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Bioinformatics Advance Access published online on September 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti044
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 19, 2004
Revised July 26, 2004
Accepted September 7, 2004

Article

A graph-theoretic approach to separation of b and y ions in tandem mass spectra

Bo Yan 1, Chongle Pan 2, Victor N. Olman 1, Robert L. Hettich 3, and Ying Xu 1*

1 Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, University of Georgia, Athens, GA 30602, USA; Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
2 Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Genome Science and Technology Graduate School, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
3 Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

* To whom correspondence should be addressed. E-mail: xyn{at}bmb.uga.edu.


  Abstract

Motivation: Ion-type identification is a fundamental problem in computational proteomics. Methods for accurate identification of ion types provide the basis for many mass spectrometry data interpretation problems, including (a) de novo sequencing, (b) identification of post-translational modifications and mutations, and (c) validation of database search results.

Results: We present here a novel graph-theoretic approach for solving the problem of separating b ions from y ions in a set of tandem mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types. The ion-separation problem is formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, representing b, y ions and others respectively, to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each partitioned subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. The tests on a large amount of simulated mass spectra and 19 sets of high quality experimental FT-ICR tandem mass spectra indicate that ~90% accuracy for separation of b and y ions was achieved.

Availability: The executable code of PRIME is available upon request.


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