Harald Barsnes

Summary

Affiliation: University of Bergen
Country: Norway

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi Protease-dependent fractional mass and peptide properties
    Harald Barsnes
    Department of Informatics, University of Bergen, Norway
    Eur J Mass Spectrom (Chichester, Eng) 14:311-7. 2008
  4. ncbi Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
    Harald Barsnes
    Department of Informatics, University of Bergen, PB 7803, N 5020 Bergen, Norway
    BMC Res Notes 1:130. 2008
  5. ncbi OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
    Harald Barsnes
    Department of Informatics, University of Bergen, N 5020 Norway
    Proteomics 9:3772-4. 2009
  6. ncbi MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
    Harald Barsnes
    Department of Informatics, University of Bergen, PB 7800, N 5020 Bergen, Norway
    BMC Bioinformatics 7:42. 2006
  7. ncbi MassSorter: peptide mass fingerprinting data analysis
    Ingvar Eidhammer
    Department of Informatics, University of Bergen, Bergen, Norway
    Methods Mol Biol 484:345-59. 2008
  8. ncbi 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
  9. ncbi A global analysis of peptide fragmentation variability
    Harald Barsnes
    Department of Informatics, University of Bergen, Bergen, Norway
    Proteomics 11:1181-8. 2011
  10. ncbi 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

Detail Information

Publications10

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi Protease-dependent fractional mass and peptide properties
    Harald Barsnes
    Department of Informatics, University of Bergen, Norway
    Eur J Mass Spectrom (Chichester, Eng) 14:311-7. 2008
    ..With the increasing accuracy of mass spectrometry instruments it is possible to exploit the information embedded in the fractional mass of unknown peaks in peptide mass fingerprint spectra...
  4. ncbi Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
    Harald Barsnes
    Department of Informatics, University of Bergen, PB 7803, N 5020 Bergen, Norway
    BMC Res Notes 1:130. 2008
    ....
  5. ncbi OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
    Harald Barsnes
    Department of Informatics, University of Bergen, N 5020 Norway
    Proteomics 9:3772-4. 2009
    ..google.com/p/omssa-parser), which parses OMSSA omx result files into easy accessible and fully functional object models. In addition, we also provide examples illustrating the usage of our library...
  6. ncbi MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
    Harald Barsnes
    Department of Informatics, University of Bergen, PB 7800, N 5020 Bergen, Norway
    BMC Bioinformatics 7:42. 2006
    ..Many small laboratories are interested in the characterization of a small number of proteins, e.g., how posttranslational modifications change under different conditions...
  7. ncbi MassSorter: peptide mass fingerprinting data analysis
    Ingvar Eidhammer
    Department of Informatics, University of Bergen, Bergen, Norway
    Methods Mol Biol 484:345-59. 2008
    ..MassSorter functions as a database of all the detected peptides. It includes tools for visualization of the results, such as sequence coverage, accuracy plots, statistics, and 3D models...
  8. ncbi 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...
  9. ncbi 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...
  10. ncbi 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...