Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis

Authors:
L. Lancashire;O. Schmid;H. Shah;G. Ball
Affiliations:
The Nottingham Trent University Nottingham, NG11 8NS, UK;Molecular Identification Services Unit, Central Public Health Laboratory Health Protection Agency, 61 Colindale Avenue, London, NW9 5HT, UK;Molecular Identification Services Unit, Central Public Health Laboratory Health Protection Agency, 61 Colindale Avenue, London, NW9 5HT, UK;The Nottingham Trent University Nottingham, NG11 8NS, UK
Venue:
Bioinformatics
Year:
2005

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Abstract

Motivation: Robust computer algorithms are required to interpret the vast amounts of proteomic data currently being produced and to generate generalized models which are applicable to 'real world' scenarios. One such scenario is the classification of bacterial species. These vary immensely, some remaining remarkably stable whereas others are extremely labile showing rapid mutation and change. Such variation makes clinical diagnosis difficult and pathogens may be easily misidentified. Results: We applied artificial neural networks (Neuroshell 2) in parallel with cluster analysis and principal components analysis to surface enhanced laser desorption/ionization (SELDI)-TOF mass spectrometry data with the aim of accurately identifying the bacterium Neisseria meningitidis from species within this genus and other closely related taxa. A subset of ions were identified that allowed for the consistent identification of species, classifying 97% of a separate validation subset of samples into their respective groups. Availability: Neuroshell 2 is commercially available from Ward Systems. Contact: graham.balls@ntu.ac.uk