proteomics

Summary

Summary: The systematic study of the complete complement of proteins (PROTEOME) of organisms.

Top Publications

  1. pmc The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 41:D1063-9. 2013
  2. doi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
  3. pmc Human Protein Reference Database--2009 update
    T S Keshava Prasad
    Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
    Nucleic Acids Res 37:D767-72. 2009
  4. doi Andromeda: a peptide search engine integrated into the MaxQuant environment
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 10:1794-805. 2011
  5. ncbi In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
  6. doi Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
  7. pmc Systematic and quantitative assessment of the ubiquitin-modified proteome
    Woong Kim
    Department of Cell Biology, Harvard Medical School, Boston, MA, USA
    Mol Cell 44:325-40. 2011
  8. doi Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
  9. ncbi Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    Yasushi Ishihama
    Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
    Mol Cell Proteomics 4:1265-72. 2005
  10. doi Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010

Detail Information

Publications358 found, 100 shown here

  1. pmc The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 41:D1063-9. 2013
    The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data...
  2. doi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
    ..for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, ..
  3. pmc Human Protein Reference Database--2009 update
    T S Keshava Prasad
    Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
    Nucleic Acids Res 37:D767-72. 2009
    ..Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins...
  4. doi Andromeda: a peptide search engine integrated into the MaxQuant environment
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 10:1794-805. 2011
    A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model...
  5. ncbi In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
    In-gel digestion of proteins isolated by gel electrophoresis is a cornerstone of mass spectrometry (MS)-driven proteomics. The 10-year-old recipe by Shevchenko et al. has been optimized to increase the speed and sensitivity of analysis...
  6. doi Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
    ..FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry-based proteomics. We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard ..
  7. pmc Systematic and quantitative assessment of the ubiquitin-modified proteome
    Woong Kim
    Department of Cell Biology, Harvard Medical School, Boston, MA, USA
    Mol Cell 44:325-40. 2011
    ..We identify ~19,000 diGly-modified lysine residues within ~5000 proteins. Using quantitative proteomics we monitored temporal changes in diGly site abundance in response to both proteasomal and translational ..
  8. doi Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
    ..Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications...
  9. ncbi Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    Yasushi Ishihama
    Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
    Mol Cell Proteomics 4:1265-72. 2005
    ..The values of emPAI are easily calculated and add important quantitation information to proteomic experiments; therefore we suggest that they should be reported in large scale proteomic identification projects...
  10. doi Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
    ..We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 ..
  11. pmc Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
    LUKAS KALL
    Center for Genomics and Bioinformatics, Karolinska Institutet, S 17177 Stockholm, Sweden
    Nucleic Acids Res 35:W429-32. 2007
    ..We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius...
  12. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  13. ncbi The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra
    Ignat V Shilov
    Applied Biosystems MDS Sciex, Foster City, CA 94404, USA
    Mol Cell Proteomics 6:1638-55. 2007
    ..Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space...
  14. doi Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
    Michiel Vermeulen
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Cell 142:967-80. 2010
    ..These chromatin "readers" are assigned to complexes by interaction proteomics of full-length BAC-GFP-tagged proteins...
  15. ncbi Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    Juri Rappsilber
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
    Nat Protoc 2:1896-906. 2007
    Mass spectrometry (MS)-based proteomics measures peptides derived from proteins by proteolytic cleavage...
  16. ncbi Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    Shao En Ong
    Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
    Mol Cell Proteomics 1:376-86. 2002
    Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated ..
  17. pmc The impact of microRNAs on protein output
    Daehyun Baek
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 455:64-71. 2008
    ..The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output...
  18. pmc Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    Brendan Maclean
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 26:966-8. 2010
    Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use...
  19. pmc Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
    Ignacio Medina
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Autopista del Saler 16, Valencia, Spain
    Nucleic Acids Res 38:W210-3. 2010
    ..This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org...
  20. pmc iRefIndex: a consolidated protein interaction database with provenance
    Sabry Razick
    The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
    BMC Bioinformatics 9:405. 2008
    ..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
  21. ncbi Global analysis of protein expression in yeast
    Sina Ghaemmaghami
    Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
    Nature 425:737-41. 2003
    ..Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements...
  22. ncbi Substrate and functional diversity of lysine acetylation revealed by a proteomics survey
    Sung Chan Kim
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Mol Cell 23:607-18. 2006
    ..The combined data sets offer a rich source for further characterization of the contribution of this modification to cellular physiology and human diseases...
  23. doi Widespread changes in protein synthesis induced by microRNAs
    Matthias Selbach
    Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, D 13125 Berlin, Germany
    Nature 455:58-63. 2008
    ..Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes...
  24. pmc Estimating accuracy of RNA-Seq and microarrays with proteomics
    Xing Fu
    Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China
    BMC Genomics 10:161. 2009
    ..At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown...
  25. ncbi Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
    John Rush
    Cell Signaling Technology Inc, 166B Cummings Center, Beverly, Massachusetts 01915, USA
    Nat Biotechnol 23:94-101. 2005
    ....
  26. pmc A guide to the Proteomics Identifications Database proteomics data repository
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:4276-83. 2009
    The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data...
  27. doi Mechanisms of plant salt response: insights from proteomics
    Heng Zhang
    Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
    J Proteome Res 11:49-67. 2012
    ..Current proteomics provides a high-throughput approach to study sophisticated molecular networks in plants...
  28. ncbi Interpretation of shotgun proteomic data: the protein inference problem
    Alexey I Nesvizhskii
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 4:1419-40. 2005
    ..However, the peptide-centric nature of shotgun proteomics complicates the analysis and biological interpretation of the data especially in the case of higher eukaryote ..
  29. ncbi Gateway-compatible vectors for plant functional genomics and proteomics
    Keith W Earley
    Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
    Plant J 45:616-29. 2006
    ..Antibodies detecting the FLAG, HA, cMyc and AcV5 tags show relatively little cross-reaction with endogenous proteins in a variety of monocotyledonous and dicotyledonous plants, suggesting broad utility for the tags and vectors...
  30. pmc Purification of proteins associated with specific genomic Loci
    Jérôme Déjardin
    Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 136:175-86. 2009
    ..Here, we describe a protocol called proteomics of isolated chromatin segments (PICh) that addresses this issue...
  31. doi Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology
    T S Keshava Prasad
    Institute of Bioinformatics, Bangalore, India
    Methods Mol Biol 577:67-79. 2009
    ..As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, classical genetics, and ..
  32. pmc Large-scale proteomics and phosphoproteomics of urinary exosomes
    Patricia A Gonzales
    Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Am Soc Nephrol 20:363-79. 2009
    ..The proteomic data are publicly accessible at http://dir.nhlbi.nih.gov/papers/lkem/exosome/...
  33. pmc SLiMSearch 2.0: biological context for short linear motifs in proteins
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W56-60. 2011
    ..Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html...
  34. pmc InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
    Gabriel Ostlund
    Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
    Nucleic Acids Res 38:D196-203. 2010
    ..To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters...
  35. pmc A tissue-specific atlas of mouse protein phosphorylation and expression
    Edward L Huttlin
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 143:1174-89. 2010
    ..We offer this dataset as an online resource for the biological research community...
  36. doi Mitochondrial protein import: from proteomics to functional mechanisms
    Oliver Schmidt
    Institut fur Biochemie und Molekularbiologie, ZBMZ, Universitat Freiburg, Stefan Meier Strabetae 17, 79104 Freiburg, Germany
    Nat Rev Mol Cell Biol 11:655-67. 2010
    ..Protein translocases do not function as independent units but are integrated into dynamic networks and are connected to machineries that function in bioenergetics, mitochondrial morphology and coupling to the endoplasmic reticulum...
  37. pmc MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data
    Hiren J Joshi
    Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Plant Physiol 155:259-70. 2011
    b>Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level...
  38. pmc The quantitative proteome of a human cell line
    Martin Beck
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:549. 2011
    ..We discuss how protein abundance is linked to function and evolution...
  39. pmc Comparing protein abundance and mRNA expression levels on a genomic scale
    Dov Greenbaum
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Genome Biol 4:117. 2003
    ..We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories...
  40. pmc De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
    Catherine Adamidi
    Max Delbruck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert Rossle Strasse 10, Berlin, Germany
    Genome Res 21:1193-200. 2011
    ..mediterranea transcriptome. We then used independent assays and massive shotgun proteomics to validate the authenticity of transcripts...
  41. pmc The Proteomics Identifications database: 2010 update
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 38:D736-42. 2010
    The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data...
  42. pmc A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed
    Jesper V Olsen
    Thermo Fisher Scientific Bremen GmbH, Hanna Kunath Strasse 11, 28199 Bremen, Germany
    Mol Cell Proteomics 8:2759-69. 2009
    ..a few years ago, the linear ion trap Orbitrap (LTQ Orbitrap) instrument has become a powerful tool in proteomics research...
  43. pmc Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fiber and Arabidopsis root hair elongation
    Chao You Pang
    The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
    Mol Cell Proteomics 9:2019-33. 2010
    ..Using a comparative proteomics approach, we identified 104 proteins from cotton ovules 10 days postanthesis with 93 preferentially accumulated ..
  44. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
    ..The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the ..
  45. doi Less label, more free: approaches in label-free quantitative mass spectrometry
    Karlie A Neilson
    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
    Proteomics 11:535-53. 2011
    In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches...
  46. pmc Selected reaction monitoring for quantitative proteomics: a tutorial
    Vinzenz Lange
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 4:222. 2008
    ..and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches...
  47. doi Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Proteome Res 8:5674-8. 2009
    Membrane proteomics is challenging because the desirable strong detergents are incompatible with downstream analysis. Recently, we demonstrated efficient removal of SDS by the filter aided sample preparation method (FASP)...
  48. pmc Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways
    Matthew J Rardin
    Buck Institute for Research on Aging, Novato, CA 94945, USA
    Proc Natl Acad Sci U S A 110:6601-6. 2013
    ....
  49. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
    ....
  50. pmc Global kinetic analysis of proteolysis via quantitative targeted proteomics
    Nicholas J Agard
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94114, USA
    Proc Natl Acad Sci U S A 109:1913-8. 2012
    Mass spectrometry-based proteomics is a powerful tool for identifying hundreds to thousands of posttranslational modifications in complex mixtures...
  51. doi Decoding signalling networks by mass spectrometry-based proteomics
    Chunaram Choudhary
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Nat Rev Mol Cell Biol 11:427-39. 2010
    ..Signalling is often studied using antibody-based techniques such as western blots. Large-scale 'precision proteomics' based on mass spectrometry now enables the system-wide characterization of signalling events at the levels of ..
  52. doi 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
    MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high-resolution mass spectrometry (MS) data...
  53. pmc A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
    M Violet Lee
    Department of Chemistry, University of Wisconsin Madison, Madison, WI, USA
    Mol Syst Biol 7:514. 2011
    ..Our results present a picture of the coordinated physiological responses at the levels of mRNA, protein, protein-synthetic capacity, and cellular growth...
  54. pmc Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
    Paola Picotti
    Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
    Cell 138:795-806. 2009
    ..This is only partly achieved by classical mass spectrometry or affinity-based methods. We applied a targeted proteomics approach based on selected reaction monitoring (SRM) to detect and quantify proteins expressed to a ..
  55. doi Mass spectrometry in high-throughput proteomics: ready for the big time
    Tommy Nilsson
    Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
    Nat Methods 7:681-5. 2010
    ..Mass spectrometry has evolved and matured to a level where it is able to assess the complexity of the human proteome. We discuss some of the expected challenges ahead and promising strategies for success...
  56. pmc Mass spectrometry-based proteomics in cell biology
    Tobias C Walther
    Organelle Architecture and Dynamics and 2 Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    J Cell Biol 190:491-500. 2010
    ..Mass spectrometry (MS)-based proteomics has matured into an attractive technology for this purpose...
  57. 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
    ..states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, ..
  58. pmc Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods
    Lis Jakobsen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
    EMBO J 30:1520-35. 2011
    ..Pulsed labelling demonstrates a remarkable variation in the stability of centrosomal protein complexes. These spatiotemporal proteomics data provide leads to the further functional characterization of centrosomal proteins.
  59. pmc Mapping intact protein isoforms in discovery mode using top-down proteomics
    John C Tran
    Department of Chemistry and Biochemistry, and the Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nature 480:254-8. 2011
    ..The technology promises to improve the link between proteomics data and complex phenotypes in basic biology and disease research.
  60. doi Quantitative, high-resolution proteomics for data-driven systems biology
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
    Annu Rev Biochem 80:273-99. 2011
    Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins...
  61. pmc PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    EMBO Rep 9:429-34. 2008
    ..For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system ..
  62. ncbi Mass spectrometry and protein analysis
    Bruno Domon
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Science 312:212-7. 2006
    ..Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science...
  63. 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
    The field of proteomics is built on technologies to analyze large numbers of proteins--ideally the entire proteome--in the same experiment...
  64. ncbi Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    Philip L Ross
    Applied Biosystems, Framingham, MA 01701, USA
    Mol Cell Proteomics 3:1154-69. 2004
    ..We find that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression...
  65. doi Mass spectrometry-based proteomics and network biology
    Ariel Bensimon
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH 8093, Switzerland
    Annu Rev Biochem 81:379-405. 2012
    ..Mass spectrometry (MS)-based proteomics is a central life science technology that has realized great progress toward the identification, quantification, ..
  66. 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
    ..Among the many formats for quantitative proteomics, stable-isotope labelling by amino acids in cell culture (SILAC) has emerged as a simple and powerful one...
  67. ncbi Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis
    Joris J Benschop
    Molecular Genetics, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
    Mol Cell Proteomics 6:1198-214. 2007
    ..Our study presents the largest quantitative Arabidopsis phosphoproteomics data set to date and provides a new resource that can be used to gain novel insight into plant defense signal transduction and early defense response...
  68. pmc Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers
    Kristina D Micheva
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Neuron 68:639-53. 2010
    ..These results establish a means for the high-throughput acquisition of proteomic data from individual cortical synapses in situ...
  69. doi Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
    Paul J Boersema
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
    Nat Protoc 4:484-94. 2009
    Accurate quantification of protein expression in biological systems is an increasingly important part of proteomics research...
  70. pmc ProteoWizard: open source software for rapid proteomics tools development
    Darren Kessner
    Spielberg Family Center for Applied Proteomics, Cedars Sinai Medical Center, USA
    Bioinformatics 24:2534-6. 2008
    ..The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework ..
  71. pmc ExPASy: The proteomics server for in-depth protein knowledge and analysis
    Elisabeth Gasteiger
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:3784-8. 2003
    ..It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository...
  72. doi Exosomes: proteomic insights and diagnostic potential
    Richard J Simpson
    Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
    Expert Rev Proteomics 6:267-83. 2009
    ..New advances in proteomic methods, and both mass spectrometry hardware and informatics tools will be covered briefly...
  73. ncbi A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    Hongbin Liu
    Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Anal Chem 76:4193-201. 2004
    ..We demonstrate a linear dynamic range over 2 orders of magnitude by using the number of spectra (spectral sampling) acquired for each protein...
  74. doi 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
    Mass spectrometry-based proteomics critically depends on algorithms for data interpretation...
  75. pmc Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma
    Michael A Kuzyk
    University of Victoria Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
    Mol Cell Proteomics 8:1860-77. 2009
    ..A mixture of 45 peptide standards, easily adaptable to common plasma proteomics work flows, was created to permit absolute quantitation of 45 endogenous proteins in human plasma trypsin ..
  76. pmc An automated method for finding molecular complexes in large protein interaction networks
    Gary D Bader
    Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
    BMC Bioinformatics 4:2. 2003
    Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks...
  77. pmc PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    Nancy Y Yu
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
    Bioinformatics 26:1608-15. 2010
    ..Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program...
  78. pmc A quantitative atlas of mitotic phosphorylation
    Noah Dephoure
    Department of Cell Biology, Harvard University Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:10762-7. 2008
    ..Analysis of non-proline site-containing phosphopeptides identified two unique motifs that suggest there are at least two undiscovered mitotic kinases...
  79. ncbi Mass spectrometry-based proteomics
    Ruedi Aebersold
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nature 422:198-207. 2003
    Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology...
  80. doi Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions
    Paola Picotti
    Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
    Nat Methods 9:555-66. 2012
    Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is emerging in the field of proteomics as a complement to untargeted shotgun methods...
  81. pmc A proteogenomic update to Yersinia: enhancing genome annotation
    Samuel H Payne
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 11:460. 2010
    ..The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins...
  82. pmc Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics
    Eric J Bennett
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Cell 143:951-65. 2010
    ..Here, we report the development of a quantitative proteomics platform centered on multiplex absolute quantification (AQUA) technology to elucidate the architecture of the ..
  83. ncbi Trypsin cleaves exclusively C-terminal to arginine and lysine residues
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 3:608-14. 2004
    Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert protein mixtures into more readily analyzable peptide populations...
  84. pmc Network organization of the human autophagy system
    Christian Behrends
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 466:68-76. 2010
    ..These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway...
  85. ncbi Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
    Juri Rappsilber
    Center of Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Anal Chem 75:663-70. 2003
    b>Proteomics is critically dependent on optimal sample preparation. Particularly, the interface between protein digestion and mass spectrometric analysis has a large influence on the overall quality and sensitivity of the analysis...
  86. pmc MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
    Lily Ting
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 8:937-40. 2011
    Quantitative mass spectrometry-based proteomics is highly versatile but not easily multiplexed...
  87. doi Next-generation proteomics: towards an integrative view of proteome dynamics
    A F Maarten Altelaar
    Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Nat Rev Genet 14:35-48. 2013
    ..Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample ..
  88. pmc The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    Andreas Ruepp
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 32:5539-45. 2004
    ..is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as 'gold standard' for functional ..
  89. ncbi The International Protein Index: an integrated database for proteomics experiments
    Paul J Kersey
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Proteomics 4:1985-8. 2004
    ..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
  90. doi Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle
    Henrik Daub
    Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell 31:438-48. 2008
    ..This proteomics approach enabled us to quantify 219 protein kinases from S and M phase-arrested human cancer cells...
  91. pmc Deep proteome and transcriptome mapping of a human cancer cell line
    Nagarjuna Nagaraj
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 7:548. 2011
    ..type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. Online liquid chromatography coupled to high-resolution MS and MS/MS yielded 166 420 peptides with unique amino-..
  92. doi Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried D 82152, Germany
    Cell 141:897-907. 2010
    ..The N-glycoproteome contains a plethora of modification sites on factors important in development, organ-specific functions, and disease...
  93. ncbi Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    John R S Newman
    Howard Hughes Medical Institute, San Francisco, California, USA
    Nature 441:840-6. 2006
    ..Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation...
  94. pmc The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics
    Shinya Ohta
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Cell 142:810-21. 2010
    ..Here, we have integrated quantitative proteomics with bioinformatic analysis to generate a series of independent classifiers that describe the approximately 4,..
  95. pmc An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host
    Mark W Robinson
    Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Ultimo, Sydney, New South Wales 2007, Australia
    Mol Cell Proteomics 8:1891-907. 2009
    ..Here we integrated a transcriptomics and proteomics approach to profile Fasciola secretory proteins that are involved in host-pathogen interactions and to correlate ..
  96. pmc Proteomics characterization of extracellular space components in the human aorta
    Athanasios Didangelos
    King s British Heart Foundation Centre, King s College, London, United Kingdom
    Mol Cell Proteomics 9:2048-62. 2010
    ..Although proteomics has been previously applied to vascular tissues, few studies have specifically targeted the vascular ECM and its ..
  97. pmc Large-scale proteomics analysis of the human kinome
    Felix S Oppermann
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 8:1751-64. 2009
    ..In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis.
  98. ncbi Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition
    Jeffrey C Silva
    Waters Corporation, Milford, Massachusetts 01757 3696, USA
    Mol Cell Proteomics 5:144-56. 2006
    Relative quantification methods have dominated the quantitative proteomics field...
  99. pmc Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
    Annette Michalski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 10:M111.011015. 2011
    Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years...
  100. pmc Defining the human deubiquitinating enzyme interaction landscape
    Mathew E Sowa
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Cell 138:389-403. 2009
    ....
  101. doi Comparison of protein enrichment strategies for proteome analysis of plasma
    Julia E Bandow
    Pfizer Global Research and Development, Pfizer Inc, Ann Arbor, MI, USA
    Proteomics 10:1416-25. 2010
    ..However, detectable protein spots in the different plasma fractions contained exclusively high-abundant proteins normally present in plasma at concentrations between 1 microg and 40 mg/mL...

Research Grants79

  1. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Furthermore, the application of DMP to peptidases will demonstrate the generality of this approach for the future characterization of medically relevant enzymes and signaling pathways. ..
  2. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  3. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ABSTRACT Paradigm shifts in biology are often catalyzed by innovations in measurement technologies. Genomics and proteomics have revolutionized biology but would not have been possible without developments in capillary sequencing, cDNA ..
  4. NIH Director's Pioneer Award
    ERICH JARVIS; Fiscal Year: 2009
    ..Repairing the pathway in vocal learners, when damaged, would have profound impact for correcting neurological disorders of speech. ..
  5. Chymase-Mediated MMP Activation in Ishemia Reperfusion Injury
    LOUIS JOSEPH DELL'ITALIA; Fiscal Year: 2013
    ..Objective 1. Determine whether I/R results in activation of novel cardiomyocyte nuclear MMPs using proteomics and mass spectrometry approaches...
  6. Mapping for Specialized Domains for FCeRI Signaling &Internalization
    Bridget S Wilson; Fiscal Year: 2013
    ..We will use a combination of proteomics, live cell and electron microscopy, pharmacologic, and molecular biology approaches to identify and characterize ..
  7. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2010
    ..Intravenous injection of this fraction causes proteinuria in rats. We have recently used state-of-the-art proteomics techniques to study the proteins in the active plasma fraction from a FSGS patient...
  8. Pilot and definitive studies to evaluate Insertional Mutagenesis
    LU TAYLOR; Fiscal Year: 2012
    ..glutathione, clinical pathology, hepatic RNA isolation and subsequent microarray profiling, liver proteomics and serum multiple analyte profiles (MAPs) will be determined in this study...
  9. Studies to Evaluate the Toxicological Potential of Test Articles
    LU TAYLOR; Fiscal Year: 2010
    ..glutathione, clinical pathology, hepatic RNA isolation and subsequent microarray profiling, liver proteomics and serum multiple analyte profiles (MAPs) will be determined in this study...
  10. Novel Mitochondrial Mechanisms of Ethanol-Induced Cardiac Injury in Aged Females
    DONNA HOPE KORZICK; Fiscal Year: 2010
    ..isolated heart and in vivo mitochondrial respiration studies in conjunction with the newly emerging iTRAQ 8plex proteomics approach, LC MS/MS and PANTHER ontological analysis to characterize alterations in mitochondrial signaling ..
  11. Role of Txnip in adapting fuel metabolism to nutritional state
    SIMON HUI; Fiscal Year: 2013
    ..In addition, proteomics approach will be used to identify partners interacting with Txnip...
  12. Immunomodulatory and regenerative effects of mesenchymal stem cells on allografts
    Norma S Kenyon; Fiscal Year: 2013
    ..models of cellular (Project 1) and solid organ (Project 2) allotransplantation, in conjunction with genomics and proteomics to define MSC product release criteria and potential biomarkers (Core B), as well as sophisticated tools for ..
  13. Functional Genomics of the Mitochondrial Proteome
    Dennis R Winge; Fiscal Year: 2011
    ..The growing interest in mitochondria has stimulated large-scale proteomics efforts to define the mitochondrial proteome...
  14. Molecular Markers for Progression of Pulmonary Fibrosis in Systemic Sclerosis
    Shervin Assassi; Fiscal Year: 2013
    ..complements the candidate's prior training in the Master's program with courses in genomics and proteomics, longitudinal and Bayesian data analysis, bioethics and advanced grant writing...
  15. Genomics of Antiviral Responses of Anopheles gambiae Against O'nyong-nyong Virus
    Young S Hong; Fiscal Year: 2010
    ..from virus-infected midgut epithelial cells, 2) 60- mer oligo-microarrays, and 3) iTRAQ", a quantitative proteomics analysis...
  16. A quantitative proteomics approach to understand viral immune evasion strategies
    Michele E Hardy; Fiscal Year: 2010
    ..Our proteomics approach predicts that convergent signaling pathways will be revealed by quantitation of changes in relative ..
  17. Lipid Droplet Metabolism
    Fredric B Kraemer; Fiscal Year: 2013
    ..in our understanding of LD metabolism have been made through a variety of approaches, including microscopy, proteomics, and genome-wide screens...
  18. Functional Analysis of the Dual Specificity Kinase NEK1 in Mammalian Meiosis
    JOANNA KIM HOLLOWAY; Fiscal Year: 2011
    ..molecular biology and cytogenetics (with an emphasis on mammalian gametogenesis);my goal is to strengthen my proteomics skills in order to execute this project and move toward independent research...
  19. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    ..b>Proteomics is a powerful state-of-the-art strategy in genetic dissection of complex diseases, such as osteoporosis...
  20. Interplay Between Tissue Architecture and Nuclear Organization in the DNA Damage
    Pierre Alexandre Vidi; Fiscal Year: 2013
    ..S. Badve and K. Hodges at the IU School of Medicine). It would also provide me training in proteomics and micromechanics that I could directly apply to my project. Importantly, I will seek advice from my Mentor (Dr...
  21. Non-coding RNA engineers antibody diversity
    Uttiya Basu; Fiscal Year: 2011
    ..Here, we use a combination of modern computational biology, proteomics, high-throughput genomics and mouse genetics to identify and functionally characterize ncRNA generated in the Ig ..
  22. Biochemical Characterization of Cytochrome b5 Reductase in Candida albicans
    MARY JOLENE PATRICIA HOLLOWAY; Fiscal Year: 2010
    ..I find it particularly exciting that this project merges infectious disease with biochemistry and proteomics, with the overall goal of identifying novel drug targets for an important human pathogen...
  23. Growth Hormone Regulation of SH2B1
    Christin Carter-Su; Fiscal Year: 2013
    ..State-of-the-art microscopes, photoactivable probes, proteomics, cell lines and both primary macrophages and MEFs from SH2B1-/- mice, will also be used...
  24. Novel Biomarkers in Aortic Aneurysms and Acute Aortic Dissection
    JENNIFER E contact VAN EYK; Fiscal Year: 2010
    ..The current proposal will use proteomics techniques in an advanced animal model of aortic aneurysms and dissections to gain insight into these mechanisms ..
  25. BRAINSTEM MATURATION IN THE SUDDEN INFANT DEATH SYNDROME
    HANNAH CHASE KINNEY; Fiscal Year: 2013
    ..In the present cycle, we performed state-of-the-art proteomics to identify candidate proteins which could provide novel insight into the cause(s) and pathogenesis of the ..
  26. Proteomic signatures of an early life asthma-protective exposure
    Serrine S Lau; Fiscal Year: 2010
    ..In order to achieve our goals, we will rely on our synergistic expertise in proteomics (Lau), epidemiology (Halonen), allergy biology and immunology (Vercelli), and biostatistics (Billheimer) as well ..
  27. Role of SIRT3 in fetal programming and kidney dysfunction
    Karen R Jonscher; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): An Applied Physicist and proteomics expert at the University of Colorado Denver, Dr...
  28. Role of Oxidative Stress in Post-MI Cardiac Failure Associated with Diabetes
    MICHAEL FREDERICK HILL; Fiscal Year: 2013
    ..encompass diverse techniques (integrative physiology, protein chemistry, biochemistry, immunohistochemistry, proteomics, pathology, and histology) and will integrate proteomic and biochemical information at the molecular level with ..
  29. Nonenzymatic glycation, bone quality, and microdamage in type 2 diabetic bone
    Eve Donnelly; Fiscal Year: 2013
    ..UPLC), and core facilities for Biochemistry, Bioimaging, Cell &Molecular Biology, Microscopy, and Proteomics. Training Plan: The training plan includes research training in the Mentor's laboratory in techniques for ..
  30. Genome-wide measurement of bacterial transcriptional regulatory states
    Peter L Freddolino; Fiscal Year: 2013
    ..In the era of genomics, proteomics, and metabolomics, however, biologists are still bereft of a generally applicable method for rapid determination ..
  31. Surgical Revascularization's Impact on Mitochondria in Hibernating Myocardium
    ROSEMARY FRANCES KELLY; Fiscal Year: 2013
    ..Adaptations to hibernation are complex and involve alterations in the bioenergetics and proteomics of the mitochondria that allow the tissue to maintain its viability while sacrificing myocardial function...
  32. Molecular physiology of voltage-gated Ca2+ channels
    Jian Yang; Fiscal Year: 2013
    ..proteolysis, and the fate and function of the resulting hemi-channels, using a combination of biochemistry, proteomics, fixed cell and live cell imaging, and electrophysiology...
  33. Functional roles of Nrf2 and NQO1 genetic variants in hyperoxic lung injury-ARDS
    Bhagavatula Moorthy; Fiscal Year: 2013
    ..Omics'approaches, including genomics (microarrays) and proteomics approaches will be used to determine the molecular mechanisms by which Nrf2 or NQO1 variants contribute to lung ..
  34. Biomarkers of Fusarium biofilm formation in vitro and in vivo
    PRANAB KUMAR MUKHERJEE; Fiscal Year: 2012
    ..the ability of outbreak isolates to form biofilms and disease severity in the murine keratitis model, (5) proteomics analysis identified 29 proteins that were differentially expressed in Fusarium biofilms compared to ..
  35. Examination of the Final Stages of Platelet Production
    JONATHAN NOAH THON; Fiscal Year: 2013
    ..Professor, University of British Columbia;Vice President, Canadian Blood Services), entailed the application of proteomics, molecular biology, and biochemistry to identify mechanisms involved in regulating the storage-related ..
  36. Abdominal Symptom Phenotypes: Pathways to New Biomarkers
    Robert Shulman; Fiscal Year: 2010
    ..3) Advances in high throughput genomics and proteomics have increased the potential for new biomarkers including urine proteomics...
  37. Retinoid Mediated Protection Against Reactive Oxygen Species Induced Cytotoxicity
    Serrine S Lau; Fiscal Year: 2013
    ..b>Proteomics analyses revealed that cytoprotection is associated with the increased synthesis of a select number of proteins, ..
  38. Functional Analysis of the Dual Specificity Kinase NEK1 in Mammalian Meiosis
    JOANNA KIM HOLLOWAY; Fiscal Year: 2013
    ..molecular biology and cytogenetics (with an emphasis on mammalian gametogenesis);my goal is to strengthen my proteomics skills in order to execute this project and move toward independent research...
  39. Research Career Development in Child Health
    Michael W Konstan; Fiscal Year: 2012
    ..The technologies and methodologies to address these questions include genomics, proteomics, metabolomics, bioimaging, cell and molecular biology, bioinformatics, in vivo approaches including mutant mouse ..
  40. cGMP-dependent Protein Kinase Function in Osteoblast Mechanotransduction
    Renate B Pilz; Fiscal Year: 2013
    ..and bimolecular fluorescence complementation to characterize the PKG-regulated Src signaling complex, and use a proteomics approach to identify novel PKG II substrates and interacting partners in osteoblast membranes...
  41. Influence of Heme on Hepatic Cytochrome P450 Turnover
    Maria Almira Correia; Fiscal Year: 2013
    ..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 synthesis and/or degradation are so dramatically altered...
  42. Role of AIB1 in malignant progression
    Anna Tate Riegel; Fiscal Year: 2013
    ..We will identify the AIB1-controlled signaling pathways activated in endothelial cells by by biochemical and proteomics approaches as well as gene expression pattern analysis...
  43. Proteome Bead-Display for Discovery of Tumor Antigens
    Mark Lim; Fiscal Year: 2013
    ..progress towards overcoming these limitations through the development of a next generation approach to proteomics, termed Bead-based Global Proteomic Screening (Bead-GPSTM)...
  44. Acquisition of a MALDI-TOF/TOF MS for Glycomic and Lipidomic Research
    Larry S Schlesinger; Fiscal Year: 2010
    ..The instrument will be located and administered by the Mass Spectrometry and Proteomics Facility (MS&P) in the Campus Chemical Instrument Center at The Ohio State University (OSU)...
  45. Resolving the role of nicotine-mediated phosphorylation on pancreatic fibrosis
    Joao A Paulo; Fiscal Year: 2013
    ..of focus in his lab include developing and applying new technologies in the fields of mass spectrometry and proteomics and investigating dynamic responses (e.g...
  46. Lipocalin 2 in Inflammation and Metabolic Control
    Xiaoli Chen; Fiscal Year: 2012
    ..Through the proteomics and microarray screening, we recently identified lipocalin 2 (LCN2) as a new adipokine that potentially connects ..
  47. Studying a Human Stem Cell Disease Using iPS Technology
    Steven E Artandi; Fiscal Year: 2010
    ..We will study self-renewal and differentiation, and employ proteomics to understand the specific nature of the defect in this disease...
  48. Roles of Host Kinases in Paramyxovirus RNA Synthesis
    Biao He; Fiscal Year: 2010
    ..We will determine the AKT1 phosphorylation site(s) within the P protein utilizing a proteomics approach as well as the in vitro kinase assay using purified P from bacteria in combination with mutational ..
  49. Sex Differences in Complement during Myocarditis/DCM
    Delisa Fairweather; Fiscal Year: 2013
    ..activation and immune complex (IC) deposition in the heart is observed in myocarditis/DCM patients, and a recent proteomics study found that 2 of the top 3 pathways in myocarditis/DCM patients involved the classical and alternative ..
  50. Identification and Validation of Alcohol Biomarker Signatures by Proteomics
    Emanuel Rubin; Fiscal Year: 2010
    ..Early diagnosis of this condition by specific biomarkers will offer the opportunity for treatment and prevention of heart enlargement, congestive heart failure and death. ..
  51. Systems Analysis of Cardiac Chromatin Structure
    Thomas M Vondriska; Fiscal Year: 2013
    ..chromatin packing), chromatin immunoprecipitation and DNA sequencing (localize proteins across the genome) and proteomics (determine proteins necessary for targeting)...
  52. A Systems Biology Approach to the Model Apicomplexan Toxoplasma gondii
    William J Sullivan Jr; Fiscal Year: 2010
    ..The development of new high-throughput technologies has enabled collection of large genomic and proteomics datasets...
  53. Bacterial Immunosuppression: Host Target Identification Through Chemical Probes
    Kim D Janda; Fiscal Year: 2013
    ..chemical probes will be employed to identify the mammalian cell receptor(s) of C12 via a click chemistry-based, proteomics-mediated approach...
  54. The Effect of Gastric Bypass Surgery on Renal Function and Metabolism
    Benjamin K Canales; Fiscal Year: 2013
    ..of renal injury and nephrolithiasis, with special focus on renal histology, transport physiology, tissue proteomics, and genomics...
  55. DAMP-RAGE Signaling and Fetal Injury in Inflammation-Induced Preterm Birth
    Irina A Buhimschi; Fiscal Year: 2013
    ..Using proteomics we discovered that S100A12 plays a key role in orchestrating the intra-amniotic inflammatory response to ..
  56. PROTEIN CARBONYLATION AND AXONAL DAMAGE IN EAE
    Oscar A Bizzozero; Fiscal Year: 2012
    ..We will then identify the oxidized proteins in the inflammatory and degenerative stages of the disease by redox proteomics, and will ascertain both the chemical nature and origin of the oxidizing species from the type of carbonylated ..
  57. Bioengineering of Novel Synthetic Lipid-Peptide Lung Surfactants
    Robert H Notter; Fiscal Year: 2013
    ..Aims 1 and 2 study the bioengineering, proteomics, synthesis, purification, molecular biophysics, and scale-up of synthetic peptides/lipopeptides and novel RL ..
  58. Regulations of DNA Alkylation/Deamination Damage Repair
    Rabindra Roy; Fiscal Year: 2013
    ..In the next funding cycle, this repair assay method in combination with biochemical, proteomics and mammalian genetic approach (knock-out, mutant and siRNA knock-down) will be a valuable tool to identify ..
  59. Skin Regeneration with Stem Cells and Scaffolds
    SUSAN RENEE OPALENIK; Fiscal Year: 2013
    ..will be accomplished by the collaboration of a seasoned team of investigators with expertise in tissue analysis, proteomics, stem cell biology, microfluidics, and polymer chemistry...
  60. Molecular Biology of Eukaryotic Viruses
    Bert L Semler; Fiscal Year: 2012
    ..An expansion of interdisciplinary research and training programs in the areas of structural biology/proteomics, virus-host interactions, and viruses requiring BSL-3 containment is proposed for the next five years...
  61. Liver Cell Membrane Protein-Expression and Function
    Allan W Wolkoff; Fiscal Year: 2012
    ..The Molecular Cytology Core (Core B) provides state-of-the-art microscopy and imaging services. A new Proteomics Core (Core C) has been added based upon the substantial use of this technology by each of the four Projects...
  62. HDL Dysfunction and Vascular Inflammation
    Kirkwood A Pritchard; Fiscal Year: 2010
    ..outcomes will be tested at the level of survival, mechanisms of ischemic injury, organ pathobiology and proteomics of HDL interactions with other inflammatory mediators...
  63. LTQ Orbitrap XL ETD Mass Spectrometer
    Haining Zhu; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The Proteomics Core Facility at the University of Kentucky (UK) College of Medicine requests $947,163 to acquire a LTQ Orbitrap XL/ETD hybrid mass spectrometer with an Eksigent nano-HPLC...
  64. Acquisition of a Hybrid Quadrupole, Ion Mobility Separation, Orthogonal Accelerat
    Sheng Zhang; Fiscal Year: 2009
    ..This state-of-the-art instrument will be utilized as a shared research resource in the Cornell Proteomics and Mass Spectrometry (MS) Facility and will be essential to 28 active NIH supported grants...
  65. Multiplex Fluorescent Dyes for Ultrasensitive Proteomics
    Edward A Dratz; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The broad long-term goals of this project are to develop more powerful proteomics detection technology with greatly improved sensitivity, that will reveal the global patterns of biologically ..
  66. A high-resolution in situ proteomics atlas of salivary gland development
    Melinda Larsen; Fiscal Year: 2010
    ..The end product will include a high- resolution in situ proteomics-based atlas, which categorizes and quantifies active signaling protein expression levels within specific cell ..
  67. High Performance Computational System to Support LCMS/Proteomics Analysis
    ROBERT STRAUBINGER; Fiscal Year: 2009
    ..Key instruments generating proteomics data for our consortium of investigators include a Waters LC-QTOF Premier (RPCI), a Thermo LTQ-XL linear ion ..
  68. Acquisition of a LTQ Orbitrap XL ETD Hybrid FT Mass Spectrometer
    George Tsaprailis; Fiscal Year: 2010
    ..and whole protein accurate measurements coupled to top-down protein gas-phase sequencing, are highly needed proteomics capabilities for existing NIH-funded investigators at the University of Arizona...
  69. Center for Computational Mass-Spectrometry
    Pavel A Pevzner; Fiscal Year: 2011
    ..of excellence in computational mass spectrometry and a national and international resource in the broad area of proteomics. It proposes to enlarge the current research activities, to branch into previously unexplored areas of ..
  70. Two-Dimensional Electrophoresis Device for Biomarker Detection
    Z Hugh Fan; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The goal of the proposed research is to develop proteomics technology for drug discovery and medical diagnostics...
  71. Symposium on Proteomics and Toxicology
    Ian Blair; Fiscal Year: 2003
    Description (provided by applicant) This proposal is a request for financial support for a half-day symposium on "Proteomics and Toxicology: Recent Advances in Technology and Applications" to be presented at the American Chemical Society ..
  72. Functional Proteomic Analysis of Cardiac Mitochondria
    Peipei Ping; Fiscal Year: 2005
    ..One focuses on broad-scale annotation of proteins (i.e., expression proteomics) and the second undertakes not only the identification but also the functional characterization of a sub-group ..
  73. CENTER FOR STRUCTURAL BIOLOGY
    Vernon Reinhold; Fiscal Year: 2003
    This proposal describes three interrelated Core activities (Proteomics, Bioinformatics, Outreach) that have been cast bo build a multi- disciplinary research team to address the next, more challenging phase of genomics, how gene products ..
  74. Ultraspec III TOF/TOF 200 MALDI-TOF Mass Spectrometry Imaging System
    Djuro Josic; Fiscal Year: 2009
    ..This instrument will be located in the Proteomics Core, which is part of the NIH/NCRR-funded Centers of Biomedical Research Excellence (COBRE) Center for Cancer ..
  75. Quantative and Phospho Proteomics Instrumentation
    Jay Fox; Fiscal Year: 2006
    ..As the field of proteomics moves beyond the level of simple identification into the more challenging realm of changes in protein structure ..
  76. GENOMICS, PROTEOMICS, BIOINFORMATICS & DEVELOPMENTAL TOX
    Philip Mirkes; Fiscal Year: 2000
    Recent developments in the fields of genomics, proteomics, and bioinformatics offer the potential to undertake global analyses of gene and protein expression...
  77. Novel Micro-X-ray Translucent Flow Cell Technology for Proteomics, a Broadly Appl
    EVA BIRNBAUM; Fiscal Year: 2009
    ..a broadly applicable, quantitative research tool which addresses core technical challenges in the field of proteomics, including protein-drug interactions, protein-protein interactions, and post-translational modifications...
  78. Proteomics/Genomics of Opiate Analgesia and Addiction
    Vivian Hook; Fiscal Year: 2004
    ..Therefore, this R21 application for pilot, innovative studies utilizing state-of-the-art technologies in both proteomics and genomics, will elucidate molecular components involved in morphine-induced analgesia compared to tolerance ..
  79. Proteomics of Auditory Brainstem Circuitry During Development and in Deafness
    Raphael Pinaud; Fiscal Year: 2010
    ..We propose to use high-throughput quantitative proteomics and mass spectrometric approaches to uncover the cascade of protein regulatory events associated with the post-..