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Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Genedata GmbH, Lena-Christ-Strasse 50, 82152 Martinsried, Germany.
Computing Science, Chalmers University of Technology, SE-412 96 Göteborg.
Department of Protein Technology, Lund University, Sölvegatan 33A.
Halmstad University, School of Information Technology, Halmstad Embedded and Intelligent Systems Research (EIS), Intelligent systems (IS-lab).
2004 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 20, no 18, p. 3628-3635Article in journal (Refereed) Published
Abstract [en]

A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.

Place, publisher, year, edition, pages
Oxford: Oxford University Press , 2004. Vol. 20, no 18, p. 3628-3635
Keywords [en]
Fingerprints, Automated analysis, Tools
Identifiers
URN: urn:nbn:se:hh:diva-244DOI: 10.1093/bioinformatics/bth460ISI: 000225786600038PubMedID: 15297302Scopus ID: 2-s2.0-12344287002Local ID: 2082/539OAI: oai:DiVA.org:hh-244DiVA, id: diva2:237422
Available from: 2006-11-24 Created: 2006-11-24 Last updated: 2018-03-23Bibliographically approved

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Rögnvaldsson, Thorsteinn

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
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  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
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Output format
  • html
  • text
  • asciidoc
  • rtf