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

Bo Yan, Chongle Pan, Victor N. Olman, Robert L. Hettich, Ying Xu

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

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: Here, we present 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: type-1 edge connecting two peaks probably of the same ion types and type-2 edge connecting two peaks probably of different ion types. The problem of ion-separation is formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, representing b, y and others ions, respectively, through maximizing 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 (PaRtition of Ion types in tandem Mass spEctra). The tests on a large amount of simulated mass spectra and 19 sets of high-quality experimental Fourier transform ion cyclotron resonance tandem mass spectra indicate that an accuracy level of ∼90% for the separation of b and y ions was achieved.

Original languageEnglish
Pages (from-to)563-574
Number of pages12
JournalBioinformatics
Volume21
Issue number5
DOIs
StatePublished - Mar 1 2005

Funding

We want to thank the anonymous reviewers whose comments have helped to improve the content and the presentation of this paper. This research was supported in part by National Science Foundation (#NSF/DBI-0354771, #NSF/ITR-IIS-0407204), and by the US Department of Energy’s Genomes to Life program (http://doegenomestolife.org/) under project, ‘Carbon Sequestration in Synechococcus sp.: From Molecular Machines to Hierarchical Modeling’ (www.genomes2life.org).

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