Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms

Automatic peptide identification from collision‐induced dissociation tandem mass spectrometry data using optimization techniques is made difficult by large plateaus in the fitness landscapes of scoring functions, by the fuzzy nature of constraints from noisy data and by the existence of diverse but...

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Bibliographic Details
Published in:Concurrency and computation Vol. 17; no. 14; pp. 1687 - 1704
Main Authors: Malard, J. M., Heredia-Langner, A., Cannon, W. R., Mooney, R., Baxter, D. J.
Format: Journal Article
Language:English
Published: Chichester, UK John Wiley & Sons, Ltd 10.12.2005
Subjects:
data-intensive computation
genetic algorithms
multiobjective optimization
peptide identification
tandem mass spectrometry
ISSN:1532-0626, 1532-0634
Online Access:Get full text
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Summary:Automatic peptide identification from collision‐induced dissociation tandem mass spectrometry data using optimization techniques is made difficult by large plateaus in the fitness landscapes of scoring functions, by the fuzzy nature of constraints from noisy data and by the existence of diverse but equally justifiable probabilistic models of peak matching. Here, two different scoring functions are combined into a parallel multi‐objective optimization framework. It is shown how multi‐objective optimization can be used to empirically test for independence between distinct scoring functions. The loss of selection pressure during the evolution of a population of putative peptide sequences by a Pareto‐driven genetic algorithm is addressed by alternating between two definitions of fitness according to a numerical threshold. Copyright © 2005 John Wiley & Sons, Ltd.
Bibliography:Office of Biological and Environmental Research in the U.S. Department of Energy - No. 41966A
ark:/67375/WNG-T1JN0519-V
istex:6FC701074AFB45BDC3C2FDB6AC4B8DAB04FC0008
ArticleID:CPE953
ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ISSN:1532-0626
1532-0634
DOI:10.1002/cpe.953