. 2011
    ..isotope-coded protein labeling, tandem mass tags, isobaric tags for relative and absolute quantitation, stable isotope labeling of amino acids in cell culture and label-free), as well as recent examples of each strategy, are described.
  53. ncbi Quantitative proteomics by amino acid labeling in C. elegans
    Julius Fredens
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
    Nat Methods 8:845-7. 2011
    ..elegans. The combined use of quantitative proteomics and selective gene knockdown is a powerful tool for C. elegans biology...
  54. pmc Metabolic turnover analysis by a combination of in vivo 13C-labelling from 13CO2 and metabolic profiling with CE-MS/MS reveals rate-limiting steps of the C3 photosynthetic pathway in Nicotiana tabacum leaves
    Tomohisa Hasunuma
    Research institute of Innovative Technology for the Earth RITE, 9 2 Kizugawadai, Kizugawa shi, Kyoto 619 0292 Japan
    J Exp Bot 61:1041-51. 2010
    ..The pool size of G1P is 12 times lower than that of G6P. These results indicate that the conversion of G6P to G1P is one of the rate-limiting steps in the sugar phosphate pathway...
  55. ncbi Use of a combination of isotopically coded cross-linkers and isotopically coded N-terminal modification reagents for selective identification of inter-peptide crosslinks
    Evgeniy V Petrotchenko
    University of Victoria Genome British Columbia Protein Centre, Department of Biochemistry and Microbiology, University of Victoria, No 3101 4464 Markham Street, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
    Anal Chem 82:817-23. 2010
    ..This procedure, combined with software for data analysis, provides a simple and rapid method for specific detection of inter-peptide crosslinks...
  56. ncbi Cyclic minigastrin analogues for gastrin receptor scintigraphy with technetium-99m: preclinical evaluation
    Elisabeth von Guggenberg
    Department of Nuclear Medicine, Innsbruck Medical University, Anichstrasse 35, A 6020 Innsbruck, Austria
    J Med Chem 52:4786-93. 2009
    ..i. for both 99mTc-EDDA-HYNIC-cyclo-MG1 and 99mTc-EDDA-HYNIC-cyclo-MG2. In an imaging study with 99mTc-EDDA-HYNIC-cyclo-MG1, the tumor was clearly visualized. The metabolite analysis indicated rapid enzymatic degradation in vivo...
  57. pmc Comparison of three radiolabelled peptide analogues for CCK-2 receptor scintigraphy in medullary thyroid carcinoma
    Alida C Fröberg
    Department of Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, s Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
    Eur J Nucl Med Mol Imaging 36:1265-72. 2009
    ..However, these studies are mostly limited and difficult to compare. The aim of this study was to evaluate the diagnostic and therapeutic potential of three promising CCK-2 receptor-binding radiopeptides in patients with MTC...
  58. pmc Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides
    Chandar S Thakur
    Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences, Bldg 296, College Park, MD 20742 3360, USA
    Appl Microbiol Biotechnol 88:771-9. 2010
    ..These studies should benefit efforts to make selective 13C-15N isotopic-labeled nucleotides for synthesizing biologically important RNAs...
  59. pmc A genetic engineering solution to the "arginine conversion problem" in stable isotope labeling by amino acids in cell culture (SILAC)
    Claudia C Bicho
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    Mol Cell Proteomics 9:1567-77. 2010
    Stable isotope labeling by amino acids in cell culture (SILAC) provides a straightforward tool for quantitation in proteomics...
  60. ncbi Species differences of bombesin analog interactions with GRP-R define the choice of animal models in the development of GRP-R-targeting drugs
    Theodosia Maina
    Institute of Radioisotopes Radiodiagnostic Products, National Center for Scientific Research Demokritos, 152 10 Ag Paraskevi Arrikis, Athens, Greece
    J Nucl Med 46:823-30. 2005
    ....
  61. ncbi Development and characterization of clinical-grade 89Zr-trastuzumab for HER2/neu immunoPET imaging
    Eli C F Dijkers
    Department of Hospital and Clinical Pharmacy, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    J Nucl Med 50:974-81. 2009
    ..The PET radiopharmaceutical (89)Zr-trastuzumab was compared with the SPECT tracer (111)In-trastuzumab, which we have tested in the clinic already...
  62. pmc The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses
    Corey E Bakalarski
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Proteome Res 7:4756-65. 2008
    ..Finally, we demonstrate that S/N can be a useful surrogate for relative abundance ratios when only a single species is detected...
  63. ncbi SPECT and PET amino acid tracer influx via system L (h4F2hc-hLAT1) and its transstimulation
    Tony Lahoutte
    Department of Nuclear Medicine, Academic Hospital Free University Brussels, Brussels, Belgium
    J Nucl Med 45:1591-6. 2004
    ....
  64. ncbi A HER2-binding Affibody molecule labelled with 68Ga for PET imaging: direct in vivo comparison with the 111In-labelled analogue
    Vladimir Tolmachev
    Division of Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala University, 751 81, Uppsala, Sweden
    Eur J Nucl Med Mol Imaging 37:1356-67. 2010
    ..The goal of this study was to prepare and characterize (68)Ga-labelled ABY-002...
  65. ncbi Delineating mechanisms of dissociation for isomeric heparin disaccharides using isotope labeling and ion trap tandem mass spectrometry
    Ola M Saad
    Department of Chemistry, University of California at Berkeley, Berkeley, California 94720 1460, USA
    J Am Soc Mass Spectrom 15:1274-86. 2004
    ....
  66. pmc A novel facile method of labeling octreotide with (18)F-fluorine
    Peter Laverman
    Department of Nuclear Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    J Nucl Med 51:454-61. 2010
    ..The method is characterized by the labeling of NOTA-octreotide (NOTA-d-Phe-cyclo[Cys-Phe-d-Trp-Lys-Thr-Cys]-Throl (MH(+) 1305) [IMP466]) with (18)F...
  67. ncbi Mapping the integrin-linked kinase interactome using SILAC
    Iveta Dobreva
    Department of Cancer Genetics, British Columbia Cancer Research Centre, 675 West 10th Avenue, V5Z 1L3, Vancouver, BC, Canada
    J Proteome Res 7:1740-9. 2008
    ..Here, we applied a SILAC (stable isotope labeling with amino acids in cell culture)-based proteomics approach to discover novel ILK-interacting proteins...
  68. ncbi Referencing strategies and techniques in stable isotope ratio analysis
    R A Werner
    Max Planck Institute for Biogeochemistry, P O Box 100164, 07701 Jena, Germany
    Rapid Commun Mass Spectrom 15:501-19. 2001
    ..The implementation of the principle in our laboratory, the monitoring of our measurement quality, the status of the international scales and reference materials and necessary correction procedures are discussed...
  69. ncbi The dynamic state of protein turnover: It's about time
    Izumi V Hinkson
    Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
    Trends Cell Biol 21:293-303. 2011
    ..This review examines several recent developments in protein turnover research, emphasizing the combination of metabolic labeling and mass spectrometry...
  70. pmc Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery
    Kenneth H Yu
    Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    J Proteome Res 8:1565-76. 2009
    ..Secreted proteins from CAPAN-2 human pancreatic cancer derived cells were collected after conducting stable isotope labeling by amino acids in cell culture (SILAC). The resulting SILAP standard contained <0...
  71. ncbi Measurement of protein turnover rates by heavy water labeling of nonessential amino acids
    Robert Busch
    KineMed, Inc, Emeryville, CA 94608, USA
    Biochim Biophys Acta 1760:730-44. 2006
    ..In conclusion, 2H2O labeling permits sensitive, quantitative, operationally simple measurements of protein turnover in vivo by the rise-to-plateau approach, especially for proteins with slow constitutive turnover...
  72. ncbi Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique
    Pragya Singh
    Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195 7610, USA
    Anal Chem 82:2636-42. 2010
    ..We review here a number of computer programs available to address these problems...
  73. pmc A statistics-based platform for quantitative N-terminome analysis and identification of protease cleavage products
    Ulrich auf dem Keller
    Department of Biochemistry and Molecular Biology, Centre for Blood Research, University of British Columbia, 4 401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Mol Cell Proteomics 9:912-27. 2010
    ....
  74. pmc Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners
    Séverine Boulon
    The Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
    Mol Cell Proteomics 9:861-79. 2010
    ..Stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry has been shown to provide a powerful ..
  75. ncbi Identifying dynamic interactors of protein complexes by quantitative mass spectrometry
    Xiaorong Wang
    Departments of Physiology and Biophysics and Developmental and Cell Biology, University of California, Irvine, California 92697 4560, USA
    Mol Cell Proteomics 7:46-57. 2008
    ..In this work, we developed a new method, MAP (mixing after purification)-SILAC (stable isotope labeling of amino acids in cell culture), to quantitatively investigate the interactions of protein complexes by mass ..
  76. ncbi Nontargeted elucidation of metabolic pathways using stable-isotope tracers and mass spectrometry
    Karsten Hiller
    Massachusetts Institute of Technology, Department of Chemical Engineering, 77 Massachusetts Ave, 56 439, Cambridge, Massachusetts 02140, USA
    Anal Chem 82:6621-8. 2010
    ..This novel method adds a new dimension to the metabolomics tool box and provides a framework for global analysis of metabolic fluxes...
  77. pmc Stable isotope labeling by amino acids in cell culture and differential plasma membrane proteome quantitation identify new substrates for the MARCH9 transmembrane E3 ligase
    Simon Hor
    Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
    Mol Cell Proteomics 8:1959-71. 2009
    ..novel MARCH9 substrates, we used high throughput flow cytometry and quantitative mass spectrometry by stable isotope labeling by amino acids in cell culture (SILAC) to determine the differential expression of plasma membrane proteins ..
  78. pmc Quantitative proteomics in plants: choices in abundance
    Jay J Thelen
    Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA
    Plant Cell 19:3339-46. 2007
  79. ncbi Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients
    Tillmann Lueders
    Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043 Marburg, Germany
    Environ Microbiol 6:73-8. 2004
    ..This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems...
  80. pmc Quantitative proteomics using stable isotope labeling with amino acids in cell culture reveals changes in the cytoplasmic, nuclear, and nucleolar proteomes in Vero cells infected with the coronavirus infectious bronchitis virus
    Edward Emmott
    Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
    Mol Cell Proteomics 9:1920-36. 2010
    ..Stable isotope labeling with amino acids in cell culture (SILAC) was used in conjunction with LC-MS/MS to identify and quantify 1830 ..
  81. ncbi A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease
    Chia Li Han
    Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
    Mol Cell Proteomics 7:1983-97. 2008
    ....
  82. pmc 68Ga-labeled inhibitors of prostate-specific membrane antigen (PSMA) for imaging prostate cancer
    Sangeeta Ray Banerjee
    Russell H Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Medical Institutions, 1550 Orleans Street, Baltimore, Maryland 21231, USA
    J Med Chem 53:5333-41. 2010
    ..Both compounds delineated tumor clearly by small animal PET. The urea series of imaging agents for PSMA can be radiolabeled with (68)Ga, a cyclotron-free isotope useful for clinical PET studies, with maintenance of target specificity...
  83. pmc Prevention of amino acid conversion in SILAC experiments with embryonic stem cells
    Sean C Bendall
    Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
    Mol Cell Proteomics 7:1587-97. 2008
    Recent studies using stable isotope labeling with amino acids in culture (SILAC) in quantitative proteomics have made mention of the problematic conversion of isotope-coded arginine to proline in cells...
  84. ncbi Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy
    Vitali Tugarinov
    Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building, 1 King s College Circle, Toronto, Ontario, M5S 1A8 Canada
    Nat Protoc 1:749-54. 2006
    The development of isotope labeling methodology has had a significant impact on NMR studies of high-molecular-weight proteins and macromolecular complexes...
  85. pmc In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling
    Paul J Boersema
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Mol Cell Proteomics 9:84-99. 2010
    ..Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated...
  86. pmc Pharmacoproteomics of a metalloproteinase hydroxamate inhibitor in breast cancer cells: dynamics of membrane type 1 matrix metalloproteinase-mediated membrane protein shedding
    Georgina S Butler
    Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, Canada
    Mol Cell Biol 28:4896-914. 2008
    ..Hence, this approach describes the dynamic pattern of cell membrane ectodomain shedding and its perturbation upon metalloproteinase drug treatment...
  87. pmc Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes
    Laura Trinkle-Mulcahy
    Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, UK
    J Cell Biol 183:223-39. 2008
    ..These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments...
  88. ncbi Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis
    Nina C Hubner
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 8:4862-72. 2008
    ..Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics...
  89. ncbi SILIP: a novel stable isotope labeling method for in planta quantitative proteomic analysis
    Jennifer E Schaff
    Department of Plant Pathology, Center for the Biology of Nematode Parasitism, North Carolina State University, Raleigh, NC 27695 7253, USA
    Plant J 56:840-54. 2008
    ..To address this issue in plant biology, we developed SILIP (stable isotope labeling in planta) using tomato plants (Solanum lycopersicum cv...
  90. ncbi Stoichiometry and absolute quantification of proteins with mass spectrometry using fluorescent and isotope-labeled concatenated peptide standards
    Dhaval Nanavati
    Laboratory of Neurotoxicology, National Institute of Mental Health, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Cell Proteomics 7:442-7. 2008
    ....
  91. pmc Quantitative membrane proteomics reveals new cellular targets of viral immune modulators
    Eric Bartee
    Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
    PLoS Pathog 2:e107. 2006
    ..Using stable isotope labeling by amino acids, we compared the proteome of plasma, Golgi, and endoplasmic reticulum membranes in the ..
  92. ncbi Proteomic analysis of post-translational modifications
    Matthias Mann
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK 5230 Denmark
    Nat Biotechnol 21:255-61. 2003
    ..Finally, stable isotope labeling strategies in combination with mass spectrometry have been applied successfully to study the dynamics of ..
  93. ncbi Proteome dynamics in complex organisms: using stable isotopes to monitor individual protein turnover rates
    Mary K Doherty
    Department of Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK
    Proteomics 5:522-33. 2005
    ..For the first time, it is feasible to contemplate the analysis of turnover of individual proteins in intact animals...
  94. pmc Intrapopulation variability shaping isotope discrimination and turnover: experimental evidence in arctic foxes
    Nicolas Lecomte
    Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
    PLoS ONE 6:e21357. 2011
    ....
  95. ncbi Qualitative and quantitative analysis of tumor cell metabolism via stable isotope labeling assisted microfluidic chip electrospray ionization mass spectrometry
    Qiushui Chen
    Beijing Key Laboratory of Analytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, People s Republic of China
    Anal Chem 84:1695-701. 2012
    In this work, a stable isotope labeling assisted microfluidic chip electrospray ionization mass spectrometry (SIL-chip-ESI-MS) platform for qualitative and quantitative analysis of cell metabolism was developed...
  96. ncbi Isotope dilution strategies for absolute quantitative proteomics
    Virginie Brun
    CEA, DSV, iRTSV, Laboratoire d Etude de la Dynamique des Proteomes, Grenoble, F 38054, France
    J Proteomics 72:740-9. 2009
    ..In this review, we present a critical overview of these isotope dilution methodologies...
  97. ncbi Analysis of carbon and nitrogen co-metabolism in yeast by ultrahigh-resolution mass spectrometry applying 13C- and 15N-labeled substrates simultaneously
    Lars M Blank
    Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
    Anal Bioanal Chem 403:2291-305. 2012
    ..The results indicate that not only glutamate but also alanine acts as an amino donor during alanine and valine synthesis. Metabolic studies using FTICR-MS can exploit new possibilities by the use of multiple-labeled elemental isotopes...
  98. ncbi Isotopic incorporation rates for shark tissues from a long-term captive feeding study
    Sora Lee Kim
    Department of Earth and Planetary Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    J Exp Biol 215:2495-500. 2012
    ..In spite of their large size and unusual physiology, the rates of isotopic incorporation in sharks seem to follow the same patterns found in other aquatic ectotherms...
  99. ncbi Designer labels for plant metabolism: statistical design of isotope labeling experiments for improved quantification of flux in complex plant metabolic networks
    Shilpa Nargund
    Department of Chemical and Biomolecular Engineering, University of Maryland, 1208D, Chemical and Nuclear Engineering Building 090, College Park, MD 20742, USA
    Mol Biosyst 9:99-112. 2013
    ..of isotope-assisted MFA to them, principally because of poor identifiability of fluxes from the measured isotope labeling patterns...
  100. pmc Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS
    Sebastian Behrens
    Department of Chemical Engineering and of Civil, Stanford University, Stanford, California 94305 5429, USA
    Appl Environ Microbiol 74:3143-50. 2008
    ..Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities...
  101. pmc Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation
    Florian Alexander Herbst
    Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany
    Mol Cell Proteomics 12:2060-9. 2013
    ..For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast ..

Research Grants69

  1. A quantitative proteomics approach to understand viral immune evasion strategies
    Michele E Hardy; Fiscal Year: 2010
    ..We will employ stable isotope labeling of amino acids in culture (SILAC) followed by high resolution chromatographic separation and tandem mass ..
  2. Role of Glutathione S-Transferase P in Heart Failure
    Sumanth D Prabhu; Fiscal Year: 2013
    ..In isolated, perfused sham-operated and failing hearts from WT, GSTP-/- and hGSTP Tg mice, using isotope labeling and mass spectrometry, we will characterize the metabolism and detoxification of unsaturated aldehydes...
  3. Influence of Heme on Hepatic Cytochrome P450 Turnover
    Maria Almira Correia; Fiscal Year: 2013
    ..Studies are proposed in Hri-/- and Hri+/+ hepatocytes using SILAC (stable isotope labeling of amino acids in culture) coupled with proteomics to identify and quantify the hepatic proteins whose ..
  4. Melanopsin Signal Transduction Studied by FTIR Spectroscopy
    Kenneth J Rothschild; Fiscal Year: 2012
    ..difference techniques, many developed in our laboratory, in conjunction with site-directed mutagenesis and isotope labeling. Application of this approach has led previously to several milestones including the first detailed ..
  5. ANALYSIS OF MEIOTIC CHROMOSOME SYNAPSIS IN YEAST
    Nancy M Hollingsworth; Fiscal Year: 2013
    ..Development of a novel protocol has allowed the powerful proteomic approach of Stable Isotope Labeling by Amino acids in Cell culture or SILAC, to be applied to meiotic budding yeast cells for the first time...
  6. Photocleavable Bead Technology for Glycomics
    Mark Lim; Fiscal Year: 2013
    ..Blixt and Costello). ..
  7. Glucocorticoid Receptor and Lipid Homeostasis
    Jen Chywan Wang; Fiscal Year: 2013
    ..In addition to measure metabolic parameters, we will also monitor the rate of lipid metabolism using stable isotope labeling technique...
  8. Functional analysis of Chk2 in DNA damage response
    Jun Hyun Kim; Fiscal Year: 2013
    ..Methods For attempts to identify new Chk2 substrates, I have performed SILAC (Stable Isotope Labeling with Amino acids in Cell culture) screening using cells with analog-sensitive Chk2 allele...
  9. The application of human collagen kinetic biomarkers to anti-fibrotic drug develo
    SCOTT M contact TURNER; Fiscal Year: 2010
    ..KineMed has developed a proprietary technology, using stable isotope labeling and mass spectrometric analysis, to accurately measure changes in tissue collagen synthesis in vivo in humans ..
  10. Neuroprotective immunity and HIV dementia
    Howard E Gendelman; Fiscal Year: 2013
    ..Coordinate magnetic resonance imaging and behavioral testing for screening of brain impairments and stable isotope labeling of amino acids in mammals for mechanistic study will anchor protein chemistry, histology, cognition and ..
  11. Determining the Function of PNPLA3 Utilizing Metabolomics and Stable Isotope Labe
    MATTHEW ALVIN MITSCHE; Fiscal Year: 2013
    ..Alternative stable isotope labeling strategies, such as 13C-glycerol or 13C-fatty acid incorporation, will also be employed to compliment the D2O ..
  12. Role of miRNA-375 in Invasive Phenotype of Head and Neck Squamous Cell Carcinoma
    Lizandra Jimenez; Fiscal Year: 2013
    ..with whole genome microarrays and translationally repressed putative targets of miR-375 by SILAC (stable isotope labeling of cells in cell culture)...
  13. Factors Mediating Host Resistance to Chlamydia trachomatis
    Michael N Starnbach; Fiscal Year: 2013
    ..trachomatis, we are applying two novel screening methods called "stable isotope labeling with amino acids in cells culture" (SILAC) and "Global Protein Stability" (GPS) to analyze, on a global scale,..
  14. Mechanisms of HbF Activation by Non-deletional HPFH
    Kenneth R Peterson; Fiscal Year: 2013
    ..protein complexes in the A?-globin promoter using proteomics of isolated chromatin segments (PICh) and Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) coupled with mass spectrometry (MS)...
  15. High Resolution Mass Spectrometry System
    John M Asara; Fiscal Year: 2012
    ..of peptides/proteins and modified peptides/proteins from cell lines and tumor tissues using stable isotope labeling (e.g., SILAC, iTRAQ, TMT) and label-free strategies (e.g...
  16. Analysis of Candida albicans filamentation using SILAC
    DEREK PAUL THOMAS; Fiscal Year: 2012
    ..The basis of the proposed experimentation is to use Stable Isotope Labeling with Amino acids in Cell culture (SILAC) in conjunction with Immobilized Metal Affinity Chromatography (IMAC) ..
  17. Regulation of spermatogenesis by sumoylation
    Margarita Vigodner; Fiscal Year: 2011
    ..experiments using freshly isolated cells will be supplemented and extended using cell lines and stable isotope labeling with amino acids in cell culture (SILAC) to study changes in the sumoylated proteomes of spermatogonia as ..
  18. Analysis of Protein Dynamics in C. elegans by mLC/MS/MS
    Michael MacCoss; Fiscal Year: 2013
    ..elegans using stable isotope labeling and isotopomer distribution analysis...
  19. 950 MHz NMR Spectrometer with Cryogenic Probe
    DAVID JOSEPH WEBER; Fiscal Year: 2010
    ..Dr. Vitali Tugarinov (project 10;Title: "Development of NMR and isotope labeling methodology for the studies of structure and dynamics of high molecular weight proteins) was recently hired ..
  20. Drosophila model of oxalate nephrolithiasis
    Michael F Romero; Fiscal Year: 2013
    ..eYFP-Cl-sensing and microCT with gut- or tubule-specific dPrestin knockdown, (c) using SILAC (stable isotope labeling by amino acids in cell culture) mass spectroscopy to elucidate protein compensation for the above tissue-..
  21. Mechanisms of odor detection and transduction
    Austin Yang; Fiscal Year: 2013
    ..We will use stable isotope labeling of mice expressing different levels of the either bait, followed by immunoprecipitation of interacting ..
  22. Orbitrap Elite Mass Spectrometer for Chromatin Biology and Epigenetics Research
    Benjamin A Garcia; Fiscal Year: 2013
    ..include Top and Middle Down analyses of histone and non-histone combinatorial PTM codes, pulse stable isotope labeling of amino acids in cell culture (pulse SILAC) for determining PTM-specific turnover/dynamics, global proteome ..
  23. CNS and Plasma Amyloid--Beta Kinetics in Alzheimer's Disease
    Randall J Bateman; Fiscal Year: 2013
    ..In order to understand A[unreadable] kinetics in the pathophysiology of AD, the applicant will use Stable Isotope Labeling Kinetics (SILK) to metabolically label and quantify proteins in the human CNS...
  24. Biomarkers of exposure and response to environmental tobacco smoke in the pancrea
    Kenneth H Yu; Fiscal Year: 2013
    ..2) To develop panels of biomarkers using stable isotope labeling methodology in order to rigorously assess pancreatic ETS exposure and biological response...
  25. Stable isotope-based fate mapping to quantify adipogenesis in obesity
    MATTHEW STEINHAUSER; Fiscal Year: 2013
    ..To address the central hypothesis, novel approaches to quantitate adipogenesis in vivo using stable isotope labeling and two mass spectrometry based platforms will be utilized...
  26. A Method to Stop HIV Replication:Inhibition of Human Purine Utilizing Proteins
    Jesse J Kwiek; Fiscal Year: 2013
    ..The proposed research will proceed in four broad steps: use SILAC (stable isotope labeling with amino acids in cell culture) to quantify purinome proteins induced by HIV-1 infection of THP1 and Jurkat ..
  27. Genetic Discovery of New Regulators of Fatty Acid Synthesis
    Daniel E Gottschling; Fiscal Year: 2012
    ..In this application, we will carry out experiments to more thoroughly characterize how these novel regulators impart their effects on fat synthesis and storage. ..
  28. Interrogating and manipulating mitochondrial ROS, energetics and proteomics
    Peter S Rabinovitch; Fiscal Year: 2010
    ..and mitochondrial proteome-wide differences in protein syntheses and turnover rates using in vivo heavy isotope labeling. In each of these aims we will apply and validate the tools developed using two tissues for which there is ..
  29. DEVELOPMENT OF A PRIMATE GENOMIC RESOURCE
    Michael G Katze; Fiscal Year: 2012
    ..Quantitative proteomic analyses will be performed using stable isotope labeling and a label-free comparative absolute quantification method in combination with the AMT tag approach...
  30. Multiplex Fluorescent Dyes for Ultrasensitive Proteomics
    Edward A Dratz; Fiscal Year: 2010
    ..proteins are present in the gel spots targeted, and demonstrate fluorescence enhanced targeted-SILAC (stable isotope labeling with amino acids in cell culture) to pin-point proteins for mass spectral analysis-- resulting in more ..
  31. New Technologies for Quantitative Phosphorylation Analysis
    Steven P Gygi; Fiscal Year: 2011
    ..This includes combining and integrating a robust stable isotope labeling strategy, new enrichment approaches, and new software tools with our existing platform...
  32. Glutamine Synthetase and the Mechanism of Seizures in Mesial Temporal Lobe Epilep
    Tore Eid; Fiscal Year: 2013
    ..in continuous video intracranial EEG monitoring, microdialysis, immunogold electron microscopy, 13C- and 15N-isotope labeling, and tandem mass spectrometry, the role of the glutamine synthetase deficiency in the generation of seizures ..
  33. Identification of Histone Modification Interaction Networks
    MARK R contact PARTHUN; Fiscal Year: 2010
    ..Our proposal is to combine yeast genetics, stable isotope labeling and mass spectrometry to comprehensively and quantitatively identify the network of interactions that exist ..
  34. Development of novel assays for measuring concentration and metabolism of Tau in
    Tim West; Fiscal Year: 2012
    ..Randall Bateman and David Holtzman at the Washington University School of Medicine developed a novel stable isotope labeling kinetics (SILK) methodology for measuring the metabolism of amyloid beta (AB) in the human central nervous ..
  35. Global protein palmitoylation and DHHC proteins in T cell activation and anergy
    Amnon Altman; Fiscal Year: 2013
    ..control T cells, and identify physiological PAT substrates of DHHC15 in PAT knockdown T cells by using stable isotope labeling with amino acids in cell culture (SILAC) coupled to metabolic labeling with the alkynyl fatty acid analog 17-..
  36. Proteo-genomic Discovery, Prioritization and Verification of Cancer Biomarkers
    Amanda G Paulovich; Fiscal Year: 2013
    ..In the first stage of our pipeline, we employ state-of-the-art LC-MS/MS together with iTRAQ stable isotope labeling to deeply characterize with precise relative quantification the proteomes and phospho-proteomes of cancer and ..
  37. Discovery of Cancer Biomarkers Through Metabolic Engineering
    Brian Smart; Fiscal Year: 2009
    ..Develop a method to quantify changes in protein and glycosylation levels in complex lysates through stable isotope labeling and mass spectrometry. (3) Analyze changes in mucin-type glycosylation levels in a murine liver cancer model...
  38. CITALOPRAM DECREASES AMYLOID-B SYNTHESIS IN HUMAN CSF
    Yvette I Sheline; Fiscal Year: 2012
    ..This is made possible by the recent development of a stable isotope labeling kinetic (SILK) technique by our colleagues here at Washington University...
  39. Role of Microglia in Ethanol-induced Oxidative Stress
    Stanley M Stevens; Fiscal Year: 2013
    ..In SA1, we will employ stable isotope labeling with amino acids in cell culture (SILAC) followed by quantitative mass spectrometric analysis to profile ..
  40. Dissection of Mycobacterium tuberculosis metabolic and regulatory pathways to per
    Lanbo Shi; Fiscal Year: 2010
    ..tuberculosis persistent infection. The program is expected to lead to new knowledge about the persistent mechanism of the tubercle bacilli and offer new strategies to tackle the persistent infection. ..
  41. GCx(py)GCC-IRMS for Isotope Metabolomics
    JAMES T BRENNA; Fiscal Year: 2013
    ..Finally, the expansion of rapid, highly sensitive intramolecular analysis capabilities to stable isotope labeling studies expands the use of a routine method in biomedical research.
  42. Comparative Proteomics to Study Age-Related Maculopathy
    Yetrib Hathout; Fiscal Year: 2009
    ..Using a cutting edge proteomics approach (stable isotope labeling by amino acids) we show that RPE cells secrete a variety of proteins that have been reported to be major ..
  43. LEF-1 translation in chronic myelegenous leukemia
    Marian L Waterman; Fiscal Year: 2010
    ..The goal is to develop the method to make it reproducible, reliable and able to be established in cell lines, primary cells and whole organisms. Vectors for tagging RNA and proteins will be developed for general use. ..
  44. Structural Characterization of Amyloid Fibrils Using Deep UV Raman Spectroscopy
    Igor K Lednev; Fiscal Year: 2013
    ..This new method, recently pioneered in our laboratory, does not require isotope labeling and creates the opportunity for bridging the gap between our extended knowledge in the structural variations ..
  45. Inhibition of TOR and de novo protein synthesis: a pulsed SILAC database
    Peter K Vogt; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): We propose to apply the new technique of pulsed SILAC (pulsed stable isotope labeling by amino acids in cell culture) to generate and make freely available a global database of the effects of TOR ..
  46. Cell-free expression of human integral membrane proteins for structural studies
    Senyon Choe; Fiscal Year: 2013
    ..We will improve the combinatorial dual-isotope labeling (CDL) strategy developed in our lab and use CF to incorporate site-specific unnatural amino acids...
  47. LTQ-Orbitrap-XL-ETD Mass Spectrometer for LLU Mass Spectrometry Facility
    Kangling Zhang; Fiscal Year: 2010
    ..of peptides, top-down and middle-down analysis, and protein quantification via label-free or stable isotope labeling such as iTRAQ and TMT. As the cost of purchasing this mass spectrometer is $729,000, we request $499,999...
  48. Acquisition of a Hybrid Quadrupole, Ion Mobility Separation, Orthogonal Accelerat
    Sheng Zhang; Fiscal Year: 2009
    ..high resolution instrument will be critical to the success of quantitative proteomics studies using stable isotope labeling (SILAC and iTRAQ)...
  49. Solid-state NMR methods for investigating native and aggregated eye lens proteins
    RACHEL WAGNER MARTIN; Fiscal Year: 2013
    ..Differential isotope labeling of peptide binders and variant crystallins can be used to identify crystallin residues involved in altered ..
  50. Proteomic Analysis of Synaptic Vesicle Pools
    Robert H Edwards; Fiscal Year: 2013
    ..pools by quantitative proteomics using isobaric tag for relative and absolute quantitation (iTRAQ) or stable isotope labeling in mammals (SILAM)...
  51. Sequence Distribution of Tabacco Carcinogen-DNA Adducts
    Natalia Tretyakova; Fiscal Year: 2007
    ..We now propose to determine the structural basis for these effects by conducting stable isotope labeling studies with a series of MeC analogs...
  52. Membrane catalyzed amyloid formation in diabetes studied with 2D IR spectroscopy
    Martin T Zanni; Fiscal Year: 2013
    ..of hIAPP with lipid membranes, we propose to use FTIR and 2D IR spectroscopy, in conjunction with 1-13C=18O isotope labeling, to yield site-specific structural information on hIAPP during the kinetics of folding in the presence of ..
  53. Measuring metabolism of C-terminal fragments of amyloid beta in the human central
    Tim West; Fiscal Year: 2011
    ..has licensed the platform technology from Washington University to carry out the company's stable isotope labeling kinetic (SILK) assay. This assay is used to measure production and clearance rates of proteins in the brain...
  54. Membrane protein structures by solution NMR
    James J Chou; Fiscal Year: 2013
    ..and MP refolding methods;(3) non-uniform sampled high resolution 4D NOESYs;(4) new strategies for selective isotope labeling of methyl groups for acquiring long-range NOEs;(5) novel reagent for site-directed paramagnetic tagging and ..
  55. GWAS to drugs: small molecule screen for inhibitors of CD40 signaling pathway
    Jose R Perez; Fiscal Year: 2013
    ..We will test hit compounds in primary B-cells. Specific Aim 3: Apply SILAC (stable isotope labeling by amino acids in cell culture)-based target identification technology to identify the protein target from ..
  56. Post-Expression Isotope Labeling: NMR Insights into Glycoprotein Structure
    MEGAN ALANE MACNAUGHTAN; Fiscal Year: 2010
    ..is to provide isotope-labeling and assignment methodologies for NMR, which are not limited to uniform, isotope labeling. These assignment strategies will become the underpinnings for structural data and functional assays on a ..
  57. Solution structure and dynamics of TCR in free and peptide-MHC-bound states
    John Orban; Fiscal Year: 2013
    ..Because TCR is a heterodimer of ?- and ?-chains, separate isotope labeling of each chain will reduce spectral complexity and facilitate NMR analysis...
  58. A proteomic approach for early diagnosis of diabetes
    Julian Watts; Fiscal Year: 2005
    ..their absolute concentration ranges in a large sample pool by use of synthetic peptide standards and stable isotope labeling; 4) the generation of immunological reagents to validated markers and their testing in immunoassays for ..
  59. High-speed NMR methods for membrane protein analysis
    Senyon Choe; Fiscal Year: 2013
    ..In particular, we will further develop the combinatorial dual-isotope labeling strategy in order to make the resonance assignment process fast and robust (Aim 1);incorporate unnatural ..
  60. DIRECTLY MEASURED T CELL DYNAMICS IN HIV PATHOGENESIS
    Marc Hellerstein; Fiscal Year: 2004
    ..Two newly developed in vivo stable isotope labeling techniques will be used: 1) [2H]glucose pulse incorporation/die-away in T cell DNA, to characterize the ..
  61. Differential metabolic network analysis of tumor progression
    James P Freyer; Fiscal Year: 2011
    ..Thus the overall goal of this proposal is to take advantage of Los Alamos expertise in isotope labeling and analysis, as well as in reverse engineering (RE) of biochemical interaction networks from HTP data to ..
  62. Discovering Immediate-Early Events in Hedgehog Signal Transduction
    Matthew P Scott; Fiscal Year: 2013
    ..1: We will identify immediate-early responses to an important developmental signal, Hedgehog, applying Stable Isotope Labeling with Amino acids in Cell culture (SILAC) and mass spectrometry to developmental regulation...
  63. NMR STUDIES OF TROPONIN COMPLEX
    PAUL ROSEVEAR; Fiscal Year: 2000
    ..13C isotope labeling. During the contraction cycle, the two C- terminal Ca2+/Mg2+ sites alternate between the Ca2+-bound and Mg2+-..
  64. CHEMISTRY AND BIOCHEMISTRY OF AQUATIC TOXINS
    Yuzuru Shimizu; Fiscal Year: 1999
    ..methods, structure elucidation by modern spectroscopic methods such as 2D-NMR and X-ray crystallography, and isotope labeling studies using both stable and radioactive isotopes...
  65. METABOLISM OF B-ADRENERGIC BLOCKERS--CHEMISTRY
    WENDEL NELSON; Fiscal Year: 1990
    ..metabolites will be synthesized, and identification will be accomplished using the techniques of stable isotope labeling, hplc separation and GC-mass spectral determination...
  66. HEPATOCYTE ASIALOGLYCOPROTEIN RECEPTOR ASSAY
    Ernest Groman; Fiscal Year: 2000
    ..Receptor-targeted diagnostic agents combined with stable isotope labeling and neutron activation represent a technologically novel and potentially general approach to the design of ..
  67. NMR AND UV STUDIES OF ANTISENSE OLIGONUCLEOTIDES
    Xiaolian Gao; Fiscal Year: 2002
    ..complex molecules, we will use site specific nucleobase deuteration, which is an efficient and cost effective isotope labeling method recently reported by this laboratory for the studies of large nucleic acid molecules, as a primary ..
  68. SYNTHESES OF HEMES FOR PROTEIN STUDIES
    Kevin Smith; Fiscal Year: 2003
    ..systems of biological interest, with special emphasis on development of completely new methodology for isotope labeling of hemes so as to provide access to unique spectroscopic probes of structure-activity relationships in heme ..
  69. SYNTHESES OF HEMES FOR PROTEIN STUDIES
    Kevin Smith; Fiscal Year: 2002
    ..systems of biological interest, with special emphasis on development of completely new methodology for isotope labeling of hemes so as to provide access to unique spectroscopic probes of structure-activity relationships in heme ..