Zeitschrift für Proteomik und Bioinformatik
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Two-phase Filtering Strategy for Efficient Peptide Identification from Mass Spectrometry

Hoong Kee Ng, Kang Ning and Hon Wai Leong

Peptide identification by tandem mass spectrometry (MS/MS) is one of the most important problems in proteomics. Recent advances in high throughput MS/MS experiments result in huge amount of spectra, and the peptide identification process should keep pace. In this paper, we strive to achieve high accuracy and efficiency for peptide identification with the presence of noise by a two-phase filtering strategy. Our algorithm transforms spectra to high dimensional vectors, and then uses self-organizing map (SOM) and multi-point range query (MPRQ) as very efficient coarse filters to select a number of candidate peptides from database. These candidate peptides are subsequently scored and ranked by an accurate tag-based scoring function S?. Experiments showed that our approach is both fast and accurate for peptide identification.