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PIUMS® - A new algorithm for protein identification using peptide fingerprints
BioBridge Computing, Lund, Sweden.
BioBridge Computing, Lund, Sweden.
Lund Graduate School of Biomedical Sciences/Biomol. Res., Lund, Sweden.
Halmstad University, School of Information Technology, Halmstad Embedded and Intelligent Systems Research (EIS).ORCID iD: 0000-0001-5163-2997
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2002 (English)In: Proceedings 50th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS , 2002, p. 783-784Conference paper, Published paper (Refereed)
Abstract [en]

Piums®, a new protein identification tool for peptide fingerprints, is presented. Piums includes both a peak extraction tool (Pepex®) and a new protein scoring algorithm (Piped®). The basic ideas underlying the scoring algorithm are presented and it is demonstrated on some real sample spectra. It is shown, using simulated peak lists, how the scoring performance varies with contamination levels and protein sequence coverage, and that there is a boundary for when scoring is possible. Piums is fully scriptable and modularised. Each individual module can be used by itself, with input and output in XML format, to e.g. include it in an analysis chain. Piums is benchmarked against the Mascot software from Matrix Science LLC, The results indicate that Piums is more precise than the Mascot score, and about 5-10% more efficient than Mascot for real peak lists, for the same level of false positives.

Place, publisher, year, edition, pages
ASMS , 2002. p. 783-784
Keywords [en]
Peptide fingerprints, Piums, Protein identification, Protein scoring algorithms, Algorithms, Computer simulation, Computer software, Contamination, Database systems, Monte Carlo methods, Probability density function, Vectors, Proteins
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:hh:diva-40865Scopus ID: 2-s2.0-2442688063OAI: oai:DiVA.org:hh-40865DiVA, id: diva2:1392766
Conference
50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida, United States, June 2-6, 2002
Available from: 2020-02-10 Created: 2020-02-10 Last updated: 2020-02-17

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CiteExportLink to record
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