Difference between revisions of "Publications:Improving automatic peptide mass fingerprint protein identification by combining many peak sets"
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{{PublicationSetupTemplate|Author=Thorsteinn Rögnvaldsson, Jari Häkkinen, Claes Lindberg, György Marko-Varga, Frank Potthast, Jim Samuelsson | {{PublicationSetupTemplate|Author=Thorsteinn Rögnvaldsson, Jari Häkkinen, Claes Lindberg, György Marko-Varga, Frank Potthast, Jim Samuelsson | ||
|PID=237403 | |PID=237403 | ||
| − | |Name=Rögnvaldsson, Thorsteinn | + | |Name=Rögnvaldsson, Thorsteinn (denni) (0000-0001-5163-2997) (Högskolan i Halmstad (2804), Sektionen för Informationsvetenskap, Data– och Elektroteknik (IDE) (3905), Halmstad Embedded and Intelligent Systems Research (EIS) (3938));Häkkinen, Jari (Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden);Lindberg, Claes (Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden);Marko-Varga, György (Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden);Potthast, Frank (Funct. Genomics Center Zürich, Winterthurerstr. 190 Y32 H52, CH-8057 Zürich, Switzerland);Samuelsson, Jim (Genedata GmbH, Lena-Christ-Str. 50, D-82152 Martinsried, Germany) |
|Title=Improving automatic peptide mass fingerprint protein identification by combining many peak sets | |Title=Improving automatic peptide mass fingerprint protein identification by combining many peak sets | ||
|PublicationType=Journal Paper | |PublicationType=Journal Paper | ||
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| Title | Improving automatic peptide mass fingerprint protein identification by combining many peak sets |
|---|---|
| Author | |
| Year | 2004 |
| PublicationType | Journal Paper |
| Journal | Journal of chromatography. B |
| HostPublication | |
| Conference | |
| DOI | http://dx.doi.org/10.1016/j.jchromb.2004.04.010 |
| Diva url | http://hh.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:237403 |
| Abstract | An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. The set of spectra contain samples ranging from strong to weak spectra, and the proposed multiple-scale method is shown to be much better on weak spectra than the industry standard method and a human operator, and equal in performance to these on strong and medium strong spectra. It is also demonstrated that peak sets selected by a human operator display a considerable variability and that it is impossible to speak of a single “true” peak set for a given spectrum. The described multiple-scale strategy both avoids time-consuming parameter tuning and exceeds the human operator in protein identification efficiency. The strategy therefore promises reliable automated user-independent protein identification using peptide mass fingerprints. |
