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Title PIUMS® - A new algorithm for protein identification using peptide fingerprints
Author Jim Samuelsson and Daniel Dalevi and Rikard Aim and Thorsteinn Rögnvaldsson and Fránk Potthast
Year 2002
PublicationType Conference Paper
Journal
HostPublication Proceedings 50th ASMS Conference on Mass Spectrometry and Allied Topics
Conference 50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida, United States, June 2-6, 2002
DOI
Diva url http://hh.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:1392766
Abstract 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.