A J Heck

Summary

Affiliation: Utrecht University
Country: The Netherlands

Publications

  1. 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
  2. ncbi request reprint Modification and inhibition of vancomycin group antibiotics by formaldehyde and acetaldehyde
    A J Heck
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    Chemistry 7:910-6. 2001
  3. ncbi request reprint Investigation of intact protein complexes by mass spectrometry
    Albert J R Heck
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    Mass Spectrom Rev 23:368-89. 2004
  4. 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
  5. 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
  6. 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
  7. ncbi request reprint Cofactor-dependent assembly of the flavoenzyme vanillyl-alcohol oxidase
    Nora Tahallah
    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 Biol Chem 277:36425-32. 2002
  8. 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
  9. ncbi request reprint Formation and efficacy of vancomycin group glycopeptide antibiotic stereoisomers studied by capillary electrophoresis and bioaffinity mass spectrometry
    P J Bonnici
    Department of Biomolecular Mass Spectrometry, Utrecht University, The Netherlands
    Anal Biochem 290:292-301. 2001
  10. 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

Detail Information

Publications87

  1. 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...
  2. ncbi request reprint Modification and inhibition of vancomycin group antibiotics by formaldehyde and acetaldehyde
    A J Heck
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    Chemistry 7:910-6. 2001
    ....
  3. ncbi request reprint Investigation of intact protein complexes by mass spectrometry
    Albert J R Heck
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
    Mass Spectrom Rev 23:368-89. 2004
    ..In this review, we describe some of the latest developments and several highlights...
  4. 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...
  5. 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...
  6. 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...
  7. ncbi request reprint Cofactor-dependent assembly of the flavoenzyme vanillyl-alcohol oxidase
    Nora Tahallah
    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 Biol Chem 277:36425-32. 2002
    ..We speculate that upon FAD binding, small conformational changes in the ADP-binding pocket of the dimeric VAO species are transmitted to the protein surface, promoting oligomerization...
  8. 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...
  9. ncbi request reprint Formation and efficacy of vancomycin group glycopeptide antibiotic stereoisomers studied by capillary electrophoresis and bioaffinity mass spectrometry
    P J Bonnici
    Department of Biomolecular Mass Spectrometry, Utrecht University, The Netherlands
    Anal Biochem 290:292-301. 2001
    ..Minimum inhibitory concentrations (Micrococcus flavus) were determined and confirmed the decrease in antibacterial efficacy upon heating...
  10. 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...
  11. ncbi request reprint Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling
    Annemieke Kolkman
    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 4:255-66. 2005
    ..89. Although the correlation between DiGE and metabolic stable isotope labeling is exceptionally good, we do observe and discuss (dis)advantages of both methods as well as in relation to other (quantitative) approaches...
  12. 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...
  13. ncbi request reprint Ligand-induced changes in the conformational dynamics of a bacterial cytotoxic endonuclease
    Ewald T J van den Bremer
    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
    Biochemistry 43:4347-55. 2004
    ..Furthermore, the results point out that the Im9-induced changes in the conformational dynamics of E9 DNase are predominant and occur independently of the Zn(2+)-induced conformational effects...
  14. pmc Probing metal ion binding and conformational properties of the colicin E9 endonuclease by electrospray ionization time-of-flight mass spectrometry
    Ewald T J van den Bremer
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Protein Sci 11:1738-52. 2002
    ..In addition, our metal ion binding studies and gas-phase dissociation experiments of the ternary E9 DNase-Zn(2+)-Im9 complex have provided further evidence that electrostatic interactions govern the gas phase ion stability...
  15. 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
    ....
  16. 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...
  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. pmc Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry
    Robert H H van den Heuvel
    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
    Nucleic Acids Res 33:e96. 2005
    ..The method described is of general use to analyze the reactivity and specificity of nucleases...
  19. ncbi request reprint The two biosynthetic routes leading to phosphatidylcholine in yeast produce different sets of molecular species. Evidence for lipid remodeling
    Henry A Boumann
    Department of Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Biochemistry 42:3054-9. 2003
    ..Remodeling was found to be required to generate the steady-state species distribution of PC. This is the first study demonstrating a functional difference between the two biosynthetic routes in yeast...
  20. ncbi request reprint Coenzyme binding during catalysis is beneficial for the stability of 4-hydroxyacetophenone monooxygenase
    Robert H H van den Heuvel
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University
    J Biol Chem 280:32115-21. 2005
    ..The interaction with the coenzyme analog 3-aminopyridine adenine dinucleotide phosphate (AADP(+)) strongly enhanced the thermal stability of wild type HAPMO. This coenzyme-induced stabilization may also be important for related enzymes...
  21. ncbi request reprint Development and application of proteomics technologies in Saccharomyces cerevisiae
    Annemieke Kolkman
    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
    Trends Biotechnol 23:598-604. 2005
    ..The model system Saccharomyces cerevisiae is considered to be the optimal vehicle for proteomics and we review studies investigating yeast adaptation to changes in (nutritional) environment...
  22. 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...
  23. 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...
  24. ncbi request reprint The selective utilization of substrates in vivo by the phosphatidylethanolamine and phosphatidylcholine biosynthetic enzymes Ept1p and Cpt1p in yeast
    Henry A Boumann
    Department Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Padualaan 8, 3584 CH Utrecht, The Netherlands
    FEBS Lett 569:173-7. 2004
    ....
  25. 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...
  26. ncbi request reprint Interaction of the K+ channel KcsA with membrane phospholipids as studied by ESI mass spectrometry
    Jeroen A A Demmers
    Department of Biochemistry of Membranes, Center for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, The Netherlands
    FEBS Lett 541:28-32. 2003
    ..These preferred interactions may reflect the differences in affinity of these phospholipids for KcsA in the membrane...
  27. 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...
  28. ncbi request reprint Structural studies on flavin reductase PheA2 reveal binding of NAD in an unusual folded conformation and support novel mechanism of action
    Robert H H van den Heuvel
    Department of Genetics and Microbiology, University of Pavia, via Abbiategrasso 207, 27100 Pavia, Italy
    J Biol Chem 279:12860-7. 2004
    ..In conclusion, the structural data provide evidence that PheA2 contains a dual binding cleft for NADH and FAD substrate, which alternate during catalysis...
  29. 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
    ....
  30. ncbi request reprint Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination
    Jeroen A A Demmers
    Contribution from the 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 Am Chem Soc 124:11191-8. 2002
    ..e., protonated B and Y' ' ions, and sodiated A and Y' ions). Our results strongly suggest that scrambling may be reduced by using alkali metal cationization instead of protonation in the ionization process...
  31. 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...
  32. 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...
  33. ncbi request reprint Lipid II is an intrinsic component of the pore induced by nisin in bacterial membranes
    Eefjan Breukink
    Center of Biomembranes and Lipid Enzymology, Department of Biochemistry of Membranes, Institute for Biomembranes, University of Utrecht, Padualaan 8 3584 CH Utrecht, The Netherlands
    J Biol Chem 278:19898-903. 2003
    ..We show here that Lipid II is not only the receptor for nisin but an intrinsic component of the pore formed by nisin, and we present a new model for the pore complex that includes Lipid II...
  34. 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...
  35. 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...
  36. ncbi request reprint Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex
    Silvia A Synowsky
    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 5:1581-92. 2006
    ..The described multiplexed mass spectrometry-based procedure is generic and thus applicable to many different types of cellular molecular machineries even if they are expressed at endogenous levels...
  37. 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...
  38. 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
    ....
  39. 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...
  40. 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
    ....
  41. 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
    ....
  42. 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...
  43. 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...
  44. 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
    ....
  45. 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...
  46. ncbi request reprint Native protein mass spectrometry: from intact oligomers to functional machineries
    Robert H H van den Heuvel
    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
    Curr Opin Chem Biol 8:519-26. 2004
    ....
  47. pmc Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides
    Berend Jan Bosch
    Division of Virology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, and Institute of Biomembranes, Utrecht University, 3584 CL Utrecht, The Netherlands
    Proc Natl Acad Sci U S A 101:8455-60. 2004
    ..The inhibitory potency of the SARS-CoV HR2-peptides provides an attractive basis for the development of a therapeutic drug for SARS...
  48. 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
    ....
  49. 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...
  50. 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...
  51. 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...
  52. 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
    ....
  53. 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...
  54. 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
    ....
  55. 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)...
  56. pmc The yeast Ski complex is a hetero-tetramer
    Silvia A Synowsky
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Protein Sci 17:119-25. 2008
    ..Combining all data we construct an improved structural model of the Ski complex...
  57. ncbi request reprint Sequential waves of functionally related proteins are expressed when B cells prepare for antibody secretion
    Eelco van Anken
    Department of Bio organic Chemistry 1, Bijvoet Center, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
    Immunity 18:243-53. 2003
    ..Metabolic capacity and secretory machinery expand first to accommodate the mass production of IgM that follows...
  58. pmc Regulated increase in folding capacity prevents unfolded protein stress in the ER
    Chantal Christis
    Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
    J Cell Sci 123:787-94. 2010
    ..Thyrocytes set an example of physiological adaptation of cells to a future potentially stress-causing situation, which suggests a general strategy for both non-secretory and specialized secretory cells...
  59. 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...
  60. doi request reprint Ion mobility mass spectrometry of proteins and protein assemblies
    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
    Chem Soc Rev 39:1633-55. 2010
    ..Here, we critically review the development, instrumentation, approaches and applications of ion mobility in combination with mass spectrometry, focusing on the analysis of larger proteins and protein assemblies (185 references)...
  61. 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...
  62. ncbi request reprint Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy
    Paul J Boersema
    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 6:937-46. 2007
    ..With this extended flexibility, we conclude that ZIC-HILIC is a very good alternative for the more conventional SCX in multidimensional peptide separation strategies...
  63. ncbi request reprint Transcriptional activation by CprK1 is regulated by protein structural changes induced by effector binding and redox state
    Hortense Mazon
    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 Biol Chem 282:11281-90. 2007
    ....
  64. ncbi request reprint Uptake and remodeling of exogenous phosphatidylethanolamine in E. coli
    Matthijs A Kol
    Department of Biochemistry of Membranes, Institute of Biomembranes, Ctr Biomem and Lipid Enz CBLE, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Biochim Biophys Acta 1636:205-12. 2004
    ....
  65. ncbi request reprint The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-of-flight instrument
    N Tahallah
    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
    Rapid Commun Mass Spectrom 15:596-601. 2001
    ..This pressure effect should be carefully addressed when relating ion abundance in the mass spectra to solution phase abundance of noncovalent protein assemblies...
  66. ncbi request reprint Stability of thioTEPA and its metabolites, TEPA, monochloroTEPA and thioTEPA-mercapturate, in plasma and urine
    M J van Maanen
    Department of Pharmaceutical Analysis, Faculty of Pharmacy, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands
    Int J Pharm 200:187-94. 2000
    ..The monochloro derivative of thioTEPA-mercapturate was formed in urine, whereas for monochloroTEPA no degradation products could be detected...
  67. ncbi request reprint Robust and cost-effective capillary electrophoresis-mass spectrometry interfaces suitable for combination with on-line analyte preconcentration
    J C Waterval
    Faculty of Pharmacy, Department of Biomedical Analysis, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, The Netherlands
    Electrophoresis 22:2701-8. 2001
    ..The described setup has a wide applicability as is demonstrated by the analysis of larger peptides, such as insulin and cytochrome c. Detailed information is given on critical factors in the preparation of the described interfaces...
  68. 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...
  69. ncbi request reprint Macromolecular assembly of Helicobacter pylori urease investigated by mass spectrometry
    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 Mass Spectrom 38:315-20. 2003
    ..In vitro, the alpha and beta subunits are capable of re-assembling to (alphabeta)(3), but not further to the dodecameric complex...
  70. ncbi request reprint Interactions between the toxin Kid of the bacterial parD system and the antitoxins Kis and MazE
    Monique B Kamphuis
    Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Utrecht, The Netherlands
    Proteins 67:219-31. 2007
    ..The functional roles of the identified Kid-Kis and Kid-MazE interaction sites and complexes in toxin neutralization and repression of transcription are discussed...
  71. ncbi request reprint A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase
    Roberto T Bossi
    Dipartimento di Genetica e Microbiologia, Universita di Pavia, via Abbiategrasso 207, 27100 Pavia, Italy
    Biochemistry 41:8807-18. 2002
    ..The physiological significance of this reaction is presently unknown. However, it could assist with drug-design studies in that the modified NADP+ could serve as a lead compound for the development of specific inhibitors...
  72. ncbi request reprint Differential oxidation of protein-tyrosine phosphatases
    Arnoud Groen
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    J Biol Chem 280:10298-304. 2005
    ..In conclusion, PTPs are differentially oxidized at physiological pH and H(2)O(2) concentrations, and the PTP loop arginine is an important determinant for susceptibility to oxidation...
  73. 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...
  74. 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...
  75. pmc Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b
    Luis F Garcia-Alles
    CNRS, UMR5089, Département Mécanismes Moléculaires des Infections Mycobactériennes, Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
    EMBO J 25:3684-92. 2006
    ..The data presented herein explain how the CD1b groove is preserved, and provide a rationale for the in vivo antigen-binding properties of CD1b...
  76. 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...
  77. ncbi request reprint The hinge region operates as a stability switch in cGMP-dependent protein kinase I alpha
    Arjen Scholten
    Department of Pharmacology, College of Medicine, University of Vermont, Burlington, VT 05405, USA
    FEBS J 274:2274-86. 2007
    ..The R77L mutation not only stabilized the N-terminus but extended a stabilizing effect on the remaining domains of the enzyme as well. These findings support the concept that the hinge region of PKG acts as a stability switch...
  78. 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...
  79. pmc Inter-ring communication allows the GroEL chaperonin complex to distinguish between different substrates
    Esther van Duijn
    Department of Biochemistry and Molecular Biology, Faculty of Sciences, Free University, Amsterdam, The Netherlands
    Protein Sci 16:956-65. 2007
    ..The data indicate that the size of the substrate is an important factor that determines the degree of stabilization of the chaperonin complex...
  80. 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
  81. pmc The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels
    Pascale Daran-Lapujade
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Proc Natl Acad Sci U S A 104:15753-8. 2007
    ..Within the 50-20% hierarchical regulation of fluxes, transcription played a minor role, whereas regulation of protein synthesis or degradation was the most important. These also contributed to 75-100% of the regulation of protein levels...
  82. ncbi request reprint Stoichiometry of the peripheral stalk subunits E and G of yeast V1-ATPase determined by mass spectrometry
    Norton Kitagawa
    Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
    J Biol Chem 283:3329-37. 2008
    ..Results from both approaches are in excellent agreement and reveal that the subunit composition of yeast V(1)-ATPase is A(3)B(3)DE(3)FG(3)H...
  83. 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...
  84. pmc Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases
    Mariëlle J H Moonen
    Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
    J Bacteriol 190:5199-209. 2008
    ..HQDO is a novel member of the family of nonheme-iron(II)-dependent dioxygenases. The enzyme shows insignificant sequence identity with known dioxygenases...
  85. ncbi request reprint Probing noncovalent protein-ligand interactions of the cGMP-dependent protein kinase using electrospray ionization time of flight mass spectrometry
    Martijn W H Pinkse
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
    J Am Soc Mass Spectrom 15:1392-9. 2004
    ..These measurements indicated that autophosphorylation mainly occurs within the first 80 aminoterminal residues and involves in total 3-4 phosphates per subunit...
  86. 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...
  87. ncbi request reprint Carbohydrate chain of ganglioside GM1 as a ligand: identification of the binding strategies of three 15 mer peptides and their divergence from the binding modes of growth-regulatory galectin-1 and cholera toxin
    Hans Christian Siebert
    Institut fur Physiologische Chemie, Tierarztliche Fakultat, Ludwig Maximilians Universitat Munchen, Veterinarstrasse 13, 80539 Munchen, Germany
    Chemistry 12:388-402. 2005
    ....