JOHN ROBERT contact YATES

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. ncbi request reprint Performance of a linear ion trap-Orbitrap hybrid for peptide analysis
    John R Yates
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Anal Chem 78:493-500. 2006
  2. pmc Identification of novel targets for miR-29a using miRNA proteomics
    Rhishikesh Bargaje
    Functional Genomics Unit, Council of Scientific Industrial Research Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e43243. 2012
  3. pmc A chaperone trap contributes to the onset of cystic fibrosis
    Judith A Coppinger
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 7:e37682. 2012
  4. pmc Differential proteomic analysis of mammalian tissues using SILAM
    Daniel B McClatchy
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 6:e16039. 2011
  5. pmc Large-scale differential proteome analysis in Plasmodium falciparum under drug treatment
    Judith Helena Prieto
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
    PLoS ONE 3:e4098. 2008
  6. pmc Digestion and depletion of abundant proteins improves proteomic coverage
    Bryan R Fonslow
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
    Nat Methods 10:54-6. 2013
  7. pmc The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation
    Dong Xia
    Department of Pre clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK
    Genome Biol 9:R116. 2008
  8. pmc Isolation of novel coregulatory protein networks associated with DNA-bound estrogen receptor alpha
    Jennifer R Schultz-Norton
    Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Mol Biol 9:97. 2008
  9. pmc PatternLab for proteomics: a tool for differential shotgun proteomics
    Paulo C Carvalho
    Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    BMC Bioinformatics 9:316. 2008
  10. doi request reprint Proteomics by mass spectrometry: approaches, advances, and applications
    John R Yates
    Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biomed Eng 11:49-79. 2009

Collaborators

Detail Information

Publications70

  1. ncbi request reprint Performance of a linear ion trap-Orbitrap hybrid for peptide analysis
    John R Yates
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Anal Chem 78:493-500. 2006
    ..Tandem mass spectra from the linear ion trap and from the Orbitrap have very similar ion abundance ratios. We conclude this instrument will be well suited for shotgun proteomic types of analyses...
  2. pmc Identification of novel targets for miR-29a using miRNA proteomics
    Rhishikesh Bargaje
    Functional Genomics Unit, Council of Scientific Industrial Research Institute of Genomics and Integrative Biology, Delhi, India
    PLoS ONE 7:e43243. 2012
    ..However, this approach was valuable for rapid assessment of the impact of the miRNAs on the cellular proteome and its biological role in apoptosis...
  3. pmc A chaperone trap contributes to the onset of cystic fibrosis
    Judith A Coppinger
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 7:e37682. 2012
    ..We propose that stalled folding intermediates could define a critical proteostasis pathway branch-point(s) responsible for the loss of function in misfolding diseases as observed in CF...
  4. pmc Differential proteomic analysis of mammalian tissues using SILAM
    Daniel B McClatchy
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 6:e16039. 2011
    ..Our findings provide a valuable resource as a starting point for further understanding of tissue specific gene regulation and demonstrate SILAM as a useful strategy for the differential proteomic analysis of mammalian tissues...
  5. pmc Large-scale differential proteome analysis in Plasmodium falciparum under drug treatment
    Judith Helena Prieto
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
    PLoS ONE 3:e4098. 2008
    ..falciparum to study the response to drug treatment or environmental changes. Only 100 microg of protein is required for the analysis suggesting that the method can also be transferred to other apicomplexan parasites...
  6. pmc Digestion and depletion of abundant proteins improves proteomic coverage
    Bryan R Fonslow
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
    Nat Methods 10:54-6. 2013
    ..This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines...
  7. pmc The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation
    Dong Xia
    Department of Pre clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK
    Genome Biol 9:R116. 2008
    ....
  8. pmc Isolation of novel coregulatory protein networks associated with DNA-bound estrogen receptor alpha
    Jennifer R Schultz-Norton
    Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Mol Biol 9:97. 2008
    ....
  9. pmc PatternLab for proteomics: a tool for differential shotgun proteomics
    Paulo C Carvalho
    Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    BMC Bioinformatics 9:316. 2008
    ..The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired...
  10. doi request reprint Proteomics by mass spectrometry: approaches, advances, and applications
    John R Yates
    Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biomed Eng 11:49-79. 2009
    ..We illustrate MudPIT application to quantitative phosphoproteomics of the beta adrenergic pathway. We discuss several biological discoveries made via mass spectrometry pipelines with a focus on cell signaling proteomics...
  11. ncbi request reprint Proteomics of organelles and large cellular structures
    John R Yates
    Department of Cell Biology, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Rev Mol Cell Biol 6:702-14. 2005
    ..Here, we review the state-of-the-art proteomics techniques for the analysis of subcellular structures and discuss the biological insights that have been derived from such studies...
  12. ncbi request reprint Mass spectral analysis in proteomics
    John R Yates
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biophys Biomol Struct 33:297-316. 2004
    ..Applications of mass spectrometry-based approaches for contemporary proteomic analyses are described...
  13. ncbi request reprint Protein identification using 2D-LC-MS/MS
    Claire Delahunty
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Methods 35:248-55. 2005
    ..This review describes the most recent advances in methodologies for protein identification by mass spectrometry and describes the limitations of the application of the technologies...
  14. pmc Cancer proteomics by quantitative shotgun proteomics
    Emily I Chen
    Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037, USA
    Mol Oncol 1:144-59. 2007
    ..In this review, progress in shotgun proteomics technologies for examining the molecular basis of cancer development will be presented and discussed...
  15. pmc Regulation of cell migration and survival by focal adhesion targeting of Lasp-1
    Yi Hsing Lin
    Department of Immunology, SP231, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
    J Cell Biol 165:421-32. 2004
    ..Thus, Lasp-1 is a dynamic focal adhesion protein necessary for cell migration and survival in response to growth factors and ECM proteins...
  16. pmc Pharmacological inhibition of BMK1 suppresses tumor growth through promyelocytic leukemia protein
    Qingkai Yang
    Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cancer Cell 18:258-67. 2010
    ..Inhibition of BMK1 by XMD8-92 blocked tumor cell proliferation in vitro and significantly inhibited tumor growth in vivo by 95%, demonstrating the efficacy and tolerability of BMK1-targeted cancer treatment in animals...
  17. ncbi request reprint A streamlined platform for high-content functional proteomics of primary human specimens
    Nadim Jessani
    The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, California 92037, USA
    Nat Methods 2:691-7. 2005
    ....
  18. ncbi request reprint Multidimensional separations for protein/peptide analysis in the post-genomic era
    Hongbin Liu
    The Scripps Research Institute, La Jolla, CA 92037, USA
    Biotechniques 32:898, 900, 902 passim. 2002
    ..Additional applications and developments of multidimensional liquid separations for proteomics are expected in the future...
  19. pmc Combined integrin phosphoproteomic analyses and small interfering RNA--based functional screening identify key regulators for cancer cell adhesion and migration
    Yanling Chen
    Department of Immunology, The Scripps Research Institute, La Jolla, California 92037, USA
    Cancer Res 69:3713-20. 2009
    ..Altogether, we not only depict an integrin-modulated phosphorylation network during cell-ECM protein interactions but also reveal novel regulators for cell adhesion and migration...
  20. ncbi request reprint Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT)
    Emily I Chen
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Mol Cell Proteomics 5:53-6. 2006
    ..As a result, we were able to reduce sample complexity by protein fractionation and increase the possibility of detecting proteins with lower abundance in the complex protein mixture...
  21. pmc Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway
    Greg T Cantin
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd SR11, La Jolla, California 92037, USA
    J Proteome Res 5:127-34. 2006
    ....
  22. pmc Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes
    Bryan R Fonslow
    Department of Chemical Physiology, The Scripps Research Institute, 10550 N Torrey Pines Rd La Jolla, California 92037, USA
    Anal Chem 82:6643-51. 2010
    ....
  23. pmc Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progression [corrected]
    Yingchun Wang
    Department of Pathology, Moores Cancer Center, University of California, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 107:10920-5. 2010
    ..Our findings indicate that PEAK1 is an important cytoskeletal regulatory kinase and possible target for anticancer therapy...
  24. ncbi request reprint Adaptation of energy metabolism in breast cancer brain metastases
    Emily I Chen
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Cancer Res 67:1472-86. 2007
    ....
  25. ncbi request reprint The biological impact of mass-spectrometry-based proteomics
    Benjamin F Cravatt
    Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 450:991-1000. 2007
    ....
  26. ncbi request reprint PRAK is essential for ras-induced senescence and tumor suppression
    Peiqing Sun
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 128:295-308. 2007
    ..Furthermore, we show that PRAK activates p53 by direct phosphorylation. We propose that phosphorylation of p53 by PRAK following activation of p38 MAPK by ras plays an important role in ras-induced senescence and tumor suppression...
  27. ncbi request reprint Maspin and tumor metastasis
    Emily I Chen
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    IUBMB Life 58:25-9. 2006
    ....
  28. ncbi request reprint Maspin alters the carcinoma proteome
    Emily I Chen
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
    FASEB J 19:1123-4. 2005
    ..These observations reveal for the first time the far reaching effects of maspin on multiple protein networks and a new hypothesis of maspin function based on the regulation of proteasome function...
  29. ncbi request reprint Shotgun proteomics: integrating technologies to answer biological questions
    W Hayes McDonald
    Department of Cell Biology, SR 11, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92307, USA
    Curr Opin Mol Ther 5:302-9. 2003
    ....
  30. pmc RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress
    Miguel A Rodríguez-Gabriel
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    EMBO J 22:6256-66. 2003
    ..These studies reveal a novel mechanism controlling MAPK-regulated transcription factors and suggest how gene expression patterns can be customized to specific forms of stress. Csx1-like proteins in humans may perform similar tasks...
  31. pmc Shotgun proteomics and biomarker discovery
    W Hayes McDonald
    Department of Cell Biology, SR11, The Scripps Research Institute, La Jolla, CA 92037, USA
    Dis Markers 18:99-105. 2002
    ..Advances in the ability to quantitate differences between samples and to detect for an array of post-translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable...
  32. ncbi request reprint Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    John D Venable
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92014, USA
    Nat Methods 1:39-45. 2004
    ....
  33. ncbi request reprint The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector
    Robert A Screaton
    Peptide Biology Laboratories, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 119:61-74. 2004
    ..Our results illustrate how a phosphatase/kinase module connects two signaling pathways in response to nutrient and hormonal cues...
  34. ncbi request reprint The application of mass spectrometry to membrane proteomics
    Christine C Wu
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nat Biotechnol 21:262-7. 2003
    ..These latter strategies facilitate the identification of large numbers of membrane proteins and modifications, and have the potential to provide insights into protein topology and orientation in membranes...
  35. ncbi request reprint Proteomics in malaria
    Jeffrey R Johnson
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Proteome Res 3:296-306. 2004
    ..The high-throughput nature of these techniques is in accord with the pace of drug and vaccine development that have the potential to directly reduce the morbidity and mortality of disease...
  36. pmc CDC25B mediates rapamycin-induced oncogenic responses in cancer cells
    Run Qiang Chen
    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
    Cancer Res 69:2663-8. 2009
    ..Together, using rapamycin phosphoproteomics, we not only advance the global mechanistic understanding of the action of rapamycin but also show that CDC25B may serve as a drug target for improving mTOR-targeted cancer therapies...
  37. pmc Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo
    Nadim Jessani
    The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 101:13756-61. 2004
    ....
  38. pmc Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress
    Victoria Martin
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Mol Biol Cell 17:1176-83. 2006
    ..This study emphasizes the importance of a modulated mRNA stability in the eukaryotic stress response pathways and adds new information to the role of RNA-binding proteins in the oxidative stress response...
  39. pmc Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood
    Sunil M Kurian
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
    PLoS ONE 4:e6212. 2009
    ..There is a pressing need to identify and validate minimally invasive biomarkers for CAN to serve as early predictors of graft loss and as metrics for managing long-term immunosuppression...
  40. pmc Shotgun identification of protein modifications from protein complexes and lens tissue
    Michael J MacCoss
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 99:7900-5. 2002
    ..The method presented will be useful in discovering co- and posttranslational modifications of proteins...
  41. pmc RCADiA: simple automation platform for comparative multidimensional protein identification technology
    Aaron O Bailey
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, California 92037, USA
    Anal Chem 79:6410-8. 2007
    ..We demonstrate this device by performing a comparative analysis of mitochondria enriched from rat liver and spinal cord...
  42. ncbi request reprint Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry
    Hanjo Lim
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Am Soc Mass Spectrom 14:957-70. 2003
    ..This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins...
  43. pmc Identification of N-terminally arginylated proteins and peptides by mass spectrometry
    Tao Xu
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Protoc 4:325-32. 2009
    ..It is recommended for studies of arginylation and can be applied to other poorly understood post-translational modifications...
  44. pmc Capillary electrophoresis applied to proteomic analysis
    Bryan R Fonslow
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Sep Sci 32:1175-88. 2009
    ....
  45. pmc PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis
    Noriyuki Nishimura
    Division of Biological Sciences, Cell and Developmental Biology Section and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0116, USA
    Plant J 61:290-9. 2010
    ....
  46. pmc Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures
    Catherine C L Wong
    Department of Chemical Physiology, SR 11, The Scripps Research Institute, La Jolla, California 92037, USA
    J Am Soc Mass Spectrom 20:1405-14. 2009
    ....
  47. ncbi request reprint Large-scale protein identification using mass spectrometry
    Dayin Lin
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
    Biochim Biophys Acta 1646:1-10. 2003
    ..This review will discuss aspects of mass spectrometry with emphasis on methods and applications for large-scale protein identification, a fundamental tool for proteomics...
  48. ncbi request reprint Probability-based validation of protein identifications using a modified SEQUEST algorithm
    Michael J MacCoss
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Anal Chem 74:5593-9. 2002
    ..This new scoring routine is used to objectively calculate the percent confidence of protein identifications and posttranslational modifications based solely on the XCorr value...
  49. pmc Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5
    Kenichi Yamaguchi
    Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Plant Cell 14:2957-74. 2002
    ..These additional domains may interact with the S1 protein and PSRP-7 to function in aspects of mRNA recognition and translation initiation that are unique to the Chlamydomonas chloroplast...
  50. ncbi request reprint Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA
    Shigeaki Saitoh
    Department of Molecular Biology, The Scripts Research Institute, La Jolla, CA 92037, USA
    Cell 109:563-73. 2002
    ..cid13 mutants have reduced dNTP pools and are sensitive to hydroxyurea, an RNR inhibitor. We propose that Cid13 defines a cytoplasmic form of poly(A) polymerase important for DNA replication and genome maintenance...
  51. doi request reprint Census for proteome quantification
    Sung Kyu Park
    The Scripps Research Institute, La Jolla, California, USA
    Curr Protoc Bioinformatics . 2010
    ..Furthermore, Census has built-in multiple statistical filters to maintain robust quality control on quantitative results...
  52. pmc Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice
    Lujian Liao
    Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 105:15281-6. 2008
    ..These studies provide insights into the potential origins of synaptic abnormalities in FXS and a demonstration of a methodology that can be used to explore neuronal protein changes in neurological disorders...
  53. pmc Mass spectrometry for proteomics
    Xuemei Han
    Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrev Pines Road, La Jolla, CA 92037, USA
    Curr Opin Chem Biol 12:483-90. 2008
    ..Finally, stable isotope labeling strategies have transformed mass spectrometry from merely descriptive to a tool for measuring dynamic changes in protein expression, interaction, and modification...
  54. pmc The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex
    Stephanie Pebernard
    The Scripps Research Institute, Rm MB107, 10550 North Torrey Pines Rd, Molecular Biology, MB 3, La Jolla, CA 92037, USA
    Mol Cell Biol 26:1617-30. 2006
    ..We propose a role for Nse5/6 mutants in suppressing recombination that results in Holliday junction formation or in Holliday junction resolution...
  55. ncbi request reprint Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis
    Christine C Wu
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Anal Chem 76:4951-9. 2004
    ..This approach is a powerful tool for the global quantitation of proteins, is capable of measuring proteome-wide changes in response to a drug, and will be useful for studying animal models of disease...
  56. pmc Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies
    James A Wohlschlegel
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Proteome Res 5:761-70. 2006
    ....
  57. ncbi request reprint SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association
    Grazia D Raffa
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    J Biol Chem 281:27973-81. 2006
    ..In addition, mutation of Rad60 Ser(32) and Ser(34) to alanine is lethal in cells deleted for the RecQ DNA helicase Rqh1. Finally, we find that Rad60 self-associates via its C-terminal SUMO-like domain and putative SUMO-binding motifs...
  58. ncbi request reprint MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
    W Hayes McDonald
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
    Rapid Commun Mass Spectrom 18:2162-8. 2004
    ....
  59. ncbi request reprint A method for the comprehensive proteomic analysis of membrane proteins
    Christine C Wu
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nat Biotechnol 21:532-8. 2003
    ..Furthermore, coupling protease protection strategies to this method permits characterization of the relative sidedness of the hydrophilic domains of membrane proteins...
  60. pmc Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides
    Akira Motoyama
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Anal Chem 79:3623-34. 2007
    ....
  61. pmc Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development
    Daniel B McClatchy
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Genome Res 17:1378-88. 2007
    ..We report the first large-scale proteomic analysis of synaptic development in the cerebellum, and we demonstrate a useful quantitative strategy for studying animal models of neurological disease...
  62. ncbi request reprint A unique sorting nexin regulates trafficking of potassium channels via a PDZ domain interaction
    Marie Louise Lunn
    Peptide Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, California 92037, USA
    Nat Neurosci 10:1249-59. 2007
    ..The regulation of endosomal trafficking via sorting nexins reveals a previously unknown mechanism for controlling potassium channel surface expression...
  63. ncbi request reprint Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples
    Akira Motoyama
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Anal Chem 78:5109-18. 2006
    ..Advantages of the use of a relatively long reversed-phase column (approximately 50 cm) for MudPIT-type experiments are also discussed...
  64. doi request reprint Identification of proteins in complex mixtures using liquid chromatography and mass spectrometry
    Claire Delahunty
    The Scripps Research Institute, La Jolla, California, USA
    Curr Protoc Cell Biol . 2003
    ..Chromatography can be performed in-line with the mass spectrometer and data acquisition can be directly interfaced with search algorithms for identification by correlation with databases...
  65. pmc A quantitative analysis software tool for mass spectrometry-based proteomics
    Sung Kyu Park
    Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, California 92014, USA
    Nat Methods 5:319-22. 2008
    ..Census uses robust algorithms to address poor-quality measurements and improve quantitative efficiency, and it can support several input file formats. We tested Census with stable-isotope labeling analyses as well as label-free analyses...
  66. pmc Motif-specific sampling of phosphoproteomes
    Cristian I Ruse
    Department of Chemical Physiology Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Proteome Res 7:2140-50. 2008
    ..Integration of differential phosphorylation of MAPK1 with knowledge bases constructed modules that correlated well with its role as node in cross-talk of canonical pathways...
  67. pmc Organellar proteomics reveals Golgi arginine dimethylation
    Christine C Wu
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Mol Biol Cell 15:2907-19. 2004
    ....
  68. ncbi request reprint A correlation algorithm for the automated quantitative analysis of shotgun proteomics data
    Michael J MacCoss
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Anal Chem 75:6912-21. 2003
    ..Our automated approach was validated using labeled mixtures composed of known molar ratios and demonstrated in a real sample by measuring the effect of osmotic stress on protein expression in Saccharomyces cerevisiae...
  69. ncbi request reprint Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book
    Rovshan G Sadygov
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Methods 1:195-202. 2004
    ..We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification...
  70. ncbi request reprint Nuclear membrane proteins with potential disease links found by subtractive proteomics
    Eric C Schirmer
    Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 301:1380-2. 2003
    ..Furthermore, 23 of these mapped within chromosome regions linked to a variety of dystrophies...

Research Grants29

  1. Differential Proteome Analysis on Plasmodium falciparum after Drug Exposure
    John Yates; Fiscal Year: 2007
    ..Particular emphasis will be given to redox related defense and signaling pathways. ..
  2. Catalogue of Human Salivary Secretory Components
    John Yates; Fiscal Year: 2007
    ....
  3. PROTEOME ANALYSIS OF NORMAL AND CATARACTOUS LENSES
    John Yates; Fiscal Year: 2000
    ..By undertaking a systematic analysis of lens proteins, we have the opportunity to make correlations between specific proteolytic modifications and the transparent condition of lenses. ..
  4. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2009
    ..A fundamental understanding of these processes will help the development of therapeutics to alleviate the symptoms associated with affective disorders such as schizophrenia, psychosis, biopolar disorder, and depression. ..
  5. Proteomic Analysis of C. elegans Insulin Signaling
    John Yates; Fiscal Year: 2009
    ..This can form the basis of future anti-diabetic treatments. ..
  6. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2007
    ..These methods will enable the use of powerful genetic models of development and disease for whole organism proteomics. ..
  7. Proteomic Analysis of C. elegans Insulin Signaling
    John Yates; Fiscal Year: 2007
    ..This can form the basis of future anti-diabetic treatments. ..
  8. Quantitative Proteome Analysis of Brain Development
    JOHN ROBERT YATES; Fiscal Year: 2010
    ..A fundamental understanding of these processes will help the development of therapeutics to alleviate the symptoms associated with affective disorders such as schizophrenia, psychosis, biopolar disorder, and depression. ..
  9. Proteomic Analysis of C. elegans Insulin Signaling
    John Yates; Fiscal Year: 2005
    ..Proteomic analysis of the insulin signaling pathway in conjunction with C. elegans genetics will lead to a better understanding of insulin signaling and provide new therapeutic targets to battle diabetes. ..
  10. PROTEOME ANALYSIS OF NORMAL AND CATARACTOUS LENSES
    John Yates; Fiscal Year: 2002
    ..By undertaking a systematic analysis of lens proteins, we have the opportunity to make correlations between specific proteolytic modifications and the transparent condition of lenses. ..
  11. Mass Spectrometry in Systems Biology
    John Yates; Fiscal Year: 2003
    ..Topics emphasizing global measurements as well as highly specific and accurate molecular measurements will be presented. ..
  12. PROTEOME ANALYSIS OF NORMAL AND CATARACTOUS LENSES
    John Yates; Fiscal Year: 2003
    ..By undertaking a systematic analysis of lens proteins, we have the opportunity to make correlations between specific proteolytic modifications and the transparent condition of lenses. ..
  13. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2005
    ..These methods will enable the use of powerful genetic models of development and disease for whole organism proteomics. ..
  14. Proteomic Profiling of CFTR Protein Interaction
    JOHN ROBERT contact YATES; Fiscal Year: 2010
    ....
  15. Catalogue of Human Salivary Secretory Components
    John Yates; Fiscal Year: 2007
    ..abstract_text> ..
  16. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2003
    ..These methods will enable the use of powerful genetic models of development and disease for whole organism proteomics. ..
  17. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2004
    ..These methods will enable the use of powerful genetic models of development and disease for whole organism proteomics. ..
  18. Proteomic Profiling of CFTR Protein Interaction
    John Yates; Fiscal Year: 2006
    ..These studies are anticipated to provide critical insight for identification of novel drugs that will alleviate suffering of individuals afflicted with CF. ..
  19. High Performance Mass Spectrometer for Proteomics
    John Yates; Fiscal Year: 2005
    ..The research of 14 Principal Investigators will lie directly supported by the instrument with approximately 270 Investigators at TSRI having access as minor users. ..
  20. Proteomic Analysis of C. elegans Insulin Signaling
    JOHN ROBERT YATES; Fiscal Year: 2010
    ..This can form the basis of future anti-diabetic treatments. ..
  21. Proteomic Profiling of CFTR Protein Interaction
    John Yates; Fiscal Year: 2009
    ..These studies are anticipated to provide critical insight for identification of novel drugs that will alleviate suffering of individuals afflicted with CF. ..
  22. Quantitative Proteome Analysis of Brain Development
    John Yates; Fiscal Year: 2006
    ..These methods will enable the use of powerful genetic models of development and disease for whole organism proteomics. ..
  23. Dissecting the Ubiquitin-mediated DNA Damage Response
    John Yates; Fiscal Year: 2003
    ..abstract_text> ..
  24. PROTEOME ANALYSIS OF NORMAL AND CATARACTOUS LENSES
    John Yates; Fiscal Year: 2001
    ..By undertaking a systematic analysis of lens proteins, we have the opportunity to make correlations between specific proteolytic modifications and the transparent condition of lenses. ..
  25. Proteomic Profiling of CFTR Protein Interaction
    John Yates; Fiscal Year: 2007
    ..These studies are anticipated to provide critical insight for identification of novel drugs that will alleviate suffering of individuals afflicted with CF. ..