Jesper V Olsen

Summary

Publications

  1. doi request reprint Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community
    Jesper V Olsen
    Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, Blegdamsvej 3b, DK 2200 Copenhagen N, Denmark
    Sci Signal 4:pe7. 2011
  2. pmc Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns
    Alicia Lundby
    Novo Nordisk Foundation Center for Protein Research, Department for Proteomics, Faculty of Health Sciences, University of Copenhagen, Denmark
    Cell Rep 2:419-31. 2012
  3. pmc Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1578-85. 2012
  4. pmc Conformation-specific anti-Mad2 monoclonal antibodies for the dissection of checkpoint signaling
    Garry G Sedgwick
    a The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen, Denmark
    MAbs . 2016
  5. doi request reprint In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling
    Alicia Lundby
    Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Sci Signal 6:rs11. 2013
  6. doi request reprint Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation
    Kristina B Emdal
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Sci Signal 8:ra40. 2015
  7. doi request reprint TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells
    Omid Hekmat
    Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences and Sino Danish Breast Cancer Research Centre, University of Copenhagen, Dyrlægevej 88, 1, 1870 Frederiksberg C, Denmark
    J Proteome Res 12:4136-51. 2013
  8. doi request reprint Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
  9. doi request reprint Functional proteomics defines the molecular switch underlying FGF receptor trafficking and cellular outputs
    Chiara Francavilla
    Department of Proteomics, NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
    Mol Cell 51:707-22. 2013
  10. pmc Status of large-scale analysis of post-translational modifications by mass spectrometry
    Jesper V Olsen
    Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 12:3444-52. 2013

Collaborators

Detail Information

Publications35

  1. doi request reprint Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community
    Jesper V Olsen
    Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, Blegdamsvej 3b, DK 2200 Copenhagen N, Denmark
    Sci Signal 4:pe7. 2011
    ..Requirements for the reporting of quantitative data are being developed, but there are few mechanisms for community-wide sharing of these data...
  2. pmc Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns
    Alicia Lundby
    Novo Nordisk Foundation Center for Protein Research, Department for Proteomics, Faculty of Health Sciences, University of Copenhagen, Denmark
    Cell Rep 2:419-31. 2012
    ..Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity...
  3. pmc Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1578-85. 2012
    ....
  4. pmc Conformation-specific anti-Mad2 monoclonal antibodies for the dissection of checkpoint signaling
    Garry G Sedgwick
    a The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen, Denmark
    MAbs . 2016
    ..Thus, our defined mAbs provide insight into checkpoint signaling and provide useful tools for future research on Mad2 function and regulation...
  5. doi request reprint In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling
    Alicia Lundby
    Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Sci Signal 6:rs11. 2013
    ....
  6. doi request reprint Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation
    Kristina B Emdal
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Sci Signal 8:ra40. 2015
    ..Our findings suggest that Cbl-b limits NGF-TrkA signaling to control the length of neurites. ..
  7. doi request reprint TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells
    Omid Hekmat
    Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences and Sino Danish Breast Cancer Research Centre, University of Copenhagen, Dyrlægevej 88, 1, 1870 Frederiksberg C, Denmark
    J Proteome Res 12:4136-51. 2013
    ....
  8. doi request reprint Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
    ..Such regions could correspond to loci selected early during domestication...
  9. doi request reprint Functional proteomics defines the molecular switch underlying FGF receptor trafficking and cellular outputs
    Chiara Francavilla
    Department of Proteomics, NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
    Mol Cell 51:707-22. 2013
    ..Altogether, these results identify an intriguing ligand-dependent mechanism for the control of receptor fate and cellular outputs that may explain the pathogenic role of deregulated FGFR2b, thus offering therapeutic opportunities...
  10. pmc Status of large-scale analysis of post-translational modifications by mass spectrometry
    Jesper V Olsen
    Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 12:3444-52. 2013
    ..The central challenge for the field is to develop streamlined methods for determining biological functions for the myriad of modifications now known to exist...
  11. doi request reprint GeLCMS for in-depth protein characterization and advanced analysis of proteomes
    Alicia Lundby
    Faculty of Health Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, DK 2200, Denmark
    Methods Mol Biol 753:143-55. 2011
    ..If SILAC-labeled protein samples are mixed prior to gel separation, the protein content of the sample can furthermore be accurately quantified...
  12. pmc Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists
    Gitte L Christensen
    Laboratory for Molecular Cardiology, Department of Biomedical Sciences, Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 9:1540-53. 2010
    ..Quantitative mass spectrometry is a promising tool for evaluation of the signaling properties of biased agonists to other receptors in the future...
  13. doi request reprint Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins
    Enrico Cappellini
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350, Copenhagen, Denmark
    J Proteome Res 11:917-26. 2012
    ..This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics...
  14. doi request reprint Pinpointing phosphorylation sites: Quantitative filtering and a novel site-specific x-ion fragment
    Christian D Kelstrup
    Department for Proteomics, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    J Proteome Res 10:2937-48. 2011
    ..Together, these findings significantly improve phosphorylation site localization confidence...
  15. doi request reprint Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer
    Christian D Kelstrup
    Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen N, Denmark
    J Proteome Res 11:3487-97. 2012
    ....
  16. doi request reprint From Phosphosites to Kinases
    Stephanie Munk
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg 6 2, 2200, Copenhagen, Denmark
    Methods Mol Biol 1355:307-21. 2016
    ..This chapter summarizes the use of the larger phosphorylation databases, and approaches that can be applied to predict kinases that phosphorylate individual sites or that are globally modulated in phosphoproteomics datasets. ..
  17. doi request reprint Systems Analysis for Interpretation of Phosphoproteomics Data
    Stephanie Munk
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Bldg 6 1, 2200, Copenhagen, Denmark
    Methods Mol Biol 1355:341-60. 2016
    ..This chapter provides a summary of the most appropriate tools for systems analysis of phosphoproteomics datasets, and the considerations that are critical for acquiring meaningful output. ..
  18. doi request reprint Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer
    Christian D Kelstrup
    Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    J Proteome Res 13:6187-95. 2014
    ....
  19. pmc Ubiquitin-SUMO circuitry controls activated fanconi anemia ID complex dosage in response to DNA damage
    Ian Gibbs-Seymour
    Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Mol Cell 57:150-64. 2015
    ..Our results uncover a regulatory role for SUMOylation in the FA pathway, and we propose that ubiquitin-SUMO signaling circuitry is a mechanism that contributes to the balance of activated ID complex dosage at sites of DNA damage...
  20. doi request reprint SILAC-based temporal phosphoproteomics
    Chiara Francavilla
    Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
    Methods Mol Biol 1188:125-48. 2014
    ..Analysis of enriched peptides on Orbitrap-based MS results in comprehensive and accurate reconstruction of temporal changes of signaling networks. ..
  21. pmc Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID)
    Christian D Kelstrup
    From the Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 13:1914-24. 2014
    ....
  22. pmc Comprehensive identification of SUMO2/3 targets and their dynamics during mitosis
    Julie Schou
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 9:e100692. 2014
    ..Our data provide a rich resource for further exploring the role of SUMO2/3 modifications in mitosis and cell cycle regulation. ..
  23. ncbi request reprint Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4
    Anders M Hinsby
    Protein Laboratory, Panum Institute 6 1, Blegdamsvej 3C, University of Copenhagen, DK 2200, Denmark
    J Biol Chem 279:46438-47. 2004
    ..Finally, we present evidence for a complex containing insulin receptor substrate-4 and ShcA in signaling by the fibroblast growth factor receptor...
  24. pmc A direct role of Mad1 in the spindle assembly checkpoint beyond Mad2 kinetochore recruitment
    Thomas Kruse
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    EMBO Rep 15:282-90. 2014
    ..The C-terminal globular domain of Mad1 and conserved residues in this region are required for this unexpected function of Mad1. ..
  25. doi request reprint Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation
    Brian T Weinert
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Sci Signal 4:ra48. 2011
    ..This systems-level analysis of comparative posttranslational modification showed that acetylation is an anciently conserved modification and suggests that phosphorylation sites may have evolved faster than acetylation sites...
  26. doi request reprint Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity
    Rosa R Jersie-Christensen
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
    Methods Mol Biol 1355:251-60. 2016
    ..Phosphopeptides are enriched using TiO2 beads and the orbitrap mass spectrometer is operated in a sensitive mode with higher energy collisional dissociation (HCD). ..
  27. doi request reprint Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage
    Tanveer S Batth
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University ofCopenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
    Methods Mol Biol 1355:179-92. 2016
    ..Each Fraction is subsequently enriched for phosphopeptides using TiO2 followed by LC/MS analysis. ..
  28. pmc Recent findings and technological advances in phosphoproteomics for cells and tissues
    Louise von Stechow
    a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Expert Rev Proteomics 12:469-87. 2015
    ..Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed. ..
  29. pmc Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues
    Alicia Lundby
    Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Nat Commun 3:876. 2012
    ..The presented phosphoproteomic method is simple and rapid, making it applicable for screening of diseased tissue samples...
  30. doi request reprint The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores
    Gang Zhang
    The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
    J Cell Sci 125:3243-53. 2012
    ..This underscores the importance of the Ndc80 loop region in coordinating chromosome segregation through the recruitment of specific proteins to the kinetochore...
  31. pmc Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics
    Alicia Lundby
    1 Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark 2 The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark 3 The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA 4
    Nat Methods 11:868-74. 2014
    ..Overall, we present a general strategy to propose candidates in GWAS loci for functional studies and to systematically filter subtle association signals using tissue-specific quantitative interaction proteomics. ..
  32. pmc Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response
    Petra Beli
    The NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell 46:212-25. 2012
    ..Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair...
  33. doi request reprint Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics
    Tanveer S Batth
    Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    J Proteome Res 13:6176-86. 2014
    ..In conclusion, we provide a basic framework and resource for performing in-depth phosphoproteome studies utilizing off-line basic reversed-phased fractionation. Raw data is available at ProteomeXchange (PXD001404)...
  34. pmc Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods
    Luise Ørsted Brandt
    Centre for Textile Research, University of Copenhagen, Copenhagen, Denmark Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 9:e106875. 2014
    ..The mass spectrometry proteomics data were deposited in the ProteomeXchange Consortium with the dataset identifier PXD001029. ..
  35. doi request reprint Global analysis of the yeast osmotic stress response by quantitative proteomics
    Boumediene Soufi
    The Novo Nordisk Foundation Center for Protein Research, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK 2200 Copenhagen, Denmark
    Mol Biosyst 5:1337-46. 2009
    ..Although the overall relationship between our proteome and published mRNA changes is poor we find an excellent correlation between the subset of osmotic shock up-regulated proteins and their corresponding mRNA changes...