Ling Jian, Zunquan Xia
School of Mathematical Sciences
Dalian University of Technology
Dalian, 116024, P.R. CHINA
College of Science
University of Petroleum
Qingdao, 266555, P.R. CHINA

Abstract. Shotgun tandem mass spectrometry-based peptide sequencing using programs such as SEQUEST allows high-throughput identification of peptides, which in turn allows identification of corresponding proteins. This paper present a novel machine learning method based on Fuzzy Support Vector Machines (Fuzzy SVMs) to discriminate between correct and incorrect identified peptides using SEQUEST search results. Through incorporating fuzzy membership this method can reduce the effect of noise in data points. Experiments show that this approach outperforms the traditional SVMs based technique, and it's an promising algorithm for peptide identification task.

Received: February 20, 2012

AMS Subject Classification: 92B05

Key Words and Phrases: peptide identification, SEQUEST, fuzzy support vector machines, mass spectrometry

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