Kris Gevaert

Summary

Affiliation: Ghent University
Country: Belgium

Publications

  1. pmc The expression, processing and localization of polymorphic membrane proteins in Chlamydia pneumoniae strain CWL029
    Brian Berg Vandahl
    Department of Medical Microbiology and Immunology, University of Aarhus, Denmark
    BMC Microbiol 2:36. 2002
  2. ncbi Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry
    K Gevaert
    Flanders Interuniversity, Department of Medical Protein Research, Ghent University, Belgium
    Electrophoresis 22:1645-51. 2001
  3. ncbi Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    Kris Gevaert
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Nat Biotechnol 21:566-9. 2003
  4. pmc In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography
    Bart Ghesquière
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 8:2642-52. 2009
  5. pmc GalNAc/Gal-binding Rhizoctonia solani agglutinin has antiproliferative activity in Drosophila melanogaster S2 cells via MAPK and JAK/STAT signaling
    Mohamad Hamshou
    Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
    PLoS ONE 7:e33680. 2012
  6. doi Selecting protein N-terminal peptides by combined fractional diagonal chromatography
    An Staes
    Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie VIB, Ghent, Belgium
    Nat Protoc 6:1130-41. 2011
  7. doi MS-driven protease substrate degradomics
    Francis Impens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 10:1284-96. 2010
  8. doi The substrate specificity profile of human granzyme A
    Petra Van Damme
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium
    Biol Chem 391:983-97. 2010
  9. ncbi A new approach for mapping sialylated N-glycosites in serum proteomes
    Bart Ghesquière
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 6:4304-12. 2007
  10. doi Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs
    Petra Van Damme
    Department of Medical Protein Research, Flanders Institute for Biotechnology VIB, Ghent, Belgium
    Mol Cell Proteomics 8:258-72. 2009

Detail Information

Publications85

  1. pmc The expression, processing and localization of polymorphic membrane proteins in Chlamydia pneumoniae strain CWL029
    Brian Berg Vandahl
    Department of Medical Microbiology and Immunology, University of Aarhus, Denmark
    BMC Microbiol 2:36. 2002
    ..In the present study, the expression, processing and localisation of the sixteen full-length Pmps in C. pneumoniae strain CWL029 have been further investigated by two-dimensional gel electrophoresis and immunofluorescence microscopy...
  2. ncbi Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry
    K Gevaert
    Flanders Interuniversity, Department of Medical Protein Research, Ghent University, Belgium
    Electrophoresis 22:1645-51. 2001
    ..The combination of peptide mass fingerprinting and PSD and analysis described here generally leads to unambiguous protein identification in the amount of material range generally encountered in most proteome studies...
  3. ncbi Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    Kris Gevaert
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Nat Biotechnol 21:566-9. 2003
    ..Omitting the acetylation step results in the isolation of non-lysine-containing N-terminal peptides from in vivo blocked proteins...
  4. pmc In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography
    Bart Ghesquière
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 8:2642-52. 2009
    ....
  5. pmc GalNAc/Gal-binding Rhizoctonia solani agglutinin has antiproliferative activity in Drosophila melanogaster S2 cells via MAPK and JAK/STAT signaling
    Mohamad Hamshou
    Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
    PLoS ONE 7:e33680. 2012
    ..Finally, RSA affinity chromatography of membrane proteins from S2 cells allowed the identification of several cell surface receptors involved in both signaling transduction pathways...
  6. doi Selecting protein N-terminal peptides by combined fractional diagonal chromatography
    An Staes
    Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie VIB, Ghent, Belgium
    Nat Protoc 6:1130-41. 2011
    ..Completion of the N-terminal COFRADIC procedure takes ~5 d...
  7. doi MS-driven protease substrate degradomics
    Francis Impens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 10:1284-96. 2010
    ..The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS-driven protease substrate degradome studies...
  8. doi The substrate specificity profile of human granzyme A
    Petra Van Damme
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium
    Biol Chem 391:983-97. 2010
    ..Further substrate characterization was used to delineate physical properties in the substrate specificity profiles, which further highlights important aspects in protease/substrate biology...
  9. ncbi A new approach for mapping sialylated N-glycosites in serum proteomes
    Bart Ghesquière
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 6:4304-12. 2007
    ....
  10. doi Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs
    Petra Van Damme
    Department of Medical Protein Research, Flanders Institute for Biotechnology VIB, Ghent, Belgium
    Mol Cell Proteomics 8:258-72. 2009
    ....
  11. pmc Probing the efficiency of proteolytic events by positional proteomics
    Kim Plasman
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Mol Cell Proteomics 10:M110.003301. 2011
    ..Several of our proteomics results were further confirmed by substrate immunoblotting and by using peptide substrates incubated with human granzyme B...
  12. pmc Diversity in protein glycosylation among insect species
    Gianni Vandenborre
    Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
    PLoS ONE 6:e16682. 2011
    ..Although the Class of the Insecta is the largest animal taxon on Earth, almost all information concerning glycosylation in insects is derived from studies with only one species, namely the fruit fly Drosophila melanogaster...
  13. pmc Redox proteomics of protein-bound methionine oxidation
    Bart Ghesquière
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 10:M110.006866. 2011
    ..This was supported by a structural modeling of the MsrA catalytic center. Finally, we applied our method onto a serum proteome from a mouse sepsis model and identified 35 in vivo methionine oxidation events in 27 different proteins...
  14. ncbi PRIDE: the proteomics identifications database
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 5:3537-45. 2005
    ..The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation...
  15. pmc Conservation of the extended substrate specificity profiles among homologous granzymes across species
    Kim Plasman
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 12:2921-34. 2013
    ..Our results thus indicate a conserved, but hitherto underappreciated specificity-determining role of extended protease-substrate contacts in steering cleavage susceptibility. ..
  16. ncbi The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile
    Lennart Martens
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Proteomics 5:3193-204. 2005
    ....
  17. pmc The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Nucleic Acids Res 41:D333-7. 2013
    ..Across substrates, substrate orthologs and conserved sequence stretches can also be shown, with iceLogo visualization provided for the latter...
  18. ncbi Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 5:3501-5. 2005
    ..Finally, some suggestions are made for both immediate and future storage of MS data in public repositories...
  19. doi Combining quantitative proteomics data processing workflows for greater sensitivity
    Niklaas Colaert
    Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie VIB, Ghent, Belgium
    Nat Methods 8:481-3. 2011
    ..Our integrative workflow is freely available through our user-friendly, open-source Rover software (http://compomics-rover.googlecode.com/)...
  20. ncbi A la carte proteomics with an emphasis on gel-free techniques
    Kris Gevaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 7:2698-718. 2007
    ..Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed...
  21. ncbi A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes
    Xavier Hanoulle
    Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    J Proteome Res 5:3438-45. 2006
    ..When applied on a cellular level, 185 different FSBA-labeled sites in a human Jurkat cell lysate were identified. Functional and structural aspects of the use of FSBA on a proteome-wide scale are discussed...
  22. doi High entomotoxicity and mechanism of the fungal GalNAc/Gal-specific Rhizoctonia solani lectin in pest insects
    Mohamad Hamshou
    Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B 9000 Ghent, Belgium
    J Insect Physiol 59:295-305. 2013
    ..These data are discussed in relation to the physiological effects of RSA...
  23. pmc NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation
    Petra Van Damme
    Department of Medical Protein Research, Ghent University, Ghent, Belgium
    PLoS Genet 7:e1002169. 2011
    ..With the characterization of NatF, the co-translational N-Ac machinery appears complete since all the major substrate groups in eukaryotes are accounted for...
  24. ncbi Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation
    Kenny Helsens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 10:3578-89. 2011
    ..Finally, we also observed an unexpected high number of N(α)-acetylated peptides that could not be related to TIS and therefore suggest events of post-translational N(α)-acetylation...
  25. ncbi Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses
    Kris Gevaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    FEBS J 274:6277-89. 2007
    ..Additionally, we discuss an activity-based proteome study in which purine-binding proteins were profiled by diagonal chromatography...
  26. doi The actin propulsive machinery: the proteome of Listeria monocytogenes tails
    Marleen Van Troys
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Biochem Biophys Res Commun 375:194-9. 2008
    ..This work forms a new basis to expand current models of cellular protrusion...
  27. ncbi Assessing a novel microfluidic interface for shotgun proteome analyses
    An Staes
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Sep Sci 30:1468-76. 2007
    ....
  28. doi Rover: a tool to visualize and validate quantitative proteomics data from different sources
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 10:1226-9. 2010
    ....
  29. ncbi Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis
    Petra Van Damme
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Belgium
    Nat Methods 2:771-7. 2005
    ..The spliceosome complex appeared a preferred target, as 14 of its members were processed. Differential isotopic labeling further revealed specific release of nucleosomal components from apoptotic nuclei...
  30. pmc Interaction of the tobacco lectin with histone proteins
    Dieter Schouppe
    Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, B 9000 Ghent, Belgium
    Plant Physiol 155:1091-102. 2011
    ..Since the lectin-histone interaction was shown to be carbohydrate dependent, it is proposed that Nictaba might fulfill a signaling role in response to stress by interacting with O-GlcNAcylated proteins in the plant cell nucleus...
  31. doi A stringent approach to improve the quality of nitrotyrosine peptide identifications
    Bart Ghesquière
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 11:1094-8. 2011
    ..Central in our approach is the reduction of nitrotyrosine into aminotyrosine and the use of the Peptizer algorithm to inspect MS/MS quality-related assumptions...
  32. pmc Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of N(alpha)-acetyltransferases and point to hNaa10p as the post-translational actin N(alpha)-acetyltransferase
    Petra Van Damme
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 10:M110.004580. 2011
    ..Thus, complex formation of NatA might alter the substrate specificity profile as compared with its isolated catalytic subunits, and, furthermore, NatA or hNaa10p may function as a post-translational actin N(α)-acetyltransferase...
  33. doi Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
    An Staes
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 8:1362-70. 2008
    ..We further show that now close to 95% of all COFRADIC-sorted peptides are alpha-amino-acetylated and, using the same amount of starting material, our novel procedure leads to an increased number of protein identifications...
  34. ncbi Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS
    An Staes
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Anal Chem 85:11054-60. 2013
    ..Asn3 is also very easy to adopt in the lab, as it requires only minor adjustments to the analytical setup. ..
  35. pmc The C-terminus of CIS defines its interaction pattern
    Delphine Lavens
    Flanders Interuniversity Institute for Biotechnology, Department of Medical Protein Research VIB09, Faculty of Medicine and Health Sciences, Ghent University, Baertsoenkaai 3, 9000 Ghent, Belgium
    Biochem J 401:257-67. 2007
    ..Mutagenesis revealed that one single tyrosine residue at position 253 is a critical binding determinant. In contrast, substrate binding by the highly related SOCS2 protein, and also by SOCS1 and SOCS3, does not require their SOCS-box...
  36. pmc N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB
    Petra Van Damme
    Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie, Ghent University, B 9000 Ghent, Belgium
    Proc Natl Acad Sci U S A 109:12449-54. 2012
    ....
  37. ncbi Protein processing and other modifications analyzed by diagonal peptide chromatography
    Kris Gevaert
    Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Biochim Biophys Acta 1764:1801-10. 2006
    ..Additional modifications that can be analyzed include phosphorylation and N-glycosylation. The potential of COFRADIC for isolating peptides holding such modified amino acids are discussed here...
  38. doi Complementary positional proteomics for screening substrates of endo- and exoproteases
    Petra Van Damme
    Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
    Nat Methods 7:512-5. 2010
    ....
  39. doi ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
    Kenny Helsens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 10:1261-4. 2010
    ..We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses...
  40. doi Stable isotopic labeling in proteomics
    Kris Gevaert
    Department of Medical Protein Research, VIB, Ghent University, Ghent, Belgium
    Proteomics 8:4873-85. 2008
    ..In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications...
  41. pmc A quantitative proteomics design for systematic identification of protease cleavage events
    Francis Impens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 9:2327-33. 2010
    ....
  42. ncbi Peptizer, a tool for assessing false positive peptide identifications and manually validating selected results
    Kenny Helsens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 7:2364-72. 2008
    ..Peptizer is open source software under the Apache2 license and is written in Java...
  43. ncbi Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells
    Kris Gevaert
    Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B9000 Ghent, Belgium
    J Proteome Res 5:1415-28. 2006
    ....
  44. doi Hybrid N-glycans on the host protective activation-associated secreted proteins of Ostertagia ostertagi and their importance in immunogenicity
    Yves Meyvis
    Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B 9820 Merelbeke, Belgium
    Mol Biochem Parasitol 161:67-71. 2008
    ..While removal of these glycans had little effect on antibody recognition by vaccinated animals, denaturing and reducing the proteins dramatically reduced recognition, suggesting the importance of conformational protein backbone epitopes...
  45. ncbi Improved tandem mass spectrometric characterization of 3-nitrotyrosine sites in peptides
    Bart Ghesquière
    Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Rapid Commun Mass Spectrom 20:2885-93. 2006
    ..In conclusion, we here illustrate that this two-step process, heme-mediated reduction and acetylation, can be used for more efficient characterization of protein-bound nitrated tyrosines...
  46. ncbi Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC
    Kris Gevaert
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium
    Proteomics 5:3589-99. 2005
    ..The method was validated with alpha-casein phosphopeptides and consecutively applied on HepG2 cells. We identified 190 phosphorylated peptides from 152 different proteins. This dataset includes 38 novel protein phosphorylation sites...
  47. doi A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 11:1110-3. 2011
    ..We derived our test data from two well-characterized publicly available quantitative data sets...
  48. ncbi Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Proteome Res 10:3840-3. 2011
    ..All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com...
  49. doi A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods
    Sven Degroeve
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 11:1172-80. 2011
    ..We demonstrate that our results are independent of the data set used in the evaluation procedure, allowing us to provide generic guidance on the choice of normalization method to apply in a certain MS/MS pipeline application...
  50. ncbi Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18
    An Staes
    Department of Medical Protein Research, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    J Proteome Res 3:786-91. 2004
    ....
  51. ncbi Proteome-wide characterization of N-glycosylation events by diagonal chromatography
    Bart Ghesquière
    Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B9000 Ghent, Belgium
    J Proteome Res 5:2438-47. 2006
    ..These properties--high sensitivity and dependence on glycan imprinting--can be exploited for glycan-biomarker analysis...
  52. doi Contemporary positional proteomics strategies to study protein processing
    Kim Plasman
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Curr Opin Chem Biol 17:66-72. 2013
    ..Since proteases create novel termini in their substrates, positional proteomics is ideally suited for protease degradomics studies. We here review recent developments in the field of positional proteomics applied to protease research...
  53. pmc Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity
    Davina Tondeleir
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Mol Cell Proteomics 11:255-71. 2012
    ....
  54. doi A case study on the comparison of different software tools for automated quantification of peptides
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent University, B 9000, Ghent, Belgium
    Methods Mol Biol 753:373-98. 2011
    ..Recently, new tools were developed for automatic peptide quantification in quantitative proteomic experiments. Here we present a case study where the most recent and frequently used tools are analyzed and compared...
  55. doi RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification
    Niklaas Colaert
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 10:3183-9. 2011
    ..Both the accuracy and the precision of our novel methods are analyzed and compared to the existing methods to illustrate the increased robustness of our new methods over existing ones...
  56. doi Protein processing characterized by a gel-free proteomics approach
    Petra Van Damme
    Ghent University, Ghent, Belgium
    Methods Mol Biol 484:245-62. 2008
    ..As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research...
  57. pmc HyperISGylation of Old World monkey ISG15 in human cells
    Els Pattyn
    Department of Medical Protein Research, VIB, Ghent, Belgium
    PLoS ONE 3:e2427. 2008
    ..Upon the cooperative activity of specific Ubiquitinating enzymes, ISG15 can be conjugated to its substrates. Increasing evidence points to a role for protein ISGylation in anti-viral and anti-tumoral defense...
  58. doi Analysis of the translationally controlled tumour protein in the nematodes Ostertagia ostertagi and Caenorhabditis elegans suggests a pivotal role in egg production
    Yves Meyvis
    Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B 9820 Merelbeke, Belgium
    Int J Parasitol 39:1205-13. 2009
    ..elegans. Knock-down of C. elegans tctp (tct-1) transcription reduced the numbers of eggs laid by the hermaphrodite in the F(0) and F(1) generations by 90% and 72%, respectively, indicating a pivotal role of TCTP in reproduction...
  59. pmc Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events
    Gerben Menschaert
    Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
    Mol Cell Proteomics 12:1780-90. 2013
    ..The underlying mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000124. ..
  60. ncbi A catalogue of putative HIV-1 protease host cell substrates
    Francis Impens
    Department of Medical Protein Research and Biochemistry, VIB, B 9000 Ghent, Belgium
    Biol Chem 393:915-31. 2012
    ..Our results are further discussed in the context of HIV-1 infection and the complex substrate recognition by the viral protease...
  61. pmc LNCipedia: a database for annotated human lncRNA transcript sequences and structures
    Pieter Jan Volders
    Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
    Nucleic Acids Res 41:D246-51. 2013
    ..The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs...
  62. doi Angiotensin I-converting enzyme inhibitory activity of gelatin hydrolysates and identification of bioactive peptides
    Griet Herregods
    Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B 9000 Ghent, Belgium
    J Agric Food Chem 59:552-8. 2011
    ..As these peptides showed ACE inhibitory activity and were more prominent in Bh2t than in Bh2, the current data provide evidence that these contribute to the antihypertensive effect of Bh2t...
  63. ncbi A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies
    Lennart Martens
    Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium
    Proteomics 6:5076-86. 2006
    ..Finally, as any comparison between large-scale proteomics datasets is decidedly non-trivial, we also evaluate and discuss several ways to go about comparing such different result sets...
  64. ncbi Reverse-phase diagonal chromatography for phosphoproteome research
    Kris Gevaert
    Department of Medical Protein Research, Ghent University, Ghent, Belgium
    Methods Mol Biol 527:219-27, ix. 2009
    ..The complete COFRADIC sorting procedure is described here...
  65. doi The tandem PDZ protein Syntenin interacts with the aminoacyl tRNA synthetase complex in a lysyl-tRNA synthetase-dependent manner
    Kris Meerschaert
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 7:4962-73. 2008
    ..As a result, other components of the ARS complex no longer co-immunoprecipitate with syntenin-1. We further show that syntenin-1 regulates KRS activity. These findings suggest that syntenin-1 is an adaptor modulating the activity of KRS...
  66. doi Mass spectrometry-driven proteomics: an introduction
    Kenny Helsens
    Department of Medical Protein Research, VIB, Ghent University, B 9000, Ghent, Belgium
    Methods Mol Biol 753:1-27. 2011
    ..To accomplish this, many methods have been developed over the last decades, and their general principles and important recent advances in large-scale protein analysis or proteomics are discussed in this review...
  67. ncbi DBToolkit: processing protein databases for peptide-centric proteomics
    Lennart Martens
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Bioinformatics 21:3584-5. 2005
    ..In addition, DBToolkit can be used to reliably solve a range of other typical tasks in processing sequence databases...
  68. pmc A review of COFRADIC techniques targeting protein N-terminal acetylation
    Petra Van Damme
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    BMC Proc 3:S6. 2009
    ....
  69. doi Multiple isoforms of the tumor suppressor myopodin are simultaneously transcribed in cancer cells
    Ariane De Ganck
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Biochem Biophys Res Commun 370:269-73. 2008
    ..These findings shed new light on the expression of this tumor suppressor gene and necessitate closer examination of both mouse and human myopodin polypeptides currently under study...
  70. doi Protein alpha-N-acetylation studied by N-terminomics
    Petra Van Damme
    Department of Medical Protein Research, VIB, Ghent, Belgium
    FEBS J 278:3822-34. 2011
    ..In this review, we report on such emerging technologies as well as on breakthroughs in our understanding of protein N-terminal biology...
  71. ncbi Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?
    Kris Gevaert
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Anal Biochem 345:18-29. 2005
    ..We were able to identify an unexpectedly high number of intracellular proteins next to known biomarkers...
  72. ncbi MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results
    Kenny Helsens
    Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium
    Proteomics 7:364-6. 2007
    ..ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications...
  73. doi Who gets cut during cell death?
    Francis Impens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Curr Opin Cell Biol 22:859-64. 2010
    ..This review provides an overview of the results obtained at the exciting interface between proteomics, protease biology and cell death...
  74. ncbi A small heat shock protein of Ostertagia ostertagi: stage-specific expression, heat inducibility, and protection trial
    Isabel Vercauteren
    Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, 133, B 9820 Merelbeke, Belgium
    J Parasitol 92:1244-50. 2006
    ..The levels of Oo-hsp18 mRNAs are sharply induced by heat shock but not by other stressors such as levamisole and H2O2. A vaccination trial with recombinant Oo-HSP18 failed to protect calves against a challenge infection...
  75. doi Glycosylation signatures in Drosophila: fishing with lectins
    Gianni Vandenborre
    Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, Belgium
    J Proteome Res 9:3235-42. 2010
    ..Furthermore, it was demonstrated that a specific glycosylation signature can be associated with a functionally related group of glycoproteins in Drosophila, both in terms of biological process and molecular function...
  76. ncbi Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies
    Kris Gevaert
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University and Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium
    Proteomics 4:897-908. 2004
    ..In both proteomes, a significant number of low abundance proteins were identified next to extremely abundant ones. A dynamic range for protein identification spanning 4-5 orders of magnitude is demonstrated...
  77. ncbi The proteome of the human neuroblastoma cell line SH-SY5Y: an enlarged proteome
    Kambiz Gilany
    Department of Biomedical Sciences, Protein Chemistery, University of Antwerp, Universiteitsplein 1, B 2610 Antwerp, Belgium
    Biochim Biophys Acta 1784:983-5. 2008
    ..The obtained proteome profile of this cell line is discussed...
  78. ncbi Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2
    Allan C Shaw
    Department of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark
    Proteomics 2:164-86. 2002
    ..trachomatis on a large scale and the integration of our data in a 2-D PAGE database will create a basis for post genomic research, important for the understanding of chlamydial development and pathogenesis...
  79. ncbi Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins
    Kris Gevaert
    Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University and Flanders Interuniversity Institute for Biotechnology, Belgium
    Mol Cell Proteomics 1:896-903. 2002
    ..adding a new dimension to future proteome research...
  80. doi Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death
    Gro Gausdal
    Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen, Norway
    Blood 111:2866-77. 2008
    ..We propose that judiciously timed inhibition of cap-independent translation is considered for combination therapy with anthracyclines in AML...
  81. ncbi Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
    Michalis Aivaliotis
    Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    J Proteome Res 6:2195-204. 2007
    ..The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders...
  82. ncbi Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
    Kristian Flikka
    Computational Biology Unit, Bergen Center for Computational Science, Bergen, Norway
    Proteomics 6:2086-94. 2006
    ..The implementation of the classifiers is available under the GNU General Public License at http://www.bioinfo.no/software/spectrumquality...
  83. doi Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  84. ncbi Identification by two-dimensional electrophoresis of a new adhesin expressed by a low-passaged strain of Mycoplasma bovis
    Anne Thomas
    Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liege, B43A, Sart Tilman, 4000 Liege, Belgium
    Res Microbiol 156:713-8. 2005
    ..Serum from a mouse immunized with these proteins significantly reduced adherence of M. bovis to BBE cells. This result underlines the function of this new Vsp in adherence of M. bovis to host cells...
  85. ncbi Proteome-wide Identification of HtrA2/Omi Substrates
    Lieselotte Vande Walle
    Department of Molecular Biomedical Research, VIB, 9052, Ghent, Belgium
    J Proteome Res 6:1006-15. 2007
    ..Our results suggest that HtrA2/Omi has a rather narrow cleavage site preference and that cytoskeletal proteins are prime targets of this protease...