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Improved protein identification in mammalian cells using a new automatic peak detection algorithm
Halmstad University, School of Information Technology, Halmstad Embedded and Intelligent Systems Research (EIS).ORCID iD: 0000-0001-5163-2997
Department of Theoretical Physics, Lund University, Lund, Sweden.ORCID iD: 0000-0002-8466-9179
BioBridge Computing, Lund, Sweden.
AstraZeneca R and D, Lund, Sweden.
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2002 (English)In: Proceedings - 50th ASMS Conference on Mass Spectrometry and Allied Topics: June 2-6, 2002, Orlando, Florida, Santa Fe: ASMS , 2002, p. 785-786Conference paper, Published paper (Refereed)
Abstract [en]

A comparison of two automatic peak detection algorithms is presented. One algorithm comes with the Voyager 5 Data ExplorerTM program, the other is a new algorithm called Pepex® (short for PEptide Peak Extractor) from BioBridge Computing. The peak sets selected with both tools have been compared, against each other and against manual peak selections, on a large set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. It is shown how much variation there is in peak sets, both when selected by human operators and when selected by automatic peak detection algorithms. This variation has been used as an advantage to gain significantly better protein identification results, using the Pepex tool, than what an experienced mass spectroscopist has achieved on the same data. The strongest improvement has been observed in weak spectra, where the signal peak intensities are low.

Place, publisher, year, edition, pages
Santa Fe: ASMS , 2002. p. 785-786
Keywords [en]
Fibroblasts, Mammalian cells, Peak detection algorithms, Pepex peak, Algorithms, Cells, Computer software, Contamination, Gels, Mass spectrometry, Monte Carlo methods, Proteins
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:hh:diva-40864Scopus ID: 2-s2.0-2442647850OAI: oai:DiVA.org:hh-40864DiVA, id: diva2:1393211
Conference
50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida, United States, June 2-6, 2002
Available from: 2020-02-14 Created: 2020-02-14 Last updated: 2020-03-10Bibliographically approved

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Rögnvaldsson, Thorsteinn

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CiteExportLink to record
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Citation style
  • apa
  • ieee
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  • de-DE
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