Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-Symmetric Computational Model

Kang Ning*, Hon Wai Leong

Department of Computer Science, National University of Singapore, Block S15, 3 Science Drive 2, Singapore 117543, Singapore. ningkang@comp.nus.edu.sg

Proc LSS Comput Syst Bioinform Conf. August, 2007. Vol. 6, p. 19-30. Full-Text PDF

*To whom correspondence should be addressed.

Peptide sequencing by tandem mass spectrometry is a very important, interesting, yet challenging problem in proteomics. This problem is extensively investigated by researchers recently, and the peptide sequencing results are becoming more and more accurate. However, many of these algorithms are using computational models based on some unverified assumptions. We believe that the investigation of the validity of these assumptions and related problems will lead to improvements in current algorithms. In this paper, we have first investigated peptide sequencing without preprocessing the spectrum, and we have shown that by introducing preprocessing on spectrum, peptide sequencing can be faster, easier and more accurate. We have then investigated one very important problem, the anti-symmetric problem in the peptide sequencing problem, and we have proved by experiments that model that simply ignore anti-symmetric of model that remove all anti-symmetric instances are too simple for peptide sequencing problem. We have proposed a new model for anti-symmetric problem in more realistic way. We have also proposed a novel algorithm which incorporate preprocessing and new model for anti-symmetric issue, and experiments show that this algorithm has better performance on datasets examined.