Lennart Martens

Summary

Affiliation: Ghent University
Country: Belgium

Publications

  1. pmc Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Proteomics 73:2136-46. 2010
  2. pmc compomics-utilities: an open-source Java library for computational proteomics
    Harald Barsnes
    Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
    BMC Bioinformatics 12:70. 2011
  3. ncbi request reprint 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
  4. ncbi request reprint 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
  5. pmc Cell_motility: a cross-platform, open source application for the study of cell motion paths
    Lennart Martens
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A, Baertsoenkaai 3, B 9000 Ghent, Belgium
    BMC Bioinformatics 7:289. 2006
  6. ncbi request reprint 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
  7. doi request reprint Data management in mass spectrometry-based proteomics
    Lennart Martens
    Department of Medical Protein Science, Universiteit Gent VIB, B 9000 Gent, Belgium
    Methods Mol Biol 728:321-32. 2011
  8. ncbi request reprint 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
  9. ncbi request reprint 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
  10. pmc PRIDE: a public repository of protein and peptide identifications for the proteomics community
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D659-63. 2006

Detail Information

Publications115 found, 100 shown here

  1. pmc Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Proteomics 73:2136-46. 2010
    ..Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced...
  2. pmc compomics-utilities: an open-source Java library for computational proteomics
    Harald Barsnes
    Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
    BMC Bioinformatics 12:70. 2011
    ..Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool...
  3. ncbi request reprint 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...
  4. ncbi request reprint 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...
  5. pmc Cell_motility: a cross-platform, open source application for the study of cell motion paths
    Lennart Martens
    Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A, Baertsoenkaai 3, B 9000 Ghent, Belgium
    BMC Bioinformatics 7:289. 2006
    ..Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s) used...
  6. ncbi request reprint 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...
  7. doi request reprint Data management in mass spectrometry-based proteomics
    Lennart Martens
    Department of Medical Protein Science, Universiteit Gent VIB, B 9000 Gent, Belgium
    Methods Mol Biol 728:321-32. 2011
    ..Finally, the increasingly important link between a local data management system and the global, centralized dissemination of proteomics data is discussed...
  8. ncbi request reprint 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
    ....
  9. ncbi request reprint 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...
  10. pmc PRIDE: a public repository of protein and peptide identifications for the proteomics community
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D659-63. 2006
    ..Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML...
  11. pmc The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
    Richard G Côté
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1QY, UK
    BMC Bioinformatics 8:401. 2007
    ..As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs...
  12. pmc A guide to the Proteomics Identifications Database proteomics data repository
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:4276-83. 2009
    ..Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium...
  13. pmc The Proteomics Identifications database: 2010 update
    Juan Antonio Vizcaino
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 38:D736-42. 2010
    ..Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium...
  14. ncbi request reprint 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...
  15. ncbi request reprint 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...
  16. doi request reprint 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/)...
  17. doi request reprint Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
    Michael Mueller
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 8:1138-48. 2008
    ..We also evaluate the empirically observed peptides of interest against predictions of their proteotypic character...
  18. pmc PRIDE: new developments and new datasets
    Philip Jones
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:D878-83. 2008
    ..Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML...
  19. 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...
  20. ncbi request reprint 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
    ....
  21. ncbi request reprint 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...
  22. ncbi request reprint 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
    ....
  23. doi request reprint 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. ..
  24. doi request reprint Using the Proteomics Identifications Database (PRIDE)
    Lennart Martens
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge
    Curr Protoc Bioinformatics . 2008
    ..This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE...
  25. pmc The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
    Richard G Côté
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:W372-6. 2008
    ..Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries...
  26. doi request reprint PRIDE: Data submission and analysis
    Juan Antonio Vizcaino
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    Curr Protoc Protein Sci . 2010
    ..Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross-domain query capabilities available through a combination of BioMarts...
  27. pmc The Ontology Lookup Service: bigger and better
    Richard Cote
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 38:W155-60. 2010
    ..In addition, newly released software packages now provide easy means to fully integrate OLS functionality in external applications...
  28. ncbi request reprint 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...
  29. ncbi request reprint 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...
  30. doi request reprint 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...
  31. doi request reprint Sigpep: calculating unique peptide signature transition sets in a complete proteome background
    Kenny Helsens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 12:1142-6. 2012
    ..The platform has been made available under the permissive Apache 2.0 open-source license, and the web application can be accessed from http://iomics.ugent.be/sigpep...
  32. pmc The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
    Richard G Côté
    Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Cell Proteomics 11:1682-9. 2012
    ..The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories...
  33. doi request reprint 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...
  34. ncbi request reprint 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...
  35. doi request reprint 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...
  36. doi request reprint 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...
  37. doi request reprint Taking Aim at Moving Targets in Computational Cell Migration
    Paola Masuzzo
    Medical Biotechnology Center, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
    Trends Cell Biol 26:88-110. 2016
    ..Finally, we provide a list of available software tools for cell migration to assist researchers in choosing the most appropriate solution for their needs. ..
  38. doi request reprint 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...
  39. ncbi request reprint Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study
    Michael Mueller
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Proteomics 6:5059-75. 2006
    ..In the majority of cases splice variants could be unambiguously identified by unique peptides, including matches to several hypothetical transcripts of known as well as predicted genes...
  40. ncbi request reprint The minimum information about a proteomics experiment (MIAPE)
    Chris F Taylor
    The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 25:887-93. 2007
    ....
  41. ncbi request reprint 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...
  42. doi request reprint Analysis of the resolution limitations of peptide identification algorithms
    Niklaas Colaert
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Proteome Res 10:5555-61. 2011
    ....
  43. doi request reprint 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...
  44. doi request reprint 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...
  45. doi request reprint 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...
  46. pmc An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics
    Giel Vandemoortele
    VIB Medical Biotechnology Center, B 9000 Ghent, Belgium
    Sci Rep 6:27220. 2016
    ..Endogenous protein tagging for absolute quantification provides a powerful extra dimension to protein analysis, allowing the detailed characterization of endogenous proteins. ..
  47. ncbi request reprint 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...
  48. doi request reprint 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...
  49. pmc Pride-asap: automatic fragment ion annotation of identified PRIDE spectra
    Niels Hulstaert
    Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
    J Proteomics 95:89-92. 2013
    ..Pride-asap binaries, source code and additional information can be downloaded from http://pride-asa-pipeline.googlecode.com.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. ..
  50. doi request reprint Getting intimate with trypsin, the leading protease in proteomics
    Elien Vandermarliere
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium Department of Biochemistry, Ghent University, B 9000 Ghent, Belgium
    Mass Spectrom Rev 32:453-65. 2013
    ..Finally, some reflections on the future of trypsin as the workhorse protease in mass spectrometry-based proteomics will be provided...
  51. doi request reprint MS2PIP: a tool for MS/MS peak intensity prediction
    Sven Degroeve
    Department of Medical Protein Research, VIB, Ghent 9000, Belgium and Department of Biochemistry, Ghent University, Ghent 9000, Belgium
    Bioinformatics 29:3199-203. 2013
    ..The ability to predict these MS(2) signals and to understand this fragmentation process is important for sensitive high-throughput proteomics research...
  52. ncbi request reprint Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy
    Lennart Martens
    European Molecular Biology Laboratory Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Cell Proteomics 6:1666-7. 2007
  53. doi request reprint The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
    Luisa Montecchi-Palazzi
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Proteomics 9:5112-9. 2009
    ..The framework source code and its various applications can be found at http://psidev.info/validator...
  54. doi request reprint jmzML, an open-source Java API for mzML, the PSI standard for MS data
    Richard G Côté
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Proteomics 10:1332-5. 2010
    ..jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com...
  55. doi request reprint PRIDE and "Database on Demand" as valuable tools for computational proteomics
    Juan Antonio Vizcaino
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:93-105. 2011
    ..Additionally, in order to show the potential of PRIDE as a source for data mining, we also explore complex queries using federated BioMart queries to integrate PRIDE data with other resources, such as Ensembl, Reactome, or UniProt...
  56. doi request reprint Data standards and controlled vocabularies for proteomics
    Lennart Martens
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 484:279-86. 2008
    ..We describe the origins and overall concepts behind these standards, as well as the individual efforts that are ongoing in the field of mass spectrometry proteomics and protein interactions...
  57. doi request reprint Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases
    Florian Reisinger
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 9:4421-4. 2009
    ..Here we present Database on Demand, an easy-to-use web tool that can quickly produce a wide variety of customized search databases...
  58. pmc OLS dialog: an open-source front end to the ontology lookup service
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    BMC Bioinformatics 11:34. 2010
    ..However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data...
  59. doi request reprint A global analysis of peptide fragmentation variability
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    Proteomics 11:1181-8. 2011
    ..Finally, we discuss the observed variability in light of ongoing efforts to create spectral libraries and predictive software for target selection in targeted proteomics...
  60. doi request reprint Bioinformatics challenges in mass spectrometry-driven proteomics
    Lennart Martens
    Department of Medical Protein Research, VIB, Ghent University, B 9000, Ghent, Belgium
    Methods Mol Biol 753:359-71. 2011
    ..Finally, the informatics aspects of the nascent field of targeted proteomics are outlined as well...
  61. pmc jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
    Kenny Helsens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Proteome Res 10:5260-3. 2011
    ..The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml ...
  62. pmc CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
    Paola Masuzzo
    Department of Medical Protein Research, VIB and Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent 9000, Belgium
    Bioinformatics 29:2661-3. 2013
    ..CellMissy simplifies and automates data management, storage and analysis from the initial experimental set-up to data exploration...
  63. ncbi request reprint Annotating the human proteome: beyond establishing a parts list
    Michael Mueller
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Biochim Biophys Acta 1774:175-91. 2007
    ..Of special importance here is the integration of heterogeneous data to facilitate the creation of resources that go beyond a mere parts list...
  64. doi request reprint 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
    Sandra Orchard
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 8:1331-3. 2008
    ..The session ended with a lively debate on the practical implications these advances will have on daily laboratory work, on submission procedures and the tools which are being developed to assist in these activities...
  65. doi request reprint A posteriori quality control for the curation and reuse of public proteomics data
    Joseph M Foster
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 11:2182-94. 2011
    ....
  66. doi request reprint Predicting tryptic cleavage from proteomics data using decision tree ensembles
    Thomas Fannes
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 12:2253-9. 2013
    ..Moreover, the trees generated by CP-DT can make predictions efficiently and are interpretable by domain experts...
  67. doi request reprint Towards a human proteomics atlas
    Giulia Gonnelli
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Anal Bioanal Chem 404:1069-77. 2012
    ..We here therefore investigate the issues involved in using the human data currently stored in the PRIDE database to construct a robust, tissue-specific protein expression atlas from tandem-MS based label-free quantification...
  68. 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...
  69. ncbi request reprint Implementation and application of a versatile clustering tool for tandem mass spectrometry data
    Kristian Flikka
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
    Proteomics 7:3245-58. 2007
    ..An analysis of the influence of the different algorithms available and their parameters is given, as well as a number of important applications of the overall approach...
  70. doi request reprint Submitting proteomics data to PRIDE using PRIDE Converter
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    Methods Mol Biol 694:237-53. 2011
    ..ebi.ac.uk/pride), and demonstrate how a new graphical user interface tool called PRIDE Converter (http://pride-converter.googlecode.com) greatly simplifies the submission of data to PRIDE...
  71. ncbi request reprint 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. doi request reprint SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis
    Kevin Titeca
    VIB Medical Biotechnology Center, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    J Proteome Res 15:332-8. 2016
    ..SFINX outperforms alternative techniques on two benchmark data sets and is available via the Web interface at http://sfinx.ugent.be/...
  73. pmc Proteome-scale Binary Interactomics in Human Cells
    Sam Lievens
    From the Medical Biotechnology Center, VIB, Ghent, Belgium
    Mol Cell Proteomics 15:3624-3639. 2016
    ..In both cases, cell microarray screens yielded known and new potential drug targets highlighting the utility of the technology beyond fundamental biology...
  74. pmc The iceLogo web server and SOAP service for determining protein consensus sequences
    Davy Maddelein
    Department of Medical Protein Research, VIB, A Baertsoenkaai 3, B 9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Nucleic Acids Res 43:W543-6. 2015
    ..The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html. ..
  75. doi request reprint Machine learning applications in proteomics research: how the past can boost the future
    Pieter Kelchtermans
    Department of Medical Protein Research, VIB, Ghent, Belgium Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium Flemish Institute for Technological Research VITO, Boeretang, Mol, Belgium
    Proteomics 14:353-66. 2014
    ....
  76. pmc An update on LNCipedia: a database for annotated human lncRNA sequences
    Pieter Jan Volders
    Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
    Nucleic Acids Res 43:D174-80. 2015
    ..In addition, a tool to assess lncRNA gene conservation between human, mouse and zebrafish has been implemented...
  77. doi request reprint PepShell: visualization of conformational proteomics data
    Elien Vandermarliere
    Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B 9000 Ghent, Belgium
    J Proteome Res 14:1987-90. 2015
    ..Moreover, PepShell allows the comparison of experiments under different conditions, including different proteolysis times or binding of the protein to different substrates or inhibitors. ..
  78. doi request reprint ProteoCloud: a full-featured open source proteomics cloud computing pipeline
    Thilo Muth
    Department of Medical Protein Research, VIB, Ghent, Belgium
    J Proteomics 88:104-8. 2013
    ..It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com...
  79. pmc The effect of peptide identification search algorithms on MS2-based label-free protein quantification
    Sven Degroeve
    Department of Medical Protein Research, VIB, and Ghent University, Faculty of Medicine and Health Sciences, Ghent, Belgium
    OMICS 16:443-8. 2012
    ....
  80. doi request reprint FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    Proteomics 10:1087-90. 2010
    ..This enables the detection of fragmentation pattern nuances related to specific instruments or due to the presence of post-translational modifications...
  81. doi request reprint Resolution of protein structure by mass spectrometry
    Elien Vandermarliere
    Department of Medical Protein Research, VIB, B 9000, Ghent, Belgium
    Mass Spectrom Rev 35:653-665. 2016
    ..2014 Wiley Periodicals, Inc. Mass Spec Rev 35:653-665, 2016...
  82. ncbi request reprint Database Search Engines: Paradigms, Challenges and Solutions
    Kenneth Verheggen
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Adv Exp Med Biol 919:147-156. 2016
    ..This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact...
  83. doi request reprint MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform
    Surya Gupta
    Medical Biotechnology Center, VIB, Ghent, Belgium
    Bioinformatics . 2017
    ..MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments...
  84. doi request reprint Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules
    Michela Di Michele
    Department of Medical Protein Research, VIB, A Baertsoenkaai 3, 9000 Ghent, Belgium
    J Proteome Res 14:4179-93. 2015
    ..We also applied our method to monitor conformational changes upon nucleotide binding of the pseudokinase KSR1, which holds high potential for inhibition in human diseases. ..
  85. doi request reprint Unraveling the specificities of the different human methionine sulfoxide reductases
    Elien Vandermarliere
    Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
    Proteomics 14:1990-8. 2014
    ..MSRB2 and MSRB3, which are both found in mitochondria, are more specific but because of their co-occurrence they can likely repair all possible substrates...
  86. doi request reprint A decoy-free approach to the identification of peptides
    Giulia Gonnelli
    Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B 9000 Ghent, Belgium
    J Proteome Res 14:1792-8. 2015
    ..We show that Nokoi outperforms Mascot and achieves a performance very close to that of Percolator at substantially higher processing speeds. ..
  87. doi request reprint Bringing proteomics into the clinic: the need for the field to finally take itself seriously
    Lennart Martens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Proteomics Clin Appl 7:388-91. 2013
    ..A key enabling factor in this maturation process is quality control and quality assurance, with bioinformatics, in its least noticeable but most influential form, as a key underlying technology...
  88. doi request reprint Protein structure as a means to triage proposed PTM sites
    Elien Vandermarliere
    Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
    Proteomics 13:1028-35. 2013
    ..This analysis illustrates that care must be taken when simply accepting the position of a PTM without first analyzing its position within the protein structure if the latter is available...
  89. ncbi request reprint Methods to Calculate Spectrum Similarity
    Sule Yilmaz
    Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent, 9000, Belgium
    Methods Mol Biol 1549:75-100. 2017
    ..Here, we describe and evaluate these scoring functions with regards to their ability to assess spectrum similarity for theoretical versus acquired, and acquired versus acquired spectra...
  90. pmc MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation
    Sven Degroeve
    Department of Medical Protein Research, VIB, A Baertsoenkaai 3, B 9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
    Nucleic Acids Res 43:W326-30. 2015
    ..We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip. ..
  91. doi request reprint An open data ecosystem for cell migration research
    Paola Masuzzo
    Department of Medical Protein Research, VIB, A Baertsoenkaai 3, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, A Baertsoenkaai 3, 9000 Ghent, Belgium
    Trends Cell Biol 25:55-8. 2015
    ..Simultaneously, however, urgent bioinformatics needs regarding data management, standardization, and dissemination have emerged. To address these concerns, we propose to establish an open data ecosystem for cell migration research. ..
  92. ncbi request reprint 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...
  93. pmc sORFs.org: a repository of small ORFs identified by ribosome profiling
    Volodimir Olexiouk
    Lab of Bioinformatics and Computational Genomics BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
    Nucleic Acids Res 44:D324-9. 2016
    ..sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects. ..
  94. doi request reprint Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory
    Kenneth Verheggen
    Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
    Proteomics 14:367-77. 2014
    ..We thus underline the benefits of distributed computing in proteomics, while also pointing out the potential issues and pitfalls involved. ..
  95. doi request reprint Scop3D: three-dimensional visualization of sequence conservation
    Tessa Vermeire
    Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
    Proteomics 15:1448-52. 2015
    ....
  96. doi request reprint Resilience in the proteomics data ecosystem: how the field cares for its data
    Lennart Martens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 13:1548-50. 2013
    ..But with public data increasingly at the hub of the life sciences, it is a good time to look at the proteomics data ecosystem in some more detail...
  97. pmc mzML--a community standard for mass spectrometry data
    Lennart Martens
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 10:R110.000133. 2011
    ..The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology...
  98. ncbi request reprint Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
    Marcin Adamski
    University of Michigan, Ann Arbor, MI 48109 2218, USA
    Proteomics 5:3246-61. 2005
    ..Recommendations of the PPP for future large-scale proteomics endeavors are described...
  99. ncbi request reprint 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...
  100. ncbi request reprint The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies
    Michael Hamacher
    Medical Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
    Proteomics 6:1719-21. 2006
    ..The results of the reprocessing were presented and tasks forces were initiated to compile, to interpret and to summarise the data obtained...
  101. ncbi request reprint Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase
    Christian Stephan
    Medizinisches Proteom Center, Ruhr Universitat Bochum, Bochum, Germany
    Proteomics 6:5015-29. 2006
    ....