Peptide identification based on fuzzy classification and clustering.

Liang X, Xia Z, Niu X, Link AJ, Pang L, Wu FX, Zhang H
Proteome Sci. 2013 11 (Suppl 1): S10

PMID: 24564935 · PMCID: PMC3908838 · DOI:10.1186/1477-5956-11-S1-S10

BACKGROUND - The sequence database searching has been the dominant method for peptide identification, in which a large number of peptide spectra generated from LC/MS/MS experiments are searched using a search engine against theoretical fragmentation spectra derived from a protein sequences database or a spectral library. Selecting trustworthy peptide spectrum matches (PSMs) remains a challenge.

RESULTS - A novel scoring method named FC-Ranker is developed to assign a nonnegative weight to each target PSM based on the possibility of its being correct. Particularly, the scores of PSMs are updated by using a fuzzy SVM classification model and a fuzzy silhouette index iteratively. Trustworthy PSMs will be assigned high scores when the algorithm stops.

CONCLUSIONS - Our experimental studies show that FC-Ranker outperforms other post-database search algorithms over a variety of datasets, and it can be extended to solve a general classification problem with uncertain labels.

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