View source for 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
|PID=237403
|Name=Rögnvaldsson, Thorsteinn [denni] (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
|PublicationType=Journal Paper
|ContentType=Refereegranskat
|Language=eng
|Journal=Journal of chromatography. B
|JournalISSN=1570-0232
|Status=published
|Volume=807
|Issue=2
|HostPublication=
|Conference=
|StartPage=209
|EndPage=215
|Year=2004
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|Publisher=Elsevier
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|DOI=http://dx.doi.org/10.1016/j.jchromb.2004.04.010
|ISI=000222283800006
|PMID=15203031
|ScopusId=2-s2.0-2942529269
|NBN=urn:nbn:se:hh:diva-225
|LocalId=2082/520
|ArchiveNumber=
|Keywords=Peak set combining;Peptide mass fingerprinting;Protein identification
|Categories=Biokemi och molekylärbiologi (10602)
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|Abstract=<p>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.</p>
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|CreatedDate=2006-11-24
|PublicationDate=2006-11-24
|LastUpdated=2013-10-15
|diva=http://hh.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:237403}}
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