Albert J R Heck

Summary

Affiliation: Utrecht University
Country: The Netherlands

Publications

  1. doi request reprint The impact of mass spectrometry on the study of intact antibodies: from post-translational modifications to structural analysis
    Natalie J Thompson
    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
    Chem Commun (Camb) 49:538-48. 2013
  2. pmc Perspectives in stem cell proteomics
    Javier Munoz
    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
    Genome Med 1:45. 2009
  3. pmc Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
    Jos Boekhorst
    Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, The Netherlands
    Genome Biol 9:R144. 2008
  4. pmc Mapping of citrullinated fibrinogen B-cell epitopes in rheumatoid arthritis by imaging surface plasmon resonance
    Joyce J B C van Beers
    Department of Biomolecular Chemistry, Nijmegen Center for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University, PO Box 9101, NL 6500 HB Nijmegen, The Netherlands
    Arthritis Res Ther 12:R219. 2010
  5. pmc Hydrophilic interaction liquid chromatography (HILIC) in proteomics
    Paul J Boersema
    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
    Anal Bioanal Chem 391:151-9. 2008
  6. doi request reprint Proteome biology of stem cells
    Albert J R Heck
    Utrecht University, The Netherlands
    Stem Cell Res 1:7-8. 2007
  7. doi request reprint Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo
    Simone Lemeer
    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 7:1555-64. 2008
  8. doi request reprint Native mass spectrometry: a bridge between interactomics and structural biology
    Albert J R Heck
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nat Methods 5:927-33. 2008
  9. doi request reprint Comparative multiplexed mass spectrometric analyses of endogenously expressed yeast nuclear and cytoplasmic exosomes
    Silvia A Synowsky
    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 Mol Biol 385:1300-13. 2009
  10. ncbi request reprint cGMP-binding prepares PKG for substrate binding by disclosing the C-terminal domain
    Vera Alverdi
    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 Mol Biol 375:1380-93. 2008

Detail Information

Publications138 found, 100 shown here

  1. doi request reprint The impact of mass spectrometry on the study of intact antibodies: from post-translational modifications to structural analysis
    Natalie J Thompson
    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
    Chem Commun (Camb) 49:538-48. 2013
    ..Here, we review several MS-based techniques that have emerged for the analysis of intact mAbs and discuss the prospects of using these technologies for the analysis of biopharmaceuticals...
  2. pmc Perspectives in stem cell proteomics
    Javier Munoz
    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
    Genome Med 1:45. 2009
    ..ABSTRACT : A brief report on the Perspectives in Stem Cell Proteomics Conference, Hinxton, UK, 22-23 March, 2009...
  3. pmc Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
    Jos Boekhorst
    Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, The Netherlands
    Genome Biol 9:R144. 2008
    ..Here, we exploit these novel data for the comparative analysis of phosphorylation events between different species of eukaryotes...
  4. pmc Mapping of citrullinated fibrinogen B-cell epitopes in rheumatoid arthritis by imaging surface plasmon resonance
    Joyce J B C van Beers
    Department of Biomolecular Chemistry, Nijmegen Center for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University, PO Box 9101, NL 6500 HB Nijmegen, The Netherlands
    Arthritis Res Ther 12:R219. 2010
    ..To obtain insight into the B-cell response to citrullinated fibrinogen in RA, its autoepitopes were systematically mapped using a new methodology...
  5. pmc Hydrophilic interaction liquid chromatography (HILIC) in proteomics
    Paul J Boersema
    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
    Anal Bioanal Chem 391:151-9. 2008
    ..Recent work has revealed that HILIC may provide an excellent alternative to SCX, possessing several advantages in the area of separation power and targeted analysis of protein post-translational modifications. [figure: see text]..
  6. 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...
  7. doi request reprint Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo
    Simone Lemeer
    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 7:1555-64. 2008
    ..These alignments revealed conservation of phosphorylation sites in several proteins suggesting preserved function in embryonic development...
  8. doi request reprint Native mass spectrometry: a bridge between interactomics and structural biology
    Albert J R Heck
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nat Methods 5:927-33. 2008
    ..I also describe current experimental challenges in native mass spectrometry, encouraging readers to contribute to solutions...
  9. doi request reprint Comparative multiplexed mass spectrometric analyses of endogenously expressed yeast nuclear and cytoplasmic exosomes
    Silvia A Synowsky
    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 Mol Biol 385:1300-13. 2009
    ..We show that the nuclear exosome selectively copurifies with the alpha/beta importin heterodimer, which is known to be involved in the transport of proteins across the nuclear membrane...
  10. ncbi request reprint cGMP-binding prepares PKG for substrate binding by disclosing the C-terminal domain
    Vera Alverdi
    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 Mol Biol 375:1380-93. 2008
    ..More surprisingly, our data revealed a specific disclosure of the substrate-binding region of holo-PKG, shedding new light into the kinase-activation process of PKG...
  11. pmc Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels
    Andreas O Helbig
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
    BMC Genomics 11:685. 2010
    ..Using a yeast nat3Δ strain, deficient for the catalytic subunit of NatB, we employed a quantitative proteomics strategy to identify NatB substrates and to characterize downstream effects in nat3Δ...
  12. pmc Selectivity in enrichment of cAMP-dependent protein kinase regulatory subunits type I and type II and their interactors using modified cAMP affinity resins
    Thin Thin Aye
    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
    Mol Cell Proteomics 8:1016-28. 2009
    ..For some of these AKAPs our data provide the first insights into their specificity...
  13. doi request reprint A three-way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions
    Andreas O Helbig
    Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Proteomics 9:4787-98. 2009
    ..In addition, this latter approach allowed screening for possible novel complex interaction partners, since for example protein Aim38p, with a yet unknown function, was identified as a possible component of respiratory chain complex IV...
  14. doi request reprint Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography
    Houjiang Zhou
    Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nat Protoc 8:461-80. 2013
    ..It takes ∼2 weeks to complete the protocol: 1 week to prepare the Ti(4+)-IMAC material, 2 d for sample preparation, 3 d for MS analysis of the enriched sample and 2 d for data analysis...
  15. doi request reprint Probing the specificity of protein-protein interactions by quantitative chemical proteomics
    Duangnapa Kovanich
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
    Methods Mol Biol 803:167-81. 2012
    ..With this tool, several novel PKA-R/AKAP specificities can be easily resolved...
  16. pmc In-depth quantitative cardiac proteomics combining electron transfer dissociation and the metalloendopeptidase Lys-N with the SILAC mouse
    Arjen Scholten
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
    Mol Cell Proteomics 10:O111.008474. 2011
    ....
  17. ncbi request reprint Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes
    Marco J L de Groot
    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
    Microbiology 153:3864-78. 2007
    ....
  18. ncbi request reprint Protein flexibility and ligand rigidity: a thermodynamic and kinetic study of ITAM-based ligand binding to Syk tandem SH2
    Nico J de Mol
    Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University UIPS, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Chembiochem 6:2261-70. 2005
    ..Such a bivalent binding model allows high affinity and fast dissociation kinetics, which are very important in transient signal-transduction processes...
  19. pmc Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome
    Andreas O Helbig
    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
    Mol Cell Proteomics 9:928-39. 2010
    ..cerevisiae and H. salinarum is predominantly a serine. Genome-wide comparisons revealed that this effect is not related to protein N-terminal processing but can be traced back to characteristics of the genome...
  20. doi request reprint Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants
    Sharon C Mithoe
    Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
    J Proteome Res 11:438-48. 2012
    ..These include a set of 3 well-characterized flagellin responsive MAP kinases and 4 novel MAP kinases. With this targeted approach, we elucidate a new level of complexity in flagellin-induced MAP kinase activation...
  21. ncbi request reprint Tandem mass spectrometry of intact GroEL-substrate complexes reveals substrate-specific conformational changes in the trans ring
    Esther van Duijn
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    J Am Chem Soc 128:4694-702. 2006
    ....
  22. 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...
  23. doi request reprint The influence of the acyl chain composition of cardiolipin on the stability of mitochondrial complexes; an unexpected effect of cardiolipin in alpha-ketoglutarate dehydrogenase and prohibitin complexes
    Renske A van Gestel
    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
    J Proteomics 73:806-14. 2010
    ..The results indicate that the decreased level of complexes in taz1Delta and acb1Deltataz1Delta mitochondria is due to a decreased content of CL or the presence of MLCL...
  24. doi request reprint Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates
    Paul J Boersema
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan, Utrecht, The Netherlands
    Proteomics 8:4624-32. 2008
    ..Thereby, differences in abundance ratio of more than two orders of magnitude could be quantified...
  25. doi 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...
  26. doi request reprint Quantitative proteome and phosphoproteome analysis of human pluripotent stem cells
    Javier Munoz
    Bijvoet Center for Biomolecular Research, Biomolecular Mass Spectrometry and Proteomics Group, Utrecht, The Netherlands
    Methods Mol Biol 767:297-312. 2011
    ..This systems-biology-based approach provides new insights into how human pluripotent stem cells exit the pluripotent state...
  27. 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
    ....
  28. pmc Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue-specific diversity
    Reinout Raijmakers
    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
    Mol Cell Proteomics 7:1755-62. 2008
    ....
  29. ncbi request reprint Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster
    Martijn W H Pinkse
    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 7:687-97. 2008
    ..Still, as the online approach allows the complementary measurements of phosphopeptides and their nonphosphorylated counterparts in subsequent analyses, this method is well-suited for automated quantitative phosphoproteomics...
  30. pmc Evaluating experimental bias and completeness in comparative phosphoproteomics analysis
    Jos Boekhorst
    Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
    PLoS ONE 6:e23276. 2011
    ....
  31. doi request reprint Targeted phosphotyrosine profiling of glycoprotein VI signaling implicates oligophrenin-1 in platelet filopodia formation
    Onno B Bleijerveld
    Biomolecular Mass Spectrometry and Proteomics and Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Arterioscler Thromb Vasc Biol 33:1538-43. 2013
    ..Here, we explore phosphotyrosine signaling events downstream of GPVI with site-specific detail...
  32. doi request reprint Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity
    Jeffrey H Ringrose
    Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Nat Commun 4:1408. 2013
    ..Together, this Trichoplax proteomics data set offers significant new insight into the mechanisms underlying the emergence of metazoan multicellularity and provides a resource for interested researchers...
  33. doi request reprint The diversity of protein turnover and abundance under nitrogen-limited steady-state conditions in Saccharomyces cerevisiae
    Andreas O Helbig
    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
    Mol Biosyst 7:3316-26. 2011
    ..These data stress the need for inclusion of quantitative data of protein turn-over rates in yeast systems biology...
  34. ncbi request reprint Investigating the dynamic nature of the interactions between nuclear proteins and histones upon DNA damage using an immobilized peptide chemical proteomics approach
    Eef H C Dirksen
    Department of Biomolecular Mass Spectrometry, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    J Proteome Res 5:2380-8. 2006
    ....
  35. doi request reprint Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites
    Shabaz Mohammed
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Anal Chem 80:3584-92. 2008
    ..The described multiplexed proteomics approach is generic and reveals that it is possible to map a protein complex to near completion while applying less than 5 mug (approximately 10 pmol) of total starting material...
  36. doi request reprint Sphingosine kinase interacting protein is an A-kinase anchoring protein specific for type I cAMP-dependent protein kinase
    Duangnapa Kovanich
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center forBiomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
    Chembiochem 11:963-71. 2010
    ..Being the first mammalian PKA-RI-specific AKAP with cytosolic localization, SPHKAP is a very promising model for studying the function of the less explored cytosolic PKA-RI signaling nodes...
  37. doi request reprint Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer
    Reinout Raijmakers
    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
    Anal Chem 82:824-32. 2010
    ....
  38. doi request reprint Assessing biological variation and protein processing in primary human leukocytes by automated multiplex stable isotope labeling coupled to 2 dimensional peptide separation
    Reinout Raijmakers
    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
    Mol Biosyst 5:992-1003. 2009
    ..This dataset represents the largest quantitative dataset for human leukocytes proteins, which was made possible by the use of an automated labeling strategy...
  39. doi request reprint In-depth profiling of post-translational modifications on the related transcription factor complexes TFIID and SAGA
    Nikolai Mischerikow
    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 8:5020-30. 2009
    ....
  40. pmc Efficient IgM assembly and secretion require the plasma cell induced endoplasmic reticulum protein pERp1
    Eelco van Anken
    Cellular Protein Chemistry and Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
    Proc Natl Acad Sci U S A 106:17019-24. 2009
    ..pERp1 emerged as a dedicated folding factor for IgM, associating with both heavy and light chains and promoting assembly and secretion of mature IgM...
  41. doi request reprint Quantitative erythrocyte membrane proteome analysis with Blue-native/SDS PAGE
    Renske A van Gestel
    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 Proteomics 73:456-65. 2010
    ..This approach provides a new tool to detect potential biomarkers and can contribute to an improved understanding of the causes of erythrocyte membrane defects in patients suffering from hemolytic anemia...
  42. doi request reprint High precision platelet releasate definition by quantitative reversed protein profiling--brief report
    Patrick Wijten
    Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Arterioscler Thromb Vasc Biol 33:1635-8. 2013
    ..Here, we present a reversed releasate proteomics approach to determine unambiguously and quantitatively proteins released from activated platelets...
  43. doi request reprint Reorganized PKA-AKAP associations in the failing human heart
    Thin Thin Aye
    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
    J Mol Cell Cardiol 52:511-8. 2012
    ..This article is part of a Special Issue entitled "Local Signaling in Myocytes"...
  44. pmc Database independent proteomics analysis of the ostrich and human proteome
    A F Maarten Altelaar
    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
    Proc Natl Acad Sci U S A 109:407-12. 2012
    ....
  45. 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...
  46. doi request reprint Strong cation exchange-based fractionation of Lys-N-generated peptides facilitates the targeted analysis of post-translational modifications
    Nadia Taouatas
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands Proteomics Centre, Utrecht, The Netherlands
    Mol Cell Proteomics 8:190-200. 2009
    ..Overall, the combination of Lys-N proteolysis, low-pH strong cation exchange, and reversed phase separation, with CID and ETD induced fragmentation, adds a new very powerful method to the toolbox of proteomic analyses...
  47. pmc Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS
    Maria Chiara Monti
    Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nucleic Acids Res 39:8052-64. 2011
    ..PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates...
  48. pmc Mode of action of cGMP-dependent protein kinase-specific inhibitors probed by photoaffinity cross-linking mass spectrometry
    Martijn W H Pinkse
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands
    J Biol Chem 284:16354-68. 2009
    ....
  49. 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
    ....
  50. 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...
  51. doi request reprint Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides
    Salvatore Cappadona
    BiomolecularMass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, CH Utrecht, The Netherlands
    J Proteomics 74:2204-9. 2011
    ..In addition, we present a tool that can correct overlapping issues when they arise which is based on modeling isotopic distributions. We demonstrate that our approach leads to improved accuracy and precision of protein quantification...
  52. pmc In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling
    Paul J Boersema
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Mol Cell Proteomics 9:84-99. 2010
    ..Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated...
  53. doi request reprint LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation
    Bas van Breukelen
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Proteomics 10:1196-201. 2010
    ..Results of similar quantity and quality could also be obtained on a much more extensive experimental dataset, illustrating the potential for higher throughput de novo sequencing using these methods...
  54. ncbi request reprint Analysis of protein-protein interaction surfaces using a combination of efficient lysine acetylation and nanoLC-MALDI-MS/MS applied to the E9:Im9 bacteriotoxin--immunity protein complex
    Arjen Scholten
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    J Am Soc Mass Spectrom 17:983-94. 2006
    ..These findings may illustrate some of the described differences in the solution-phase structure of the E9:Im9 complex compared with the crystal structure...
  55. pmc Distinct conformational stability and functional activity of four highly homologous endonuclease colicins
    Ewald T J van den Bremer
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, The Netherlands e t j
    Protein Sci 13:1391-401. 2004
    ....
  56. ncbi request reprint Selective enrichment of Ser-/Thr-phosphorylated peptides in the presence of Ser-/Thr-glycosylated peptides
    Alex J Poot
    Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Proteomics 6:6394-9. 2006
    ..This is the first report of selective beta-elimination and enrichment of phosphorylated peptides in the presence of glycosylated peptides...
  57. pmc Interactions of Kid-Kis toxin-antitoxin complexes with the parD operator-promoter region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid-Kis oligomers
    Maria C Monti
    Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Nucleic Acids Res 35:1737-49. 2007
    ..Upon increasing the Kis concentration, (Kid2-Kis2)n complexes repress the kid-kis operon...
  58. doi request reprint Toward a comprehensive characterization of a human cancer cell phosphoproteome
    Houjiang Zhou
    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
    J Proteome Res 12:260-71. 2013
    ..In summary, we demonstrate the need to carry out extensive fractionation for deep mining of the phosphoproteome and provide a guide for appropriate strategies depending on sample amount and/or analysis time...
  59. pmc Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa
    Esther van Duijn
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Mol Cell Proteomics 11:1430-41. 2012
    ..coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes...
  60. pmc Depletion of phosphatidylcholine in yeast induces shortening and increased saturation of the lipid acyl chains: evidence for regulation of intrinsic membrane curvature in a eukaryote
    Henry A Boumann
    Department of Biochemistry of Membranes, Bijvoet Institute, Utrecht University, 3584 CH Utrecht, The Netherlands
    Mol Biol Cell 17:1006-17. 2006
    ..The shortening and increased saturation of the PE acyl chains were shown to decrease the nonbilayer propensity of PE. The results point to a regulatory mechanism in yeast that maintains intrinsic membrane curvature in an optimal range...
  61. ncbi request reprint The yeast phospholipid N-methyltransferases catalyzing the synthesis of phosphatidylcholine preferentially convert di-C16:1 substrates both in vivo and in vitro
    Henry A Boumann
    Department Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Padualaan 8, 3584 CH Utrecht, The Netherlands
    J Biol Chem 279:40314-9. 2004
    ..The combined results indicate that the selective methylation of PE species by the methyltransferases plays an important role in shaping the steady-state profile of PC molecular species in yeast...
  62. pmc The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells
    Javier Munoz
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Mol Syst Biol 7:550. 2011
    ....
  63. doi request reprint Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra
    Erik L de Graaf
    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
    J Proteome Res 10:4334-41. 2011
    ....
  64. pmc Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment
    Houjiang Zhou
    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
    Mol Cell Proteomics 10:M110.006452. 2011
    ..Collectively, our data show that the combination of SCX and Ti(4+)-IMAC is particularly advantageous for phosphopeptides with multiple basic residues...
  65. doi request reprint Evaluation of the deuterium isotope effect in zwitterionic hydrophilic interaction liquid chromatography separations for implementation in a quantitative proteomic approach
    Serena Di Palma
    Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Anal Chem 83:8352-6. 2011
    ..We demonstrate that our approach is suitable to perform unbiased quantitative proteome analysis, still quantifying more than 2500 proteins when analyzing only a few micrograms of sample...
  66. ncbi request reprint Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: a proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acid
    Edwin P Romijn
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, The Netherlands
    Mol Cell Proteomics 4:1297-310. 2005
    ..The quality of the quantitative data allowed us to even identify subclusters within functionally related classes of proteins such as in the endoplasmic reticulum proteins that are involved in antibody production...
  67. pmc Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase
    Paul J Boersema
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
    Mol Cell Proteomics 8:650-60. 2009
    ..We therefore conclude that this method that combines Lys-N, strong cation exchange enrichment, and MALDI-MS/MS analysis provides a valuable alternative proteomics strategy...
  68. 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...
  69. 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...
  70. pmc Phosphorylation of Not4p functions parallel to BUR2 to regulate resistance to cellular stresses in Saccharomyces cerevisiae
    Nga Chi Lau
    Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands
    PLoS ONE 5:e9864. 2010
    ..The evolutionarily conserved Ccr4-Not and Bur1/2 kinase complexes are functionally related in Saccharomyces cerevisiae. In this study, we further explore the relationship between the subunits Not4p and Bur2p...
  71. doi request reprint Proteome-wide protein concentrations in the human heart
    Thin Thin Aye
    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
    Mol Biosyst 6:1917-27. 2010
    ..The obtained quantitative protein library of the human left ventricle is a valuable resource to isolate signaling based, putative biomarkers with concentrations likely to be detectable in plasma...
  72. pmc Subunit exchange rates in Hepatitis B virus capsids are geometry- and temperature-dependent
    Charlotte Uetrecht
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Phys Chem Chem Phys 12:13368-71. 2010
    ..Native tandem mass spectrometry reveals marked differences in the rates at which the two polymorphic forms of the HBV capsid exchange dimeric subunits with the soluble pool...
  73. 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
  74. doi request reprint aPKC phosphorylates NuMA-related LIN-5 to position the mitotic spindle during asymmetric division
    Matilde Galli
    Developmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
    Nat Cell Biol 13:1132-8. 2011
    ..This molecular interaction between polarity and spindle-positioning proteins may be used broadly in cell cleavage plane determination...
  75. pmc Protein-tyrosine kinase activity profiling in knock down zebrafish embryos
    Simone Lemeer
    Hubrecht Institute, Utrecht, Netherlands Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
    PLoS ONE 2:e581. 2007
    ....
  76. 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...
  77. doi request reprint Dimethyl isotope labeling assisted de novo peptide sequencing
    Marco L Hennrich
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    J Am Soc Mass Spectrom 21:1957-65. 2010
    ....
  78. pmc Stability and shape of hepatitis B virus capsids in vacuo
    Charlotte Uetrecht
    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
    Angew Chem Int Ed Engl 47:6247-51. 2008
  79. doi request reprint Chip-Based Enrichment and NanoLC-MS/MS Analysis of Phosphopeptides from Whole Lysates
    Shabaz Mohammed
    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 7:1565-71. 2008
    ..Such a design proved robust, easy to use, and was capable of consistent performance over tens of analyses including minute amounts of complex cellular lysates...
  80. doi request reprint 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
    ..The labeling steps take approximately 60-90 min, whereas the full protocol including digestion and (two-dimensional) liquid chromatography-mass spectrometry takes approximately 1.5-3 days to complete...
  81. ncbi request reprint Surface-plasmon-resonance-based chemical proteomics: efficient specific extraction and semiquantitative identification of cyclic nucleotide-binding proteins from cellular lysates by using a combination of surface plasmon resonance, sequential elution and
    Natasja F C Visser
    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
    Chembiochem 8:298-305. 2007
    ..The data show that SPR-based chemical proteomics is a promising alternative for the efficient specific extraction and quantitative identification of small-molecule-binding proteins from complex mixtures...
  82. pmc Proteome analysis of yeast response to various nutrient limitations
    Annemieke Kolkman
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Mol Syst Biol 2:2006.0026. 2006
    ..These observations underline the need for multilevel analysis in yeast systems biology...
  83. doi request reprint A chemical proteomics based enrichment technique targeting the interactome of the PDE5 inhibitor PF-4540124
    Poupak Dadvar
    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
    Mol Biosyst 5:472-82. 2009
    ..The presented method provides a generic highly-specific chemical proteomics based enrichment technique for analyzing drug-protein interactions in mammalian tissue lysates...
  84. doi request reprint Interrogating viral capsid assembly with ion mobility-mass spectrometry
    Charlotte Uetrecht
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Nat Chem 3:126-32. 2011
    ..Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids...
  85. 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...
  86. doi request reprint The phosphoproteomics data explosion
    Simone Lemeer
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, The Netherlands
    Curr Opin Chem Biol 13:414-20. 2009
    ....
  87. ncbi request reprint Development of a novel chemical probe for the selective enrichment of phosphorylated serine- and threonine-containing peptides
    Pieter Van der Veken
    Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P O BOX 80082, 3508 TB Utrecht, The Netherlands
    Chembiochem 6:2271-80. 2005
    ..During the development of the beta-elimination/nucleophilic addition protocol, special attention was paid to the different experimental parameters that might affect the chemical-modification steps carried out on phosphorylated residues...
  88. doi request reprint StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
    Bas van Breukelen
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrech, The Netherlands
    Bioinformatics 25:1472-3. 2009
    ..StatQuant offers the researcher post-processing methods to achieve improved confidence on the obtained protein ratios. AVAILABILITY: StatQuant can be downloaded from: (https://gforge.nbic.nl/projects/statquant/) (binary and source code)...
  89. doi request reprint Surface plasmon resonance mass spectrometry in proteomics
    Natasja F C Visser
    Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Expert Rev Proteomics 5:425-33. 2008
    ..We evaluate the current possibilities and limitations and discuss the future developments of the SPR-MS technique...
  90. ncbi request reprint 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...
  91. 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...
  92. 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
    ....
  93. ncbi request reprint Changes in structural dynamics of the Grb2 adaptor protein upon binding of phosphotyrosine ligand to its SH2 domain
    Nico J de Mol
    Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P O BOX 80082, Sorbonnelaan 16, 3508 TB Utrecht, The Netherlands
    Biochim Biophys Acta 1700:53-64. 2004
    ....
  94. doi request reprint Exploring the membrane proteome--challenges and analytical strategies
    Andreas O Helbig
    Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    J Proteomics 73:868-78. 2010
    ..Finally, we discuss approaches to target membrane-protein complexes and lipid-protein interactions, as such approaches offer unique insights into function and architecture of cellular membranes...
  95. ncbi request reprint Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns
    Martijn W H Pinkse
    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
    Anal Chem 76:3935-43. 2004
    ..These results clearly show that TiO(2) has strong affinity for phosphorylated peptides, and thus, we conclude that this material has a high potential in the field of phosphoproteomics...
  96. ncbi request reprint Endogenous phosphotyrosine signaling in zebrafish embryos
    Simone Lemeer
    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
    Mol Cell Proteomics 6:2088-99. 2007
    ..Our experiments are the first to show that global tyrosine phosphorylation-mediated signaling can be studied at endogenous levels in complex multicellular organisms...
  97. doi request reprint Human Ccr4-Not complexes contain variable deadenylase subunits
    Nga Chi Lau
    Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands
    Biochem J 422:443-53. 2009
    ..Taken together, human Ccr4-Not complexes are heterogeneous in composition owing to differences in their deadenylase subunits, which may reflect the multi-functionality of these complexes in cellular processes...
  98. ncbi request reprint Identification of proteins in activated human neutrophils susceptible to tyrosyl radical attack. A proteomic study using a tyrosylating fluorophore
    Diana Avram
    Department of Biochemistry of Lipids, Center for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, The Netherlands
    Proteomics 4:2397-407. 2004
    ..This study shows that human neutrophils can modulate their proteome via a tyrosine oxidation pathway induced by pro-inflammatory mediators...
  99. ncbi request reprint Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol
    Annemieke Kolkman
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, The Netherlands
    Mol Cell Proteomics 4:1-11. 2005
    ..Importantly, we show here that the combined approach of chemostat cultivation and comprehensive proteome analysis allowed us to study the primary effect of single limiting conditions on the yeast proteome...
  100. 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...
  101. 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
    ....