An Accurate and Efficient Algorithm for Peptide and PTM Identification by Tandem Mass Spectrometry

Kang Ning (
Hoong Kee Ng (
Hon Wai Leong (

Department of Computer Science, School of Computing, National University of Singapore, Computing 1, Singapore 117590


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. Unfortunately, identification of these spectra is relatively slow, and the accuracies of current algorithms are not high with the presence of noises and post-translational modifications (PTMs). In this paper, we strive to achieve high accuracy and efficiency for peptide identification problem, with special concern on identification of peptides with PTMs. This paper expands our previous work on PepSOM with the introduction of two accurate modified scoring functions: Sλ for peptide identification and Sλ* for identification of peptides with PTMs. Experiments showed that our algorithm is both fast and accurate for peptide identification. Experiments on spectra with simulated and real PTMs confirmed that our algorithm is accurate for identifying PTMs.

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Japanese Society for Bioinformatics