Pierre Alain Binz

Summary

Affiliation: Swiss Institute of Bioinformatics
Country: Switzerland

Publications

  1. pmc The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'
    Pierre Alain Binz
    Proteome Informatics Group, Swiss Institute of Bioinformatics, 1 Michel Servet, Geneva 1211, Switzerland
    Comp Funct Genomics 5:148-55. 2004
  2. ncbi request reprint Mass spectrometry-based proteomics: current status and potential use in clinical chemistry
    Pierre Alain Binz
    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
    Clin Chem Lab Med 41:1540-51. 2003
  3. ncbi request reprint The molecular scanner: concept and developments
    Pierre Alain Binz
    Swiss Institute of Bioinformatics, Proteome Informatics Group, CMU, Michel Servet 1, 1211 Geneva, Switzerland
    Curr Opin Biotechnol 15:17-23. 2004
  4. ncbi request reprint Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra
    Steven Gay
    Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 2:1374-91. 2002
  5. ncbi request reprint Molecular scanner experiment with human plasma: improving protein identification by using intensity distributions of matching peptide masses
    Markus Muller
    Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 2:1413-25. 2002
  6. ncbi request reprint Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect
    Alexander Scherl
    Biomedical Proteomics Research Group, Central Clinical Chemistry Laboratory, Geneva University Hospitals, Geneva, Switzerland
    Rapid Commun Mass Spectrom 19:605-10. 2005
  7. ncbi request reprint MSight: an image analysis software for liquid chromatography-mass spectrometry
    Patricia M Palagi
    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 5:2381-4. 2005
  8. doi request reprint X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry
    Roman Mylonas
    Swiss Institute of Bioinformatics
    Anal Chem 81:7604-10. 2009
  9. ncbi request reprint The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases
    Khaled Mostaguir
    Swiss Institute of Bioinformatics, Centre Medical Universitaire CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Proteomics 3:1441-4. 2003
  10. ncbi request reprint Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session
    Pierre Alain Binz
    Swiss Institute of Bioinformatics SIB, Centre Medical Universitaire, 1 Michel Servet, CH 1211 Geneva 4, Switzerland
    Proteomics 3:1562-6. 2003

Detail Information

Publications26

  1. pmc The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'
    Pierre Alain Binz
    Proteome Informatics Group, Swiss Institute of Bioinformatics, 1 Michel Servet, Geneva 1211, Switzerland
    Comp Funct Genomics 5:148-55. 2004
    ....
  2. ncbi request reprint Mass spectrometry-based proteomics: current status and potential use in clinical chemistry
    Pierre Alain Binz
    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
    Clin Chem Lab Med 41:1540-51. 2003
    ..We also describe the major experimental workflows that are typically used in proteomics today, with a focus on those incorporating MS as a major analysis tool...
  3. ncbi request reprint The molecular scanner: concept and developments
    Pierre Alain Binz
    Swiss Institute of Bioinformatics, Proteome Informatics Group, CMU, Michel Servet 1, 1211 Geneva, Switzerland
    Curr Opin Biotechnol 15:17-23. 2004
    ..Clinical applications of the molecular scanner have also started to be developed for disease diagnosis in biological material...
  4. ncbi request reprint Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra
    Steven Gay
    Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 2:1374-91. 2002
    ..Furthermore, this datamining approach can certainly be extended to the tandem mass spectrometry domain or other mass spectrometry derived methods...
  5. ncbi request reprint Molecular scanner experiment with human plasma: improving protein identification by using intensity distributions of matching peptide masses
    Markus Muller
    Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 2:1413-25. 2002
    ..Many proteins annotated on the SWISS-2D PAGE human plasma master gel could be clearly identified and many interesting properties were observed...
  6. ncbi request reprint Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect
    Alexander Scherl
    Biomedical Proteomics Research Group, Central Clinical Chemistry Laboratory, Geneva University Hospitals, Geneva, Switzerland
    Rapid Commun Mass Spectrom 19:605-10. 2005
    ..A thin layer of gold renders the membrane conductive. This allows adequate data acquisition on MALDI-TOF/TOF systems. Therefore, this methodology extends the capacity of the molecular scanner concept to tandem mass spectrometry...
  7. ncbi request reprint MSight: an image analysis software for liquid chromatography-mass spectrometry
    Patricia M Palagi
    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
    Proteomics 5:2381-4. 2005
    ..We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison...
  8. doi request reprint X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry
    Roman Mylonas
    Swiss Institute of Bioinformatics
    Anal Chem 81:7604-10. 2009
    ..It also opens the possibility for efficient general unknown screening (GUS) against large compound libraries...
  9. ncbi request reprint The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases
    Khaled Mostaguir
    Swiss Institute of Bioinformatics, Centre Medical Universitaire CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Proteomics 3:1441-4. 2003
    ..Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data...
  10. ncbi request reprint Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session
    Pierre Alain Binz
    Swiss Institute of Bioinformatics SIB, Centre Medical Universitaire, 1 Michel Servet, CH 1211 Geneva 4, Switzerland
    Proteomics 3:1562-6. 2003
    ..Sample B was generally and correctly identified as penaeidin. However, only one group reported the full primary structure. Interestingly, the approaches were again varied and are discussed in the text...
  11. pmc Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers
    Alexander Scherl
    Biomedical Proteomics Research Group, Geneva University, Geneva, Switzerland
    BMC Genomics 7:296. 2006
    ..Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome...
  12. doi request reprint A simple workflow to increase MS2 identification rate by subsequent spectral library search
    Erik Ahrné
    Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland
    Proteomics 9:1731-6. 2009
    ..Additionally matched spectra by SpectraST included noisy spectra, spectra representing missed cleaved peptides as well as spectra from post-translationally modified peptides...
  13. doi request reprint Guidelines for reporting the use of mass spectrometry informatics in proteomics
    Pierre Alain Binz
    Nat Biotechnol 26:862. 2008
  14. 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
    ....
  15. ncbi request reprint Challenges in mass spectrometry
    Reto Stocklin
    Atheris Laboratories, Bernex Geneva, Switzerland
    Proteomics 2:825-7. 2002
    ..Although it was one of the final events of the meeting, this MS round table attracted an audience of some fifty participants of the congress who were actively involved in the debate...
  16. 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
    ....
  17. ncbi request reprint The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1006-8. 2007
    ..This should be achieved by early in 2007...
  18. ncbi request reprint Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 5:337-9. 2005
    ..Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats...
  19. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  20. doi request reprint The PSI-MOD community standard for representation of protein modification data
    Luisa Montecchi-Palazzi
    Nat Biotechnol 26:864-6. 2008
  21. doi request reprint Guidelines for reporting the use of gel electrophoresis in proteomics
    Frank Gibson
    Nat Biotechnol 26:863-4. 2008
  22. ncbi request reprint Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 6:738-41. 2006
    ..Common to all these efforts is the field of protein modifications, and work has been initiated to establish an ontology in this field that can be used by both workers in the field of proteomics and the wider scientific community...
  23. doi request reprint Guidelines for reporting the use of mass spectrometry in proteomics
    Chris F Taylor
    Nat Biotechnol 26:860-1. 2008
  24. 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...
  25. ncbi request reprint Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 7:3436-40. 2007
    ..Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets...
  26. ncbi request reprint Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 7:337-9. 2007
    ..In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community-input via the PSI website...