Jeroen Krijgsveld

Summary

Affiliation: Utrecht University
Country: The Netherlands

Publications

  1. doi request reprint Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells
    Wilma Dormeyer
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 7:2936-51. 2008
  2. ncbi request reprint Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
    Jeroen Krijgsveld
    Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Nat Biotechnol 21:927-31. 2003
  3. ncbi request reprint In-gel isoelectric focusing of peptides as a tool for improved protein identification
    Jeroen Krijgsveld
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    J Proteome Res 5:1721-30. 2006
  4. ncbi request reprint Orthogonal separation techniques for the characterization of the yeast nuclear proteome
    Sharon Gauci
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 8:3451-63. 2009
  5. pmc Quantitative proteomics by metabolic labeling of model organisms
    Joost W Gouw
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, 3584CH Utrecht, The Netherlands
    Mol Cell Proteomics 9:11-24. 2010
  6. pmc In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition
    Joost W Gouw
    Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Mol Cell Proteomics 8:1566-78. 2009
  7. doi request reprint Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labeling
    Bastiaan B J Tops
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    J Proteome Res 9:341-51. 2010
  8. doi request reprint A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells
    Wilma Dormeyer
    Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Proteomics 8:4036-53. 2008
  9. pmc An AC-5 cathepsin B-like protease purified from Haemonchus contortus excretory secretory products shows protective antigen potential for lambs
    Erik de Vries
    Division of Parasitology and Tropical Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
    Vet Res 40:41. 2009
  10. doi request reprint Proteome biology of stem cells
    Albert J R Heck
    Utrecht University, The Netherlands
    Stem Cell Res 1:7-8. 2007

Collaborators

Detail Information

Publications38

  1. doi request reprint Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells
    Wilma Dormeyer
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 7:2936-51. 2008
    ..Our data provides a surface signature for HUES-7 and NT2/D1 cells and distinguishes normal hESCs from hECCs, helping explain their 'benign' versus 'malignant' nature...
  2. ncbi request reprint Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
    Jeroen Krijgsveld
    Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Nat Biotechnol 21:927-31. 2003
    ..elegans strains, one with and one without a germ line. The methodology described provides tools for accurate quantitative proteomic studies in these model organisms...
  3. ncbi request reprint In-gel isoelectric focusing of peptides as a tool for improved protein identification
    Jeroen Krijgsveld
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    J Proteome Res 5:1721-30. 2006
    ..5%. Of these, 1751 proteins (80%) were identified after peptide IEF and FT-MS alone. Overall, we show that peptide IEF allows to increase the confidence level of protein identifications, and is more sensitive than SDS-PAGE...
  4. ncbi request reprint Orthogonal separation techniques for the characterization of the yeast nuclear proteome
    Sharon Gauci
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 8:3451-63. 2009
    ..The enrichment for specific nuclear complexes has resulted in high protein sequence coverage, which will be particularly useful for the detailed characterization of subunits...
  5. pmc Quantitative proteomics by metabolic labeling of model organisms
    Joost W Gouw
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, 3584CH Utrecht, The Netherlands
    Mol Cell Proteomics 9:11-24. 2010
    ..We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life...
  6. pmc In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition
    Joost W Gouw
    Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Mol Cell Proteomics 8:1566-78. 2009
    ....
  7. doi request reprint Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labeling
    Bastiaan B J Tops
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    J Proteome Res 9:341-51. 2010
    ..elegans and show the potential and feasibility of an approach enabling system-wide accurate quantitative proteomics experiments in this model organism...
  8. doi request reprint A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells
    Wilma Dormeyer
    Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Proteomics 8:4036-53. 2008
    ..However, as the composition of cells and membranes is highly variable we still recommend adapting the sample preparation protocol for each individual system...
  9. pmc An AC-5 cathepsin B-like protease purified from Haemonchus contortus excretory secretory products shows protective antigen potential for lambs
    Erik de Vries
    Division of Parasitology and Tropical Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
    Vet Res 40:41. 2009
    ..After challenge the cystatin-binding proteins induced significantly higher local and systemic ES specific IgA and IgG responses...
  10. doi request reprint Proteome biology of stem cells
    Albert J R Heck
    Utrecht University, The Netherlands
    Stem Cell Res 1:7-8. 2007
    ..Here we report on the rationale and goals of this initiative...
  11. pmc Novel Hsp90 partners discovered using complementary proteomic approaches
    Pavel A Tsaytler
    Department of Membrane Enzymology, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
    Cell Stress Chaperones 14:629-38. 2009
    ..Taken together, our data expand the knowledge of the Hsp90 interactome and provide a further step in our understanding of the Hsp90 chaperone system...
  12. doi request reprint Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics
    Joost W Gouw
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Anal Chem 80:7796-803. 2008
    ....
  13. ncbi request reprint Lung proteome alterations in a mouse model for nonallergic asthma
    Rene Houtman
    Department of Pharmaceutical Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    Proteomics 3:2008-18. 2003
    ....
  14. doi request reprint A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing
    Sharon Gauci
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Proteomics 8:4898-906. 2008
    ..Collectively, this peptide pI calculator is a welcome addition to the versatility and robustness of IEF for the separation and confident identification of (post-translationally modified) peptides...
  15. doi request reprint Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach
    Sharon Gauci
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Anal Chem 81:4493-501. 2009
    ....
  16. doi request reprint Proteomics and human embryonic stem cells
    Dennis Van Hoof
    Developmental Biology and Stem Cell Research, Hubrecht Institute, Utrecht, The Netherlands
    Stem Cell Res 1:169-82. 2008
    ..These findings underscore the power of mass spectrometry-based techniques to identify novel proteins associated with hESCs by studying these cells in an unbiased, discovery-oriented manner on a proteome-wide scale...
  17. doi request reprint Phosphorylation dynamics during early differentiation of human embryonic stem cells
    Dennis Van Hoof
    Developmental Biology and Stem Cell Research, Hubrecht Institute, Utrecht, The Netherlands
    Cell Stem Cell 5:214-26. 2009
    ..The findings provide new insights into how hESCs exit the pluripotent state and present the hESC (phospho)proteome resource as a complement to existing pluripotency network databases...
  18. ncbi request reprint GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7
    Jan A van der Knaap
    Department of Biochemistry, Center for Biomedical Genetics, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands
    Mol Cell 17:695-707. 2005
    ..Thus, GMPS can regulate the activity of a ubiquitin protease. Collectively, these results implicate a biosynthetic enzyme in chromatin control via ubiquitin regulation...
  19. ncbi request reprint Targeted analysis of protein termini
    Wilma Dormeyer
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 6:4634-45. 2007
    ..Our method will improve the correct annotation of genes and proteins in databases...
  20. ncbi request reprint Mass spectrometry-based quantitative proteomics
    Albert J R Heck
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Expert Rev Proteomics 1:317-26. 2004
    ..This article reviews various mass spectrometry-based technologies in quantitative proteomics, highlighting several interesting applications in areas ranging from cell biology to clinical applications...
  21. ncbi request reprint Mass spectrometric analysis of the Schistosoma mansoni tegumental sub-proteome
    Bas W M van Balkom
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 4:958-66. 2005
    ..Many of these proteins show no homology to any nonschistosomal protein, demonstrating that the schistosomal outer-surface comprises specific and unique proteins, likely to be critical for parasite survival...
  22. doi request reprint Proteome biology of stem cells: a new joint HUPO and ISSCR initiative
    Jeroen Krijgsveld
    Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Mol Cell Proteomics 7:204-5. 2008
  23. pmc Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish
    Hsin Yi Huang
    Hubrecht Institute KNAW, University Medical Centre Utrecht, Utrecht, The Netherlands
    EMBO J 30:3298-308. 2011
    ..Altogether, our data suggest that Tdrd1 acts as a molecular scaffold for Piwi proteins, bound through specific tudor domain-sDMA interactions, piRNAs and piRNA targets...
  24. pmc Identification of secreted cysteine proteases from the parasitic nematode Haemonchus contortus detected by biotinylated inhibitors
    Ana P Yatsuda
    Division of Infection Biology, Department of Infectious Diseases and Immunology, Utrecht University, Yalelaan, 1, 3584CL, Utrecht, The Netherlands
    Infect Immun 74:1989-93. 2006
    ..Mass spectrometry provided the identification of AC-4, HMCP1, HMCP2, and GCP7 as well as three novel CBLs encoded by clustered expressed sequence tags...
  25. doi request reprint A P4-ATPase protein interaction network reveals a link between aminophospholipid transport and phosphoinositide metabolism
    Catheleyne F Puts
    Membrane Enzymology, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH Utrecht, The Netherlands
    J Proteome Res 9:833-42. 2010
    ..One of these, the phosphatidylinositol-4-phosphatase Sac1p, also displays genetic interactions with Drs2p. Together, these findings suggest that aminophospholipid transport and phosphoinositide metabolism are interconnected at the Golgi...
  26. ncbi request reprint Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics
    Edwin P Romijn
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Chromatogr A 1000:589-608. 2003
    ....
  27. doi request reprint Immediate protein targets of photodynamic treatment in carcinoma cells
    Pavel A Tsaytler
    Department of Membrane Enzymology, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    J Proteome Res 7:3868-78. 2008
    ..This may not only lead to a further understanding of the complex network of cellular responses to oxidative stress, but it may also help in detailed targeting of photodynamic treatment applied to cancer...
  28. doi request reprint Searching for proteins of Mycobacterium avium subspecies paratuberculosis with diagnostic potential by comparative qualitative proteomic analysis of mycobacterial tuberculins
    Wiebren Santema
    Department of Infectious Diseases and Immunology, Immunology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
    Vet Microbiol 138:191-6. 2009
    ....
  29. pmc Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes
    Lisette Mohrmann
    Gene Regulation Laboratory, Centre for Biomedical Genetics, Department of Molecular and Cell Biology, Leiden University Medical Centre, 2300 RA Leiden, The Netherlands
    Mol Cell Biol 24:3077-88. 2004
    ..Our results support a close reciprocity of chromatin regulation by ATP-dependent remodelers and histone-modifying enzymes...
  30. ncbi request reprint An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics
    Dennis Van Hoof
    Nat Methods 4:677-8. 2007
  31. ncbi request reprint A high-quality catalog of the Drosophila melanogaster proteome
    Erich Brunner
    Center for Model Organism Proteomes, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    Nat Biotechnol 25:576-83. 2007
    ..melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism...
  32. ncbi request reprint The time is right: proteome biology of stem cells
    Anthony D Whetton
    Stem Cell and Leukemia Proteomics Laboratory, Faculty of Medical and Human Sciences, University of Manchester, Christie Hospital, Manchester M20 9BX, UK
    Cell Stem Cell 2:215-7. 2008
    ..Here we present the Proteome Biology of Stem Cells Initiative (PBSCI) and report on its goals and future activities...
  33. ncbi request reprint Embryonic stem cell proteomics
    Dennis Van Hoof
    Netherlands Institute of Developmental Biology, Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Expert Rev Proteomics 3:427-37. 2006
    ..In addition, we make concise comparisons with related transcriptome profiling reports...
  34. ncbi request reprint Mass spectrometric identification of human prostate cancer-derived proteins in serum of xenograft-bearing mice
    Gert Jan C M van den Bemd
    Department of Urology, Josephine Nefkens Institute, Erasmus MC, 3000 DR, Rotterdam, The Netherlands
    Mol Cell Proteomics 5:1830-9. 2006
    ....
  35. ncbi request reprint A quest for human and mouse embryonic stem cell-specific proteins
    Dennis Van Hoof
    Hubrecht Laboratory, Netherlands Institute of Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Mol Cell Proteomics 5:1261-73. 2006
    ..Validation by three independent conventional protein analysis techniques shows that our methodology is robust, provides an excellent tool to characterize ESCs at the protein level, and may disclose novel ESC-specific benchmarks...
  36. pmc Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cells
    Maaike Neeft
    Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
    Mol Biol Cell 16:731-41. 2005
    ..Mutations in either of the two genes prevent formation of this complex and abolish secretion...
  37. ncbi request reprint Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research
    Patrick A Everley
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Proteomics 3:729-35. 2004
    ..Western blotting provided further confirmation of the mass spectrometry-based quantification. Our results demonstrate the applicability of this novel approach toward the study of cancer progression using defined cell lines...
  38. pmc Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice
    Ernie de Boer
    Department of Cell Biology, Erasmus Medical Center, P O Box 1738, 3000 DR Rotterdam, The Netherlands
    Proc Natl Acad Sci U S A 100:7480-5. 2003
    ..Therefore, BirA-mediated biotinylation of tagged proteins provides the basis for the single-step purification of proteins from mammalian cells...