PIUMS® - A new algorithm for protein identification using peptide fingerprints

• 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.

Subject headings

NATURVETENSKAP  -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Bioinformatics (hsv//eng)

Keyword

Peptide fingerprints

Piums

Protein identification

Protein scoring algorithms

Algorithms

Computer simulation

Computer software

Contamination

Database systems

Monte Carlo methods

Probability density function

Vectors

Proteins

Publication and Content Type

ref (subject category)

kon (subject category)