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Bioinformatics Advance Access published online on November 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl561
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 27, 2006
Revised October 4, 2006
Accepted November 4, 2006

Article

Neural network prediction of peptide separation in strong anion exchange chromatography

Cheolhwan Oh 1, Stanislaw H. Zak 2, Hamid Mirzaei 3, Charles Buck 1, Fred E. Regnier 3, and Xiang Zhang 1 *

1 Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
2 School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907
3 Department of Chemistry, Purdue University, West Lafayette, IN 47907

* To whom correspondence should be addressed.
Xiang Zhang, E-mail: zhang100{at}purdue.edu


  Abstract

Motivation: The still emerging combination of technologies that enable description and characterization of all expressed proteins in a biological system is known as proteomics. Although many separation and analysis technologies have been employed in proteomics, it remains a challenge to predict peptide behavior during separation processes. New informatics tools are needed to model the experimental analysis method that will allow scientists to predict peptide separation and assist with required data mining steps, such as protein identification.

Results: We developed a software package to predict the separation of peptides in strong anion exchange (SAX) chromatography using artificial neural network based pattern classification techniques. A multi-layer perceptron is used as a pattern classifier and it is designed with feature vectors extracted from the peptides so that the classification error is minimized. A genetic algorithm is employed to train the neural network. The developed system was tested using 14 protein digests, and the sensitivity analysis was carried out to investigate the significance of each feature.

Availability: The software and testing results can be downloaded from ftp://ftp.bbc.purdue.edu.

Associate Editor: Satoru Miyano
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