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Improving automatic...
Improving automatic peptide mass fingerprint protein identification by combining many peak sets
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- Rögnvaldsson, Thorsteinn (author)
- Högskolan i Halmstad,Halmstad Embedded and Intelligent Systems Research (EIS)
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- Häkkinen, Jari (author)
- Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science,Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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- Lindberg, Claes (author)
- Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden
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- Marko-Varga, György (author)
- Molecular Sciences, AstraZeneca RandD Lund, SE-221 87 Lund, Sweden
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- Potthast, Frank (author)
- Funct. Genomics Center Zürich, Winterthurerstr. 190 Y32 H52, CH-8057 Zürich, Switzerland
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- Samuelsson, Jim (author)
- Genedata GmbH, Lena-Christ-Str. 50, D-82152 Martinsried, Germany
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(creator_code:org_t)
- Elsevier, 2004
- 2004
- English.
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In: Journal of chromatography. B. - : Elsevier. - 1570-0232 .- 1873-376X. ; 807:2, s. 209-215
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
Keyword
- Peak set combining
- Peptide mass fingerprinting
- Protein identification
- Biochemistry
- Biokemi
- peak set combining
- peptide mass fingerprinting
- protein identification
Publication and Content Type
- ref (subject category)
- art (subject category)
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