Research Topics
Genomes and Genes | Jeroen KrijgsveldSummaryAffiliation: Utrecht University Country: The Netherlands Publications
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Publications
Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cellsWilma 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...
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomicsJeroen 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...- In-gel isoelectric focusing of peptides as a tool for improved protein identificationJeroen 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... - Orthogonal separation techniques for the characterization of the yeast nuclear proteomeSharon 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... 
Quantitative proteomics by metabolic labeling of model organismsJoost 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...- In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transitionJoost W Gouw
Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
Mol Cell Proteomics 8:1566-78. 2009.... - Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labelingBastiaan 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... - A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cellsWilma 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... - An AC-5 cathepsin B-like protease purified from Haemonchus contortus excretory secretory products shows protective antigen potential for lambsErik 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... - Proteome biology of stem cellsAlbert 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... - Novel Hsp90 partners discovered using complementary proteomic approachesPavel 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... - Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomicsJoost 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.... - Lung proteome alterations in a mouse model for nonallergic asthmaRene Houtman
Department of Pharmaceutical Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
Proteomics 3:2008-18. 2003.... - A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusingSharon 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... - Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approachSharon 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.... - Proteomics and human embryonic stem cellsDennis 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... - Phosphorylation dynamics during early differentiation of human embryonic stem cellsDennis 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... - GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7Jan 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... - Targeted analysis of protein terminiWilma 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... - Mass spectrometry-based quantitative proteomicsAlbert 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... - Mass spectrometric analysis of the Schistosoma mansoni tegumental sub-proteomeBas 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... - Proteome biology of stem cells: a new joint HUPO and ISSCR initiativeJeroen Krijgsveld
Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
Mol Cell Proteomics 7:204-5. 2008 - Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafishHsin 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... - Identification of secreted cysteine proteases from the parasitic nematode Haemonchus contortus detected by biotinylated inhibitorsAna 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... - A P4-ATPase protein interaction network reveals a link between aminophospholipid transport and phosphoinositide metabolismCatheleyne 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... - Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomicsEdwin 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.... - Immediate protein targets of photodynamic treatment in carcinoma cellsPavel 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... - Searching for proteins of Mycobacterium avium subspecies paratuberculosis with diagnostic potential by comparative qualitative proteomic analysis of mycobacterial tuberculinsWiebren Santema
Department of Infectious Diseases and Immunology, Immunology Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
Vet Microbiol 138:191-6. 2009.... - Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexesLisette 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... - An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomicsDennis Van Hoof
Nat Methods 4:677-8. 2007 - A high-quality catalog of the Drosophila melanogaster proteomeErich 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... - The time is right: proteome biology of stem cellsAnthony 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... - Embryonic stem cell proteomicsDennis 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... - Mass spectrometric identification of human prostate cancer-derived proteins in serum of xenograft-bearing miceGert-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.... - A quest for human and mouse embryonic stem cell-specific proteinsDennis 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... - Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cellsMaaike 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... - Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer researchPatrick 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... - Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic miceErnie 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...