Neural network prediction of peptide separation in strong anion exchange chromatography.
BACKGROUND
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.


BACKGROUND
The software and testing results can be downloaded from ftp://ftp.bbc.purdue.edu.
Oh
Cheolhwan
C
Bindley Bioscience Center, West Lafayette, IN 47907, USA.
Zak
Stanislaw H
SH
Mirzaei
Hamid
H
Buck
Charles
C
Regnier
Fred E
FE
Zhang
Xiang
X
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000302:isolation & purification; D002417:Cattle; D002645:Chickens; D002852:Chromatography, Ion Exchange / Q000379:methods*; D006736:Horses; D006801:Humans; D008958:Models, Molecular; D016571:Neural Networks, Computer; D010449:Peptide Mapping; D010455:Peptides / Q000302:isolation & purification*; D040901:Proteomics; D011817:Rabbits
D001426:Bacterial Proteins; D010455:Peptides