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Improving automatic peptide mass fingerprint protein identification by combining many peak sets
Halmstad University, School of Information Science, Computer and Electrical Engineering (IDE), Halmstad Embedded and Intelligent Systems Research (EIS).ORCID iD: 0000-0001-5163-2997
Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden.
Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden.
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2004 (English)In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 807, no 2, p. 209-215Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2004. Vol. 807, no 2, p. 209-215
Keywords [en]
Peak set combining, Peptide mass fingerprinting, Protein identification
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:hh:diva-225DOI: 10.1016/j.jchromb.2004.04.010ISI: 000222283800006PubMedID: 15203031Scopus ID: 2-s2.0-2942529269Local ID: 2082/520OAI: oai:DiVA.org:hh-225DiVA, id: diva2:237403
Available from: 2006-11-24 Created: 2006-11-24 Last updated: 2017-12-13Bibliographically approved

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Rögnvaldsson, Thorsteinn

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CiteExportLink to record
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Citation style
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