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Bioinformatics Advance Access published online on March 6, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm062
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio

Mitsuhiro Kanazawa 1,5,*, Hisae Anyoji 1, Atsushi Ogiwara 2,3 and Umpei Nagashima 4,5

1 Reifycs Inc., Tokyo, Japan; 2Medical ProteoScope Co., Ltd., Tokyo, Japan; 3Tokyo Medical University, Tokyo, Japan; 4National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan; and 5Tsukuba University, Ibaraki, Japan

*To whom correspondence should be addressed. Mitsuhiro Kanazawa, E-mail: kanazawa{at}reifycs.com


  Abstract

Motivation: Peptide sequencing methods by mass spectrum use the following two approaches: database searching and de novo sequencing. The database searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. On the other hand, in the case of de novo sequencing, no preliminary information is necessary; however, continuous amino acid sequence peaks and the differentiation of these peaks are required. It is, however, very difficult to obtain and differentiate the peaks of all amino acids by using an actual spectrum.

We propose a novel de novo sequencing approach using not only mass-to-charge ratio but also ion peak intensity and amino acid cleavage intensity ratio (CIR).

Results: Our method compensates for any undetectable amino acid peak intervals by estimating the amino acid set and the probability of peak expression based on amino acid CIR. It provides more accurate identification of sequences than the existing methods, by which it is usually difficult to sequence.

Associate Editor: Prof. Martin Bishop

Received on September 17, 2006; revised on February 1, 2007; accepted on February 18, 2007

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