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Bioinformatics Advance Access published online on January 2, 2008
Bioinformatics, doi:10.1093/bioinformatics/btm631
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Decomp—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem

Sebastian Böcker a,*, Zsuzsanna Lipták b, Marcel Martin b and Anton Pervukhin a,{dagger}

aLehrstuhl Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany, bAG Genominformatik, Technische Fakultät, Universität Bielefeld, PF 100 131, 33501 Bielefeld, Germany

{dagger}To whom correspondence should be addressed. Anton Pervukhin, E-mail: apervukh{at}minet.uni-jena.de


  Abstract

Summary: We introduce Decomp, a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises frequently in biochemistry and mass spectrometry (MS), when we know the molecular mass of a protein, DNA, or metabolite fragment but have no other information. A closely related problem is known as the Money Changing Problem (MCP), where all masses are positive integers. Recently, efficient algorithms have been developed for the MCP, which Decomp applies to real valued MS data. The excellent performance of this method on proteomic and metabolomic MS data has recently been demonstrated. Decomp has an easy-to-use graphical interface, which caters for both types of users: those interested in solving MCP instances and those submitting MS data.

Availability:Decomp is freely accessible at http://bibiserv.techfak.uni-bielefeld.de/decomp/

Contact: apervukh{at}minet.uni-jena.de

Associate Editor: Prof. John Quackenbush

*Authors are listed alphabetically.

Received on August 13, 2007; revised on November 16, 2007; accepted on December 17, 2007

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