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Bioinformatics Advance Access originally published online on April 15, 2004
Bioinformatics 2004 20(14):2296-2304; doi:10.1093/bioinformatics/bth242
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.

Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data

Alejandro Heredia-Langner 1,*, William R. Cannon 2, Kenneth D. Jarman 1 and Kristin H. Jarman 1

1 Statistical and Mathematical Sciences and 2 Computational Biosciences, Pacific Northwest National Laboratory, Richland, WA 99352, USA

Received on December 7, 2002; revised on January 30, 2004; accepted on February 2, 2004
Advance Access Publication April 15, 2004

Motivation: Peptide identification following tandem mass spectrometry (MS/MS) is usually achieved by searching for the best match between the mass spectrum of an unidentified peptide and model spectra generated from peptides in a sequence database. This methodology will be successful only if the peptide under investigation belongs to an available database. Our objective is to develop and test the performance of a heuristic optimization algorithm capable of dealing with some features commonly found in actual MS/MS spectra that tend to stop simpler deterministic solution approaches.

Results: We present the implementation of a Genetic Algorithm (GA) in the reconstruction of amino acid sequences using only spectral features, discuss some of the problems associated with this approach and compare its performance to a de novo sequencing method. The GA can potentially overcome some of the most problematic aspects associated with de novo analysis of real MS/MS data such as missing or unclearly defined peaks and may prove to be a valuable tool in the proteomics field. We assess the performance of our algorithm under conditions of perfect spectral information, in situations where key spectral features are missing, and using real MS/MS spectral data.

Contact: Alejandro.Heredia-Langner{at}pnl.gov

* To whom correspondence should be addressed.


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 Brief BioinformHome page
B.-J. M. Webb-Robertson and W. R. Cannon
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Brief Bioinform, September 1, 2007; 8(5): 304 - 317.
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