PIUMS: A New Algorithm for Protein Identification Using Peptide Fingerprints. Samuelsson, J.; Dalevi, D.; Alm, R.; Rögnvaldsson, T.; and Potthast, F. poster handout ASMS Conf. on mass spectrometry and allied topics, 2002.
abstract   bibtex   
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 about 5-10% more efficient than Mascot for real peak lists, for the same level of false positives.
@Misc{samuelsson02piums,
  author       = {Jim Samuelsson and Daniel Dalevi and Rikard Alm and Thorsteinn R\"ognvaldsson and Frank Potthast},
  title        = {{PIUMS}: A New Algorithm for Protein Identification Using Peptide Fingerprints},
  howpublished = {poster handout ASMS Conf. on mass spectrometry and allied topics},
  year         = {2002},
  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 about 5-10\% more efficient than Mascot for real peak lists, for the same level of false positives.},
  file         = {SamuelssonEtAl_PIUMSNewAlgorithmPMF_ASMS_2002.pdf:2002/SamuelssonEtAl_PIUMSNewAlgorithmPMF_ASMS_2002.pdf:PDF},
  owner        = {Sebastian},
  timestamp    = {2006.03.28},
}
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